<86>May 4 02:22:08 userdel[2255419]: delete user 'rooter' <86>May 4 02:22:08 userdel[2255419]: removed group 'rooter' owned by 'rooter' <86>May 4 02:22:08 userdel[2255419]: removed shadow group 'rooter' owned by 'rooter' <86>May 4 02:22:08 groupadd[2255426]: group added to /etc/group: name=rooter, GID=1217 <86>May 4 02:22:08 groupadd[2255426]: group added to /etc/gshadow: name=rooter <86>May 4 02:22:08 groupadd[2255426]: new group: name=rooter, GID=1217 <86>May 4 02:22:08 useradd[2255434]: new user: name=rooter, UID=1217, GID=1217, home=/root, shell=/bin/bash, from=none <86>May 4 02:22:08 userdel[2255444]: delete user 'builder' <86>May 4 02:22:08 userdel[2255444]: removed group 'builder' owned by 'builder' <86>May 4 02:22:08 userdel[2255444]: removed shadow group 'builder' owned by 'builder' <86>May 4 02:22:08 groupadd[2255453]: group added to /etc/group: name=builder, GID=1218 <86>May 4 02:22:08 groupadd[2255453]: group added to /etc/gshadow: name=builder <86>May 4 02:22:08 groupadd[2255453]: new group: name=builder, GID=1218 <86>May 4 02:22:08 useradd[2255459]: new user: name=builder, UID=1218, GID=1218, home=/usr/src, shell=/bin/bash, from=none warning: Macro %add_tcl_lib_path not found <13>May 4 02:22:21 rpmi: libpng16-1.6.42-alt2 sisyphus+339555.100.1.1 1706781682 installed <13>May 4 02:22:21 rpmi: xorg-proto-devel-2024.1-alt1 sisyphus+343583.40.1.1 1711440649 installed <13>May 4 02:22:21 rpmi: libjpeg-2:3.0.2-alt2.1 sisyphus+340135.100.1.1 1707449145 installed <13>May 4 02:22:21 rpmi: libexpat-2.5.0-alt1 sisyphus+309227.100.1.1 1667075764 installed <13>May 4 02:22:21 rpmi: perl-HTTP-Date-6.06-alt1 sisyphus+324527.100.1.1 1688834564 installed <13>May 4 02:22:21 rpmi: perl-Unicode-Normalize-1:5.38.2-alt0.2 sisyphus+344512.40.2.1 1712358015 installed <13>May 4 02:22:21 rpmi: tex-common-0.2-alt4 sisyphus+276869.100.1.1 1625246366 installed <13>May 4 02:22:21 rpmi: perl-Term-ANSIColor-5.01-alt1 sisyphus+244783.100.1.2 1579747505 installed <13>May 4 02:22:21 rpmi: liblcms2-2.16-alt1 sisyphus+335676.100.1.1 1701682597 installed <13>May 4 02:22:21 rpmi: libidn2-2.3.7-alt1 sisyphus+339505.100.1.2 1706718968 installed <13>May 4 02:22:21 rpmi: libnettle8-3.9.1-alt1 sisyphus+322548.100.1.2 1686176879 installed <13>May 4 02:22:21 rpmi: less-633-alt1 sisyphus+328181.300.2.1 1693321749 installed <13>May 4 02:22:21 rpmi: libICE-1.1.1-alt1 sisyphus+311428.500.1.1 1670577555 installed <13>May 4 02:22:22 rpmi: libicu74-1:7.4.2-alt1 sisyphus+336372.200.1.1 1702423005 installed <13>May 4 02:22:22 rpmi: libgraphite2-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed <13>May 4 02:22:22 rpmi: libSM-1.2.4-alt1 sisyphus+312057.200.1.1 1671526916 installed <13>May 4 02:22:22 rpmi: perl-unicore-1:5.38.2-alt0.2 sisyphus+344512.40.2.1 1712358015 installed <13>May 4 02:22:22 rpmi: perl-Tie-RefHash-1.40-alt1 sisyphus+260329.100.1.1 1603548550 installed <13>May 4 02:22:22 rpmi: perl-IO-Stringy-2.113-alt1 sisyphus+289915.300.2.1 1637124493 installed <13>May 4 02:22:22 rpmi: perl-IO-Socket-IP-0.42-alt1 sisyphus+325815.100.1.2 1690571193 installed <13>May 4 02:22:22 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed <13>May 4 02:22:22 rpmi: perl-libnet-1:3.15-alt1 sisyphus+317310.100.1.1 1679580208 installed <13>May 4 02:22:22 rpmi: perl-HTML-Tagset-3.24-alt1 sisyphus+343117.100.1.3 1710883587 installed <13>May 4 02:22:22 rpmi: perl-Compress-Raw-Zlib-2.206-alt1 sisyphus+335067.600.1.1 1700901499 installed <13>May 4 02:22:22 rpmi: rpm-macros-info-install-7.1-alt1 sisyphus+338907.200.3.1 1706718831 installed <13>May 4 02:22:22 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed <13>May 4 02:22:22 rpmi: libtcl-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed <13>May 4 02:22:22 rpmi: tcl-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed <13>May 4 02:22:22 rpmi: libnspr-1:4.35-alt1 sisyphus+308164.100.1.1 1665397040 installed <13>May 4 02:22:23 rpmi: libopenblas-0.3.26-alt1 sisyphus+339579.140.3.1 1706872444 installed <13>May 4 02:22:23 rpmi: libsqlite3-3.44.2-alt1 sisyphus+335409.100.3.3 1701347810 installed <13>May 4 02:22:23 rpmi: libassuan-2.5.6-alt1 sisyphus+327218.300.1.1 1692093921 installed <13>May 4 02:22:23 rpmi: javapackages-filesystem-1:6.0.0-alt2_7jpp11 sisyphus+318644.100.1.1 1681742255 installed <13>May 4 02:22:23 rpmi: libxxhash-0.8.2-alt1 sisyphus+336514.200.7.1 1702672118 installed <13>May 4 02:22:23 rpmi: libwebp7-1.4.0-alt1 sisyphus+345159.200.1.1 1713168663 installed <13>May 4 02:22:23 rpmi: libpaper2-2:2.1.3-alt1 sisyphus+340967.100.1.1 1708276732 installed <13>May 4 02:22:23 rpmi: libopenjpeg2.0-2.5.2-alt1 sisyphus+341637.100.1.1 1709150017 installed <13>May 4 02:22:23 rpmi: liblz4-1:1.9.4-alt1 sisyphus+309416.100.1.1 1667412981 installed <13>May 4 02:22:23 rpmi: libquadmath0-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:23 rpmi: libgfortran5-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:23 rpmi: libpixman-3:0.43.4-alt2 sisyphus+344164.100.1.1 1711987977 installed <13>May 4 02:22:23 rpmi: libbrotlicommon-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed <13>May 4 02:22:23 rpmi: libbrotlidec-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed <13>May 4 02:22:23 rpmi: libharfbuzz-8.4.0-alt1 sisyphus+344161.100.1.1 1711987962 installed <13>May 4 02:22:23 rpmi: libfreetype-2.13.2-alt1 sisyphus+328677.100.1.1 1693834345 installed <13>May 4 02:22:23 rpmi: libfontconfig1-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed <13>May 4 02:22:23 rpmi: libbrotlienc-1.1.0-alt1 sisyphus+328501.100.1.1 1693598419 installed <13>May 4 02:22:23 rpmi: zlib-devel-1.3.1-alt1 sisyphus+342532.100.1.1 1710232285 installed <13>May 4 02:22:23 rpmi: libXau-1.0.11-alt1 sisyphus+311428.100.1.1 1670577439 installed <13>May 4 02:22:23 rpmi: libgdbm-1.8.3-alt10 sisyphus+278100.1600.1.1 1626058413 installed <13>May 4 02:22:23 rpmi: xml-utils-1:2.12.6-alt1 sisyphus+347327.100.1.1 1714660882 installed <13>May 4 02:22:23 rpmi: fontconfig-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed Updating fonts cache: <29>May 4 02:22:24 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>May 4 02:22:24 rpmi: libp11-kit-1:0.25.3-alt2 sisyphus+336533.100.1.1 1702645560 installed <13>May 4 02:22:24 rpmi: libtasn1-4.19.0-alt3 sisyphus+327816.100.1.1 1692802615 installed <13>May 4 02:22:24 rpmi: libreadline7-7.0.3-alt5 sisyphus+328858.200.1.1 1694010737 installed <13>May 4 02:22:24 rpmi: bc-1:1.07.1-alt1 sisyphus+278100.400.1.1 1626056612 installed <13>May 4 02:22:24 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed <13>May 4 02:22:24 rpmi: rpm-build-gir-0.7.3-alt3.1 sisyphus+319393.100.1.1 1682538783 installed <13>May 4 02:22:24 rpmi: libXau-devel-1.0.11-alt1 sisyphus+311428.100.1.1 1670577439 installed <13>May 4 02:22:24 rpmi: libpng-devel-1.6.42-alt2 sisyphus+339555.100.1.1 1706781682 installed <13>May 4 02:22:24 rpmi: libwoff2-1.0.2-alt3 sisyphus+302729.100.1.1 1656351540 installed <13>May 4 02:22:24 rpmi: libharfbuzz-icu-8.4.0-alt1 sisyphus+344161.100.1.1 1711987962 installed <13>May 4 02:22:24 rpmi: libharfbuzz-gobject-8.4.0-alt1 sisyphus+344161.100.1.1 1711987962 installed <13>May 4 02:22:24 rpmi: libquadmath13-devel-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:24 rpmi: libsystemd-1:254.10-alt2 sisyphus+345302.400.3.1 1713818564 installed <13>May 4 02:22:24 rpmi: libdbus-1.14.10-alt1 sisyphus+327286.5700.14.1 1711487401 installed <13>May 4 02:22:24 rpmi: libavahi-0.8-alt4 sisyphus+344258.100.1.1 1712133856 installed <13>May 4 02:22:24 rpmi: javapackages-tools-1:6.0.0-alt2_7jpp11 sisyphus+318644.100.1.1 1681742255 installed <13>May 4 02:22:24 rpmi: java-common-1.7.0-alt1 sisyphus+333533.100.1.1 1699037019 installed <13>May 4 02:22:24 rpmi: libopenblas-devel-0.3.26-alt1 sisyphus+339579.140.3.1 1706872444 installed <13>May 4 02:22:24 rpmi: perl-OLE-Storage_Lite-0.22-alt1 sisyphus+315433.100.1.1 1676717427 installed <13>May 4 02:22:24 rpmi: perl-autodie-2.37-alt1 sisyphus+337625.100.1.1 1704230186 installed <13>May 4 02:22:24 rpmi: perl-Net-IDN-Encode-2.500-alt2 sisyphus+335067.2600.1.1 1700901862 installed <13>May 4 02:22:24 rpmi: libgraphite2-devel-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed <13>May 4 02:22:24 rpmi: icu-utils-1:7.4.2-alt1 sisyphus+336372.200.1.1 1702423005 installed <13>May 4 02:22:24 rpmi: libicu-devel-1:7.4.2-alt1 sisyphus+336372.200.1.1 1702423005 installed <13>May 4 02:22:24 rpmi: libICE-devel-1.1.1-alt1 sisyphus+311428.500.1.1 1670577555 installed <13>May 4 02:22:24 rpmi: libSM-devel-1.2.4-alt1 sisyphus+312057.200.1.1 1671526916 installed <13>May 4 02:22:24 rpmi: libhogweed6-3.9.1-alt1 sisyphus+322548.100.1.2 1686176879 installed <13>May 4 02:22:25 rpmi: libgnutls30-3.8.4-alt1 sisyphus+343729.100.2.1 1711571288 installed <13>May 4 02:22:25 rpmi: libngtcp2.16-1.4.0-alt1 sisyphus+343912.100.1.1 1711714683 installed <13>May 4 02:22:25 rpmi: libngtcp2_crypto_gnutls8-1.4.0-alt1 sisyphus+343912.100.1.1 1711714683 installed <13>May 4 02:22:25 rpmi: perl-Data-Dump-1.25-alt1 sisyphus+276551.100.1.1 1625126880 installed <13>May 4 02:22:25 rpmi: perl-File-Listing-6.16-alt1 sisyphus+325783.100.1.1 1690559356 installed <13>May 4 02:22:25 rpmi: libturbojpeg-2:3.0.2-alt2.1 sisyphus+340135.100.1.1 1707449145 installed <13>May 4 02:22:25 rpmi: groff-base-1.22.3-alt2 sisyphus+275306.100.2.1 1624538375 installed <13>May 4 02:22:25 rpmi: zziplib-0.13.72-alt1 sisyphus+278032.100.1.2 1625982008 installed <13>May 4 02:22:25 rpmi: t1utils-1.42-alt1 sisyphus+278458.100.1.1 1626102085 installed <13>May 4 02:22:25 rpmi: ttf2pt1-3.4.4-alt1.qa1 sisyphus+275192.100.2.1 1624905844 installed <13>May 4 02:22:25 rpmi: rpm-build-tcl-0.6.2-alt1 sisyphus+299320.100.1.1 1651401392 installed <13>May 4 02:22:25 rpmi: tcl-devel-8.6.13-alt1 sisyphus+310696.100.1.1 1669548266 installed <13>May 4 02:22:25 rpmi: perl-X11-Protocol-0.56-alt1.1 1290621401 installed <13>May 4 02:22:25 rpmi: perl-TimeDate-2.33-alt1 sisyphus+252901.100.1.1 1591387378 installed <13>May 4 02:22:25 rpmi: perl-Unicode-Map-0.112-alt8 sisyphus+335067.5100.2.2 1701151359 installed <13>May 4 02:22:25 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed <13>May 4 02:22:25 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed <13>May 4 02:22:25 rpmi: perl-IPC-System-Simple-1.30-alt1 sisyphus+248544.100.1.1 1585154078 installed <13>May 4 02:22:25 rpmi: perl-IPC-Run3-0.049-alt1 sisyphus+343743.100.2.1 1711555032 installed <13>May 4 02:22:25 rpmi: psutils-2:2.10-alt2 sisyphus+336930.2400.2.1 1703147004 installed <13>May 4 02:22:25 rpmi: perl-Try-Tiny-0.31-alt1 sisyphus+290597.100.1.1 1637915507 installed <13>May 4 02:22:25 rpmi: perl-Module-Load-0.36-alt1 sisyphus+258992.100.1.1 1601543407 installed <13>May 4 02:22:25 rpmi: perl-IO-Compress-Brotli-2:0.004001-alt3 sisyphus+335067.1200.1.1 1700901589 installed <13>May 4 02:22:25 rpmi: perl-File-Which-1.27-alt1 sisyphus+271986.100.1.1 1621196035 installed <13>May 4 02:22:25 rpmi: perl-File-Copy-Recursive-0.45-alt1 sisyphus+235291.100.1.1 1564606222 installed <13>May 4 02:22:25 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+335067.4700.2.2 1701151286 installed <13>May 4 02:22:25 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed <13>May 4 02:22:25 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed <13>May 4 02:22:25 rpmi: perl-Clone-0.46-alt1 sisyphus+335067.1100.1.1 1700901562 installed <13>May 4 02:22:25 rpmi: perl-Term-Cap-1.18-alt1 sisyphus+315126.100.1.1 1676227129 installed <13>May 4 02:22:25 rpmi: perl-IO-String-1.08-alt2 1321677915 installed <13>May 4 02:22:25 rpmi: perl-Compress-Raw-Bzip2-2.210-alt1 sisyphus+343108.100.1.3 1710881036 installed <13>May 4 02:22:25 rpmi: perl-Algorithm-Diff-1:1.201-alt1 sisyphus+263447.100.1.1 1607956595 installed <13>May 4 02:22:25 rpmi: perl-Unicode-EastAsianWidth-12.0-alt1 sisyphus+237401.100.1.1 1568197363 installed <13>May 4 02:22:25 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>May 4 02:22:25 rpmi: perl-Filter-1.64-alt1 sisyphus+335067.400.1.1 1700901412 installed <13>May 4 02:22:25 rpmi: perl-Encode-3.21-alt1 sisyphus+343095.100.1.1 1710875477 installed <13>May 4 02:22:25 rpmi: perl-URI-5.27-alt1 sisyphus+340901.100.1.1 1708180683 installed <13>May 4 02:22:25 rpmi: perl-IO-Compress-2.206-alt1 sisyphus+325819.100.1.1 1690563199 installed <13>May 4 02:22:25 rpmi: perl-HTML-Parser-3.82-alt1 sisyphus+343116.100.1.3 1710883258 installed <13>May 4 02:22:25 rpmi: perl-Net-HTTP-6.23-alt1 sisyphus+323470.100.1.1 1687422469 installed <13>May 4 02:22:25 rpmi: perl-Pod-Simple-3.45-alt1 sisyphus+321554.100.1.1 1684663135 installed <13>May 4 02:22:25 rpmi: perl-Pod-Usage-2.03-alt1 sisyphus+300436.100.1.3 1653292807 installed <13>May 4 02:22:25 rpmi: perl-podlators-5.01-alt1 sisyphus+312638.100.1.1 1672339228 installed <13>May 4 02:22:25 rpmi: perl-IO-Zlib-1.15-alt1 sisyphus+343119.100.1.3 1710884191 installed <13>May 4 02:22:25 rpmi: perl-Archive-Tar-3.02-alt1 sisyphus+318647.100.1.1 1681742479 installed <13>May 4 02:22:25 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>May 4 02:22:25 rpmi: perl-libintl-1.33-alt1.1 sisyphus+335067.6600.2.2 1701152056 installed <13>May 4 02:22:25 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>May 4 02:22:25 rpmi: perl-IO-HTML-1.004-alt1 sisyphus+258983.100.1.1 1601542619 installed <13>May 4 02:22:25 rpmi: perl-HTTP-Message-6.45-alt1 sisyphus+330728.100.1.1 1696162276 installed <13>May 4 02:22:25 rpmi: perl-HTML-Form-6.11-alt1 sisyphus+315122.100.1.1 1676226686 installed <13>May 4 02:22:25 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>May 4 02:22:25 rpmi: perl-libwww-6.77-alt1 sisyphus+343120.100.1.2 1710884405 installed <13>May 4 02:22:25 rpmi: perl-HTML-Tree-5.07-alt1 sisyphus+277105.100.1.1 1625402682 installed <13>May 4 02:22:25 rpmi: perl-HTML-Formatter-2.16-alt2 sisyphus+306600.100.1.1 1663005434 installed <13>May 4 02:22:25 rpmi: perl-XML-Parser-2.47-alt1 sisyphus+337612.100.1.1 1704201438 installed <13>May 4 02:22:25 rpmi: perl-XML-Twig-3.52-alt1 sisyphus+277116.100.1.2 1625410693 installed <13>May 4 02:22:25 rpmi: perl-Net-DBus-1.2.0-alt1 sisyphus+335067.4300.2.2 1701150369 installed <13>May 4 02:22:25 rpmi: perl-XML-XPath-1.48-alt1 sisyphus+305097.100.1.2 1660226797 installed <13>May 4 02:22:25 rpmi: perl-HTTP-Cookies-6.11-alt1 sisyphus+336115.100.1.1 1702044494 installed <13>May 4 02:22:25 rpmi: perl-WWW-Mechanize-2.18-alt1 sisyphus+339965.100.1.3 1707245616 installed <13>May 4 02:22:25 rpmi: perl-Text-CSV_XS-1.53-alt1 sisyphus+335870.100.1.1 1701794985 installed <13>May 4 02:22:25 rpmi: perl-Spreadsheet-ParseExcel-1:0.66-alt1 sisyphus+337637.100.1.1 1704230912 installed <13>May 4 02:22:25 rpmi: libtre5-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed <13>May 4 02:22:25 rpmi: libtexlua5-2022-alt0_10 sisyphus+342516.200.3.2 1710234717 installed <13>May 4 02:22:25 rpmi: libteckit-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed <13>May 4 02:22:25 rpmi: libteckit-utils-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed <13>May 4 02:22:25 rpmi: libsynctex2-2022-alt0_10 sisyphus+342516.200.3.2 1710234717 installed <13>May 4 02:22:25 rpmi: libqqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed <13>May 4 02:22:25 rpmi: qqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed <13>May 4 02:22:25 rpmi: libpotrace-1.16-alt2 sisyphus+328401.100.1.1 1693483624 installed <13>May 4 02:22:25 rpmi: poppler-data-0.4.12-alt1 sisyphus+322151.100.1.1 1685438511 installed <13>May 4 02:22:25 rpmi: libpipeline-1.5.7-alt1_1 sisyphus+312433.100.1.1 1671879773 installed <13>May 4 02:22:25 rpmi: man-db-2.12.0-alt1 sisyphus+336930.2100.1.1 1703107121 installed <13>May 4 02:22:25 rpmi: liblua5.4-5.4.6-alt1 sisyphus+342744.200.2.1 1710617890 installed <13>May 4 02:22:25 rpmi: lua5.4-5.4.6-alt1 sisyphus+342744.200.2.1 1710617890 installed <13>May 4 02:22:26 rpmi: libxblas-1.0.248-alt2 sisyphus+285045.40.2.1 1631388330 installed <13>May 4 02:22:26 rpmi: liblapack-1:3.8.0-alt7 sisyphus+340675.300.1.1 1707908338 installed <13>May 4 02:22:26 rpmi: libkpathsea6-2022-alt0_10 sisyphus+342516.200.3.2 1710234717 installed <13>May 4 02:22:26 rpmi: libptexenc1-2022-alt0_10 sisyphus+342516.200.3.2 1710234717 installed <13>May 4 02:22:26 rpmi: libusb-1.0.27-alt1 sisyphus+347412.100.1.1 1714739651 installed <13>May 4 02:22:26 rpmi: libnpth-1.6.0.20.g7e45b50-alt3 sisyphus+278566.100.1.1 1626114690 installed <13>May 4 02:22:26 rpmi: libksba-1.6.4-alt1 sisyphus+327218.400.1.1 1692093956 installed <13>May 4 02:22:26 rpmi: libgomp1-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:26 rpmi: libgomp13-devel-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:26 rpmi: libnuma-2.0.14-alt2 sisyphus+278485.100.1.1 1626104244 installed <13>May 4 02:22:26 rpmi: libx265-199-3.5-alt1.1 sisyphus+277560.100.1.1 1625697230 installed <13>May 4 02:22:26 rpmi: libgdk-pixbuf-locales-2.42.11-alt1 sisyphus+345586.100.1.1 1713719119 installed <13>May 4 02:22:26 rpmi: libfribidi-1.0.14-alt1 sisyphus+345841.100.1.1 1714055921 installed <13>May 4 02:22:26 rpmi: libde265-1.0.15-alt1 sisyphus+337190.100.1.1 1703502096 installed <13>May 4 02:22:26 rpmi: libdatrie-0.2.13-alt1_7 sisyphus+328221.100.1.1 1693336966 installed <13>May 4 02:22:26 rpmi: libthai-0.1.29-alt1_6 sisyphus+328230.100.1.2 1693348044 installed <13>May 4 02:22:26 rpmi: libaom3-3.5.0-alt2 sisyphus+335780.100.1.1 1701761281 installed <13>May 4 02:22:26 rpmi: javazi-2024a-alt1 sisyphus+344801.200.1.1 1712691734 installed <13>May 4 02:22:26 rpmi: hd2u-1.0.3-alt2 sisyphus+275312.100.2.1 1624906676 installed <13>May 4 02:22:26 rpmi: gpgme-common-1.23.2-alt3 sisyphus+347209.100.1.1 1714473066 installed <13>May 4 02:22:26 rpmi: publicsuffix-list-dafsa-20240415-alt1 sisyphus+345249.100.1.1 1713270235 installed <13>May 4 02:22:26 rpmi: libpsl-0.21.5-alt1 sisyphus+338474.100.1.1 1705684769 installed <13>May 4 02:22:26 rpmi: libnghttp3.9-1.2.0-alt1 sisyphus+343912.200.1.1 1711714725 installed <13>May 4 02:22:26 rpmi: libnghttp2-1.61.0-alt1 sisyphus+344450.100.1.1 1712304117 installed <13>May 4 02:22:26 rpmi: openldap-common-2.6.7-alt1 sisyphus+343335.200.1.1 1711113916 installed <13>May 4 02:22:26 rpmi: libntlm-1.5-alt1 sisyphus+278100.3300.1.1 1626058899 installed <13>May 4 02:22:26 rpmi: libidn-1.37-alt2 sisyphus+300849.100.1.1 1653769687 installed <13>May 4 02:22:26 rpmi: libedit3-3.1.20230828-alt1 sisyphus+330914.200.3.1 1696922743 installed <13>May 4 02:22:26 rpmi: libdeflate-1.20-alt1 sisyphus+343488.100.1.1 1711323991 installed <13>May 4 02:22:26 rpmi: libtiff5-4.4.0-alt4 sisyphus+322581.100.1.2 1686180089 installed <13>May 4 02:22:26 rpmi: libverto-0.3.2-alt1_1 sisyphus+321176.2200.10.2 1684803947 installed <13>May 4 02:22:26 rpmi: liblmdb-0.9.32-alt1 sisyphus+342426.100.1.1 1710124288 installed <13>May 4 02:22:26 rpmi: libkeyutils-1.6.3-alt1 sisyphus+266061.100.1.1 1612919566 installed <13>May 4 02:22:26 rpmi: libcom_err-1.46.4.0.5.4cda-alt1 sisyphus+283826.100.1.1 1629975345 installed <13>May 4 02:22:26 rpmi: gcc-fortran-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed <13>May 4 02:22:26 rpmi: libgfortran13-devel-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:27 rpmi: gcc13-fortran-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:27 rpmi: gcc-c++-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed <13>May 4 02:22:27 rpmi: libstdc++13-devel-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:28 rpmi: gcc13-c++-13.2.1-alt3 sisyphus+339335.100.1.1 1706563486 installed <13>May 4 02:22:28 rpmi: libX11-locales-3:1.8.8-alt1 sisyphus+343583.100.1.1 1711440719 installed <13>May 4 02:22:28 rpmi: libXdmcp-1.1.5-alt1 sisyphus+343583.700.1.1 1711441061 installed <13>May 4 02:22:28 rpmi: libxcb-1.17.0-alt1 sisyphus+345308.200.1.1 1713342004 installed <13>May 4 02:22:28 rpmi: libX11-3:1.8.8-alt1 sisyphus+343583.100.1.1 1711440719 installed <13>May 4 02:22:28 rpmi: libXext-1.3.6-alt1 sisyphus+343583.1000.1.1 1711441101 installed <13>May 4 02:22:28 rpmi: libXt-1.3.0-alt1 sisyphus+331490.500.1.1 1697023310 installed <13>May 4 02:22:28 rpmi: libXmu-1.2.0-alt1 sisyphus+343583.1200.1.1 1711441172 installed <13>May 4 02:22:28 rpmi: libXrender-0.9.11-alt1 sisyphus+308841.100.1.1 1666436130 installed <13>May 4 02:22:29 rpmi: libcairo-1:1.18.0-alt1 sisyphus+330227.100.1.1 1695539090 installed <13>May 4 02:22:29 rpmi: libXft-2.3.8-alt1 sisyphus+331490.400.1.1 1697023269 installed <13>May 4 02:22:29 rpmi: libXpm-3.5.17-alt1 sisyphus+330921.100.1.1 1696400257 installed <13>May 4 02:22:30 rpmi: libxcb-devel-1.17.0-alt1 sisyphus+345308.200.1.1 1713342004 installed <13>May 4 02:22:30 rpmi: libX11-devel-3:1.8.8-alt1 sisyphus+343583.100.1.1 1711440719 installed <13>May 4 02:22:30 rpmi: libXrender-devel-0.9.11-alt1 sisyphus+308841.100.1.1 1666436130 installed <13>May 4 02:22:30 rpmi: libXext-devel-1.3.6-alt1 sisyphus+343583.1000.1.1 1711441101 installed <13>May 4 02:22:30 rpmi: libXt-devel-1.3.0-alt1 sisyphus+331490.500.1.1 1697023310 installed <13>May 4 02:22:30 rpmi: libXaw-1.0.16-alt1 sisyphus+343583.400.1.1 1711440833 installed <13>May 4 02:22:30 rpmi: libtk-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed <13>May 4 02:22:30 rpmi: tk-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed <13>May 4 02:22:30 rpmi: perl-Tk-804.036-alt1 sisyphus+335067.4600.2.2 1701151239 installed <13>May 4 02:22:30 rpmi: libharfbuzz-cairo-8.4.0-alt1 sisyphus+344161.100.1.1 1711987962 installed <13>May 4 02:22:30 rpmi: xset-1.2.4-alt1 sisyphus+275497.100.2.2 1624918317 installed <13>May 4 02:22:30 rpmi: xprop-1.2.5-alt1 sisyphus+279025.100.1.1 1626354198 installed <13>May 4 02:22:30 rpmi: xdg-utils-1.1.3-alt12 sisyphus+303279.300.3.1 1657254392 installed <13>May 4 02:22:30 rpmi: desktop-file-utils-0.26-alt6 sisyphus+331944.100.1.3 1697550026 installed <13>May 4 02:22:30 rpmi: shared-mime-info-2.4-alt1 sisyphus+334259.100.1.1 1699787316 installed <13>May 4 02:22:30 rpmi: gsettings-desktop-schemas-data-46.0-alt1 sisyphus+343025.100.4.2 1710847127 installed <13>May 4 02:22:30 rpmi: libgio-2.80.0-alt2.1 sisyphus+343856.100.1.1 1711642821 installed <13>May 4 02:22:30 rpmi: gsettings-desktop-schemas-46.0-alt1 sisyphus+343025.100.4.2 1710847127 installed <13>May 4 02:22:30 rpmi: libgdk-pixbuf-2.42.11-alt1 sisyphus+345586.100.1.1 1713719119 installed <13>May 4 02:22:30 rpmi: libheif-1.17.6-alt1 sisyphus+337190.200.1.1 1703502141 installed <13>May 4 02:22:30 rpmi: libgd3-2.3.3-alt2 sisyphus+335387.100.1.1 1701278641 installed <13>May 4 02:22:30 rpmi: libpango-1.52.2-alt1 sisyphus+344075.100.1.1 1711911777 installed <13>May 4 02:22:30 rpmi: libmpdec3-2.5.1-alt3 sisyphus+314490.500.5.1 1675432004 installed <13>May 4 02:22:30 rpmi: libb2-0.98.1-alt1_1 sisyphus+291614.100.1.1 1638962877 installed <13>May 4 02:22:30 rpmi: ed-1:0.2-alt10 sisyphus+278100.1100.1.1 1626056843 installed <13>May 4 02:22:30 rpmi: diffstat-1.64-alt1 sisyphus+278100.700.1.1 1626056683 installed <13>May 4 02:22:30 rpmi: libdialog-1.3.20171209-alt2 sisyphus+328094.100.1.1 1693228848 installed <13>May 4 02:22:30 rpmi: dialog-1.3.20171209-alt2 sisyphus+328094.100.1.1 1693228848 installed <13>May 4 02:22:30 rpmi: rpm-macros-alternatives-0.5.2-alt2 sisyphus+315270.200.2.1 1676457367 installed <13>May 4 02:22:30 rpmi: alternatives-0.5.2-alt2 sisyphus+315270.200.2.1 1676457367 installed <13>May 4 02:22:31 rpmi: ca-certificates-2024.02.24-alt1 sisyphus+341362.100.1.1 1708791001 installed <13>May 4 02:22:31 rpmi: ca-trust-0.2.0-alt1 sisyphus+344843.100.1.1 1712743326 installed <13>May 4 02:22:31 rpmi: p11-kit-trust-1:0.25.3-alt2 sisyphus+336533.100.1.1 1702645560 installed <13>May 4 02:22:31 rpmi: libcrypto3-3.1.5-alt2 sisyphus+343320.140.3.1 1711982212 installed <13>May 4 02:22:31 rpmi: libssl3-3.1.5-alt2 sisyphus+343320.140.3.1 1711982212 installed <86>May 4 02:22:31 groupadd[2270075]: group added to /etc/group: name=_keytab, GID=999 <86>May 4 02:22:31 groupadd[2270075]: group added to /etc/gshadow: name=_keytab <86>May 4 02:22:31 groupadd[2270075]: new group: name=_keytab, GID=999 <13>May 4 02:22:31 rpmi: libkrb5-1.21.2-alt2 sisyphus+338902.100.2.1 1706700934 installed <13>May 4 02:22:31 rpmi: python3-3.12.2-alt1 sisyphus+341702.200.1.1 1709232871 installed <13>May 4 02:22:32 rpmi: python3-base-3.12.2-alt1 sisyphus+341702.200.1.1 1709232871 installed <13>May 4 02:22:32 rpmi: python3-module-packaging-24.0-alt1 sisyphus+342487.100.2.1 1710407438 installed <13>May 4 02:22:32 rpmi: glib2-devel-2.80.0-alt2.1 sisyphus+343856.100.1.1 1711642821 installed <13>May 4 02:22:32 rpmi: libcairo-devel-1:1.18.0-alt1 sisyphus+330227.100.1.1 1695539090 installed <13>May 4 02:22:32 rpmi: fontconfig-devel-2.14.2-alt8 sisyphus+328444.100.1.1 1693553402 installed <13>May 4 02:22:32 rpmi: libfreetype-devel-2.13.2-alt1 sisyphus+328677.100.1.1 1693834345 installed <13>May 4 02:22:32 rpmi: libharfbuzz-devel-8.4.0-alt1 sisyphus+344161.100.1.1 1711987962 installed <13>May 4 02:22:32 rpmi: libXft-devel-2.3.8-alt1 sisyphus+331490.400.1.1 1697023269 installed <13>May 4 02:22:32 rpmi: libcups-2.4.7-alt2 sisyphus+333092.100.1.1 1698654160 installed <13>May 4 02:22:33 rpmi: libgs-10.01.1-alt2 sisyphus+337968.300.3.1 1705654974 installed <13>May 4 02:22:34 rpmi: ghostscript-common-10.01.1-alt2 sisyphus+337968.300.3.1 1705654974 installed <13>May 4 02:22:34 rpmi: ghostscript-classic-10.01.1-alt2 sisyphus+337968.300.3.1 1705654974 installed <13>May 4 02:22:35 rpmi: ghostscript-10.01.1-alt2 sisyphus+337968.300.3.1 1705654974 installed <13>May 4 02:22:35 rpmi: ghostscript-module-X-10.01.1-alt2 sisyphus+337968.300.3.1 1705654974 installed <13>May 4 02:22:35 rpmi: libgsasl-2.2.0-alt1 sisyphus+333173.100.1.1 1698696954 installed <86>May 4 02:22:35 groupadd[2271675]: group added to /etc/group: name=sasl, GID=998 <86>May 4 02:22:35 groupadd[2271675]: group added to /etc/gshadow: name=sasl <86>May 4 02:22:35 groupadd[2271675]: new group: name=sasl, GID=998 <13>May 4 02:22:35 rpmi: libsasl2-3-2.1.28-alt2 sisyphus+343335.100.1.1 1711112544 installed <13>May 4 02:22:35 rpmi: libldap2-2.6.7-alt1 sisyphus+343335.200.1.1 1711113916 installed <86>May 4 02:22:35 groupadd[2271687]: group added to /etc/group: name=_gnupg, GID=997 <86>May 4 02:22:35 groupadd[2271687]: group added to /etc/gshadow: name=_gnupg <86>May 4 02:22:35 groupadd[2271687]: new group: name=_gnupg, GID=997 <13>May 4 02:22:35 rpmi: gnupg2-2.4.3-alt1 sisyphus+327229.100.1.1 1692102992 installed <13>May 4 02:22:35 rpmi: libgpgme11-1.23.2-alt3 sisyphus+347209.100.1.1 1714473066 installed <13>May 4 02:22:35 rpmi: libgpgmepp6-1.23.2-alt3 sisyphus+347209.100.1.1 1714473066 installed <13>May 4 02:22:35 rpmi: perl-Net-SSLeay-1.94-alt1 sisyphus+340982.100.1.1 1708280650 installed <13>May 4 02:22:35 rpmi: perl-IO-Socket-SSL-2.085-alt1 sisyphus+339115.100.1.1 1706295283 installed <13>May 4 02:22:35 rpmi: perl-Net-HTTPS-6.23-alt1 sisyphus+323470.100.1.1 1687422469 installed <13>May 4 02:22:35 rpmi: perl-LWP-Protocol-https-6.14-alt1 sisyphus+343123.100.1.3 1710885316 installed <13>May 4 02:22:35 rpmi: openssh-common-9.6p1-alt1 sisyphus+338324.200.2.1 1706093654 installed <86>May 4 02:22:35 groupadd[2271720]: group added to /etc/group: name=sshagent, GID=996 <86>May 4 02:22:35 groupadd[2271720]: group added to /etc/gshadow: name=sshagent <86>May 4 02:22:35 groupadd[2271720]: new group: name=sshagent, GID=996 <13>May 4 02:22:35 rpmi: openssh-clients-9.6p1-alt1 sisyphus+338324.200.2.1 1706093654 installed <13>May 4 02:22:35 rpmi: rsync-3.2.7-alt1 sisyphus+325006.2000.1.1 1689497333 installed <13>May 4 02:22:35 rpmi: libssh2-1.11.0-alt2 sisyphus+339356.100.1.1 1706593137 installed <13>May 4 02:22:35 rpmi: libcurl-8.7.1-alt2 sisyphus+345773.100.1.1 1713974723 installed <13>May 4 02:22:36 rpmi: git-core-2.42.1-alt1 sisyphus+333661.100.1.1 1699193182 installed <13>May 4 02:22:36 rpmi: ca-trust-java-0.2.0-alt1 sisyphus+344843.100.1.1 1712743326 installed <13>May 4 02:22:36 rpmi: libnss-3.99-alt1 sisyphus+344230.420.10.1 1712504446 installed <13>May 4 02:22:36 rpmi: libpoppler130-23.08.0-alt4 sisyphus+341496.100.1.1 1709026260 installed <13>May 4 02:22:36 rpmi: poppler-23.08.0-alt4 sisyphus+341496.100.1.1 1709026260 installed <13>May 4 02:22:36 rpmi: foomatic-db-engine-4.0.12-alt1 sisyphus+278189.100.1.1 1626076171 installed <13>May 4 02:22:37 rpmi: texlive-2022-alt0_10 sisyphus+342516.200.3.2 1710234717 installed <13>May 4 02:22:50 rpmi: texlive-collection-basic-2022-alt0_12 sisyphus+342303.200.3.1 1710171325 installed <13>May 4 02:22:51 rpmi: texlive-fonts-sources-2022-alt0_12 sisyphus+342303.200.3.1 1710171325 installed <13>May 4 02:22:51 rpmi: texlive-texmf-2022-alt0_12 sisyphus+342303.200.3.1 1710171325 installed <13>May 4 02:23:37 rpmi: texlive-dist-2022-alt0_12 sisyphus+342303.200.3.1 1710171325 installed <13>May 4 02:23:37 rpmi: alsa-ucm-conf-1.2.10-alt2 sisyphus+337619.100.1.1 1704220124 installed <13>May 4 02:23:37 rpmi: alsa-topology-conf-1.2.5.1-alt1 sisyphus+274777.100.1.1 1624089141 installed <13>May 4 02:23:37 rpmi: libalsa-1:1.2.10-alt2 sisyphus+337619.200.1.1 1704220185 installed <13>May 4 02:23:40 rpmi: java-21-openjdk-headless-0:21.0.2.0.13-alt2 sisyphus+339996.100.1.1 1707300603 installed <13>May 4 02:23:41 rpmi: libcurl-devel-8.7.1-alt2 sisyphus+345773.100.1.1 1713974723 installed <13>May 4 02:23:41 rpmi: libpango-devel-1.52.2-alt1 sisyphus+344075.100.1.1 1711911777 installed <13>May 4 02:23:41 rpmi: tk-devel-8.6.13-alt1 sisyphus+310696.200.1.1 1669548530 installed <13>May 4 02:23:41 rpmi: libXmu-devel-1.2.0-alt1 sisyphus+343583.1200.1.1 1711441172 installed <13>May 4 02:23:41 rpmi: gcc-c++-13-alt1 sisyphus+323337.300.1.1 1687267966 installed <13>May 4 02:23:41 rpmi: gcc-fortran-13-alt1 sisyphus+323337.300.1.1 1687267966 installed <13>May 4 02:23:41 rpmi: libtiff-devel-4.4.0-alt4 sisyphus+322581.100.1.2 1686180089 installed <13>May 4 02:23:41 rpmi: libgomp-devel-13-alt1 sisyphus+323337.300.1.1 1687267966 installed <13>May 4 02:23:41 rpmi: liblapack-devel-1:3.8.0-alt7 sisyphus+340675.300.1.1 1707908338 installed <13>May 4 02:23:41 rpmi: libtre-devel-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed <13>May 4 02:23:41 rpmi: makeinfo-7.1-alt1 sisyphus+338907.200.3.1 1706718831 installed <13>May 4 02:23:41 rpmi: libjpeg-devel-2:3.0.2-alt2.1 sisyphus+340135.100.1.1 1707449145 installed <13>May 4 02:23:41 rpmi: texi2dvi-7.1-alt1 sisyphus+338907.200.3.1 1706718831 installed <13>May 4 02:23:41 rpmi: libreadline-devel-8.2.10-alt1 sisyphus+338911.100.4.1 1706717067 installed <13>May 4 02:23:41 rpmi: libpcre2-devel-10.43-alt1 sisyphus+340880.100.1.1 1708164071 installed <13>May 4 02:23:41 rpmi: liblzma-devel-5.4.5-alt1 sisyphus+338177.300.3.1 1707490235 installed <13>May 4 02:23:41 rpmi: bzlib-devel-1:1.0.8-alt3 sisyphus+327286.5000.14.1 1711487039 installed egrep: warning: egrep is obsolescent; using grep -E Building target platforms: x86_64 Building for target x86_64 Wrote: /usr/src/in/nosrpm/R-base-4.2.2-alt2.nosrc.rpm (w1.gzdio) Installing R-base-4.2.2-alt2.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.19740 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-4.2.2 + echo 'Source #0 (R-4.2.2.tar):' Source #0 (R-4.2.2.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-4.2.2.tar + cd R-4.2.2 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-4.2.2-alt2.patch):' Patch #0 (R-4.2.2-alt2.patch): + /usr/bin/patch -p1 patching file .gear/R-base-4.1.3-alt-fix-build-libcurl8.patch patching file .gear/rules patching file .gear/tags/090724dbb6a4b610aebe571d65fd3f728697d791 patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0 patching file .gear/tags/1af743c7e25d963067c0a7736c2f362bc1a54087 patching file .gear/tags/1c120fe0028c5f64c67f1a04eeed89140e84044a patching file .gear/tags/2c68f436cffd98cb9581510d928bea5942555c48 patching file .gear/tags/54c0af5d3e579ef9d459def6e87471043832c3ed patching file .gear/tags/70ae5201e8ecc68e51ed59c0bedcfa01dbb4b579 patching file .gear/tags/890191223501f9206c89761358c534357f6c76b8 patching file .gear/tags/927c0ab3556c90b625751594da83a9926a6014d6 patching file .gear/tags/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0 patching file .gear/tags/a267957eb382565da32225335ac89fb8c75df0da patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5 patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e patching file .gear/tags/b058f2b5de79631ea567c44d0a2ef87939a28ec5 patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020 patching file .gear/tags/d1aa04cfbb52bb55a5c03a5323d797c2bf87b6a9 patching file .gear/tags/d4cbf2db4bf99fe20d6f904178cbebb8619dab9a patching file .gear/tags/dbe24e8137437d3688e1d77cf1b67279d3099cea patching file .gear/tags/e6f3c8b737583c5e27038507647866d029bfb5e4 patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061 patching file .gear/tags/eca5e30f29900b6f8279889e83a532a8cb55697a patching file .gear/tags/eef29626bf3bf68c9462ce5f0594fedd5a80168b patching file .gear/tags/f1447dd74acee19fdf9c5adc838da57bef3c8142 patching file .gear/tags/f600e7641c9fbf40a0abc5b1cdd67c703376e847 patching file .gear/tags/fdd01de5a3b9e7e6d41e1f4f9db33a99b6973818 patching file .gear/tags/list patching file R-base.spec patching file src/extra/blas/Makefile.in patching file src/extra/xdr/Makefile.in patching file tests/d-p-q-r-tst-2.R patching file tests/reg-tests-1c.R patching file tests/reg-tests-1d.R + echo 'Patch #1 (R-base-4.1.3-alt-fix-build-libcurl8.patch):' Patch #1 (R-base-4.1.3-alt-fix-build-libcurl8.patch): + /usr/bin/patch -p1 patching file configure Hunk #1 succeeded at 47584 (offset 156 lines). Hunk #2 succeeded at 47602 (offset 156 lines). patching file m4/R.m4 Hunk #1 succeeded at 4300 (offset 29 lines). + rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f + exit 0 Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.19740 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.2.2 + export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=xdg-open ac_cv_path_R_PDFVIEWER=xdg-open 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr + lt_cv_prog_cc_static_works=no + ac_cv_path_R_ZIPCMD=zip + ac_cv_path_R_UNZIPCMD=unzip + ac_cv_path_R_BROWSER=xdg-open + ac_cv_path_R_PDFVIEWER=xdg-open + ac_cv_path_PAGER='less -isR' + ac_cv_prog_R_PRINTCMD=lpr + CFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing' + export CFLAGS + CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing' + export CXXFLAGS + FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing' + export FFLAGS + FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing' + export FCFLAGS + '[' -n '' ']' ++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing' ++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g' + ASFLAGS= + export ASFLAGS + export lt_cv_deplibs_check_method=pass_all + lt_cv_deplibs_check_method=pass_all + readlink -e -- ./configure + xargs -ri dirname -- '{}' + xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n' + sort -u + xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess + configure_runstatedir_flags= + grep -qF runstatedir=DIR ./configure + configure_runstatedir_flags=--runstatedir=/var/run + ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --disable-silent-rules --runstatedir=/var/run --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --disable-rpath --with-system-tre --with-gnu-ld --enable-long-double --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-4.2' configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules checking build system type... x86_64-alt-linux-gnu checking host system type... x86_64-alt-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /usr/bin/pwd checking whether builddir is srcdir... yes checking whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /usr/bin/ginstall -c checking for sed... /usr/bin/sed checking for which... /usr/bin/which checking for less... (cached) less -isR checking for gtar... /usr/bin/gtar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... missing configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally checking for unzip... (cached) unzip checking for zip... (cached) zip checking for gzip... /usr/bin/gzip checking for bzip2... /usr/bin/bzip2 checking for firefox... (cached) xdg-open using default browser ... xdg-open checking for acroread... (cached) xdg-open checking for working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/bin/realpath checking for pkg-config... /usr/bin/pkg-config checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether x86_64-alt-linux-gcc accepts -g... yes checking for x86_64-alt-linux-gcc option to enable C11 features... none needed checking how to run the C preprocessor... x86_64-alt-linux-gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether x86_64-alt-linux-gcc needs -traditional... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking for sys/time.h... yes checking for sys/param.h... yes checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking how to run the C preprocessor... x86_64-alt-linux-gcc -E looking for a modern Fortran compiler checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran checking whether the compiler supports GNU Fortran... yes checking whether x86_64-alt-linux-gfortran accepts -g... yes checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++ checking whether the compiler supports GNU C++... yes checking whether x86_64-alt-linux-g++ accepts -g... yes checking for x86_64-alt-linux-g++ option to enable C++11 features... none needed checking whether x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing can compile C++ code... yes checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes checking whether x86_64-alt-linux-g++ accepts -fvisibility... yes checking whether x86_64-alt-linux-gfortran accepts -fvisibility... yes checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether the compiler supports GNU Objective C... no checking whether x86_64-alt-linux-gcc accepts -g... no checking whether x86_64-alt-linux-g++ can compile ObjC++... no checking for Objective C++ compiler... no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-alt-linux-gnu file names to x86_64-alt-linux-gnu format... func_convert_file_noop checking how to convert x86_64-alt-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-alt-linux-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... (cached) pass_all checking for x86_64-alt-linux-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-alt-linux-ar... (cached) ar checking for archiver @FILE support... @ checking for x86_64-alt-linux-strip... no checking for strip... strip checking for x86_64-alt-linux-ranlib... no checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for x86_64-alt-linux-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-gcc static flag -static works... no checking if x86_64-alt-linux-gcc supports -c -o file.o... yes checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-g++ static flag -static works... no checking if x86_64-alt-linux-g++ supports -c -o file.o... yes checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes checking if x86_64-alt-linux-gfortran static flag -static works... no checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking for readline/history.h... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking for fcntl.h... yes checking for glob.h... yes checking for grp.h... yes checking for pwd.h... yes checking for sched.h... yes checking for strings.h... (cached) yes checking for sys/resource.h... yes checking for sys/select.h... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking for sys/time.h... (cached) yes checking for sys/times.h... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking for utime.h... yes checking for arpa/inet.h... yes checking for elf.h... yes checking for features.h... yes checking for floatingpoint.h... no checking for langinfo.h... yes checking for netdb.h... yes checking for netinet/in.h... yes checking for sys/param.h... (cached) yes checking for stdalign.h... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking for limits.h... yes checking for locale.h... yes checking for stdarg.h... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking for x86_64-alt-linux-gcc options needed to detect all undeclared functions... none needed checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking for C stack direction... down checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes checking for x86_64-alt-linux-gcc option to support OpenMP... -fopenmp checking how to get verbose linking output from x86_64-alt-linux-gfortran... -v checking for Fortran libraries of x86_64-alt-linux-gfortran... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from x86_64-alt-linux-gcc... -v checking for C libraries of x86_64-alt-linux-gcc... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/13/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether x86_64-alt-linux-gfortran appends underscores to external names... yes checking whether x86_64-alt-linux-gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on int and double... yes checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on double complex... yes checking for x86_64-alt-linux-gfortran option to support OpenMP... -fopenmp checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking for ObjC runtime library... checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no checking if need -fno-optimize-sibling-calls for gfortran... yes checking for type of 'hidden' Fortran character lengths... size_t checking for xmkmf... no checking whether x86_64-alt-linux-g++ supports C++11 features with -std=gnu++11... yes checking whether x86_64-alt-linux-g++ supports C++14 features with -std=gnu++14... yes checking whether x86_64-alt-linux-g++ supports C++17 features with -std=gnu++17... yes checking whether x86_64-alt-linux-g++ supports C++20 features with -std=gnu++20... yes checking for x86_64-alt-linux-g++ -std=gnu++14 option to support OpenMP... -fopenmp checking for option providing pthread_kill... none required checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwnam exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... no checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... yes checking whether mktime works correctly outside 1902-2037... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_ in -lopenblas... yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking whether iconv accepts "CP1252"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for wchar.h... (cached) yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking whether wcwidth exists and is declared... yes checking whether wcswidth exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking for X11/Xmu/Atoms.h... yes checking for XmuInternAtom in -lXmu... yes checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh checking for tcl.h... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking for rpc/types.h... no checking for tirpc/rpc/types.h... no checking for XDR support... no checking for inflateInit2_ in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking for BZ2_bzlibVersion in -lbz2... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking for pcre2.h... yes checking for pcre2_compile_8 in -lpcre2-8... yes checking if PCRE2 has Unicode support... yes checking whether PCRE support suffices... yes checking for tre_regncompb in -ltre... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 8.7.1 checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.28.0 or 8... yes checking if libcurl supports https... yes checking if pkg-config knows about libjpeg... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if pkg-config knows about libpng... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking if pkg-config knows about libtiff... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for struct stat.st_atim.tv_nsec... yes checking whether struct stat.st_atim is of type struct timespec... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for lpr... (cached) lpr checking for paperconf... false checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for x86_64-alt-linux-gfortran option to support OpenMP... (cached) -fopenmp checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a race-free mkdir -p... /usr/bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for x86_64-alt-linux-ranlib... ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... no checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.8.2, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules R is now configured for x86_64-alt-linux-gnu Source directory: . Installation directory: /usr C compiler: x86_64-alt-linux-gcc -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing Fortran fixed-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing Default C++ compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing C++11 compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing C++14 compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing C++17 compiler: x86_64-alt-linux-g++ -std=gnu++17 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing C++20 compiler: x86_64-alt-linux-g++ -std=gnu++20 -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing Fortran free-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing Obj-C compiler: x86_64-alt-linux-gcc Interfaces supported: X11, tcltk External libraries: pcre2, readline, BLAS(OpenBLAS), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, static HTML Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally + make -j8 make[1]: Nothing to be done for 'R'. make[1]: Nothing to be done for 'R'. make[2]: Nothing to be done for 'R'. make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts' creating src/scripts/R.fe make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/scripts' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/include' mkdir -p -- ../../include make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/include' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/include/R_ext' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' making xdr_float.d from xdr_float.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' making xdr_mem.d from xdr_mem.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' making xdr.d from xdr.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' making xdr_stdio.d from xdr_stdio.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making regerror.d from regerror.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making regcomp.d from regcomp.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making regexec.d from regexec.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-ast.d from tre-ast.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-match-backtrack.d from tre-match-backtrack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-match-approx.d from tre-match-approx.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-compile.d from tre-compile.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-match-parallel.d from tre-match-parallel.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-mem.d from tre-mem.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-parse.d from tre-parse.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making tre-stack.d from tre-stack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' making xmalloc.d from xmalloc.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr.c -o xdr.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_float.c -o xdr_float.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' ar -cr libxdr.a xdr.o xdr_float.o xdr_mem.o xdr_stdio.o ranlib libxdr.a make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o xmalloc.c: In function 'xrealloc_impl': xmalloc.c:358:7: warning: pointer 'ptr_19(D)' may be used after 'realloc' [-Wuse-after-free] 358 | hash_table_del(xmalloc_table, ptr); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmalloc.c:355:13: note: call to 'realloc' here 355 | new_ptr = realloc(ptr, new_size); | ^~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/extra/tre' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making interv.d from interv.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making integrate.d from integrate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making maxcol.d from maxcol.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making pretty.d from pretty.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making uncmin.d from uncmin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' making optim.d from optim.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c interv.c -o interv.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpbfa.f -o dpbfa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dchdc.f -o dchdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpbsl.f -o dpbsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c maxcol.c -o maxcol.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpodi.f -o dpodi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pretty.c -o pretty.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpoco.f -o dpoco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpofa.f -o dpofa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dposl.f -o dposl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrls.f -o dqrls.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrdc.f -o dqrdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrsl.f -o dqrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dqrutl.f -o dqrutl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c integrate.c -o integrate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrsl.f -o dtrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrco.f -o dtrco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsvdc.f -o dsvdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c uncmin.c -o uncmin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c optim.c -o optim.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/appl' #@make install-Linpack make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making fmax2.d from fmax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making mlutils.d from mlutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making d1mach.d from d1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making i1mach.d from i1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making fmin2.d from fmin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making fprec.d from fprec.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making fround.d from fround.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making ftrunc.d from ftrunc.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making sign.d from sign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making imax2.d from imax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making fsign.d from fsign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making imin2.d from imin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making chebyshev.d from chebyshev.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making lgammacor.d from lgammacor.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making log1p.d from log1p.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making gammalims.d from gammalims.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making stirlerr.d from stirlerr.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making bd0.d from bd0.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making gamma.d from gamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making lgamma.d from lgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making gamma_cody.d from gamma_cody.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making beta.d from beta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making lbeta.d from lbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making polygamma.d from polygamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making cospi.d from cospi.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making bessel_i.d from bessel_i.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making bessel_j.d from bessel_j.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making bessel_k.d from bessel_k.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making bessel_y.d from bessel_y.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making sexp.d from sexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making choose.d from choose.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making snorm.d from snorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dgamma.d from dgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pgamma.d from pgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qgamma.d from qgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rgamma.d from rgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dbeta.d from dbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pbeta.d from pbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qbeta.d from qbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rbeta.d from rbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dunif.d from dunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making punif.d from punif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qunif.d from qunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making runif.d from runif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnorm.d from dnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnorm.d from pnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnorm.d from qnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rnorm.d from rnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dlnorm.d from dlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making plnorm.d from plnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qlnorm.d from qlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rlnorm.d from rlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making df.d from df.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pf.d from pf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qf.d from qf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rf.d from rf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnf.d from dnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dt.d from dt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pt.d from pt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qt.d from qt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rt.d from rt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnt.d from dnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dchisq.d from dchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pchisq.d from pchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qchisq.d from qchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rchisq.d from rchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rnchisq.d from rnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dbinom.d from dbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pbinom.d from pbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qbinom.d from qbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rbinom.d from rbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rmultinom.d from rmultinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dcauchy.d from dcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pcauchy.d from pcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qcauchy.d from qcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rcauchy.d from rcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dexp.d from dexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pexp.d from pexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qexp.d from qexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rexp.d from rexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dgeom.d from dgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pgeom.d from pgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qgeom.d from qgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rgeom.d from rgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dhyper.d from dhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making phyper.d from phyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qhyper.d from qhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnbinom.d from dnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rhyper.d from rhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnbinom.d from pnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnbinom.d from qnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnbinom_mu.d from qnbinom_mu.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rnbinom.d from rnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dpois.d from dpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making ppois.d from ppois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qpois.d from qpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rpois.d from rpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pweibull.d from pweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dweibull.d from dweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qweibull.d from qweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rweibull.d from rweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dlogis.d from dlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making plogis.d from plogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qlogis.d from qlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making rlogis.d from rlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnchisq.d from dnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnchisq.d from pnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnchisq.d from qnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making dnbeta.d from dnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnbeta.d from pnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnbeta.d from qnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnf.d from pnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making pnt.d from pnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnf.d from qnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qnt.d from qnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making ptukey.d from ptukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making qtukey.d from qtukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making toms708.d from toms708.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making wilcox.d from wilcox.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' making signrank.d from signrank.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mlutils.c -o mlutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fmin2.c -o fmin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c i1mach.c -o i1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c d1mach.c -o d1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fmax2.c -o fmax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ftrunc.c -o ftrunc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fprec.c -o fprec.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fround.c -o fround.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sign.c -o sign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fsign.c -o fsign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c imax2.c -o imax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c imin2.c -o imin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c log1p.c -o log1p.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gammalims.c -o gammalims.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgammacor.c -o lgammacor.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chebyshev.c -o chebyshev.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stirlerr.c -o stirlerr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgamma.c -o lgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bd0.c -o bd0.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gamma.c -o gamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c beta.c -o beta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lbeta.c -o lbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c polygamma.c -o polygamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cospi.c -o cospi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c choose.c -o choose.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c snorm.c -o snorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bessel_i.c -o bessel_i.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bessel_y.c -o bessel_y.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bessel_k.c -o bessel_k.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bessel_j.c -o bessel_j.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sexp.c -o sexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgamma.c -o dgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pbeta.c -o pbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dbeta.c -o dbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rgamma.c -o rgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rbeta.c -o rbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qgamma.c -o qgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pgamma.c -o pgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dunif.c -o dunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qbeta.c -o qbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c runif.c -o runif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c punif.c -o punif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qunif.c -o qunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnorm.c -o dnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnorm.c -o pnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnorm.c -o qnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rnorm.c -o rnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dlnorm.c -o dlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plnorm.c -o plnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qlnorm.c -o qlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlnorm.c -o rlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c df.c -o df.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pf.c -o pf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qf.c -o qf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rf.c -o rf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnf.c -o dnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dt.c -o dt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pt.c -o pt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rt.c -o rt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dchisq.c -o dchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qt.c -o qt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnt.c -o dnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pchisq.c -o pchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qchisq.c -o qchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rchisq.c -o rchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rnchisq.c -o rnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dbinom.c -o dbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pbinom.c -o pbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dcauchy.c -o dcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qbinom.c -o qbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rmultinom.c -o rmultinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rbinom.c -o rbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pcauchy.c -o pcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qcauchy.c -o qcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rcauchy.c -o rcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dexp.c -o dexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rexp.c -o rexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pexp.c -o pexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qexp.c -o qexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgeom.c -o dgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pgeom.c -o pgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qgeom.c -o qgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rgeom.c -o rgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dhyper.c -o dhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c phyper.c -o phyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qhyper.c -o qhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnbinom.c -o dnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rhyper.c -o rhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnbinom.c -o pnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rnbinom.c -o rnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbinom.c -o qnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbinom_mu.c -o qnbinom_mu.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpois.c -o dpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ppois.c -o ppois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qpois.c -o qpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpois.c -o rpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dweibull.c -o dweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pweibull.c -o pweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qweibull.c -o qweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rweibull.c -o rweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dlogis.c -o dlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plogis.c -o plogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlogis.c -o rlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qlogis.c -o qlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnchisq.c -o dnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnchisq.c -o qnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dnbeta.c -o dnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnchisq.c -o pnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnbeta.c -o qnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnbeta.c -o pnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnf.c -o pnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnf.c -o qnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pnt.c -o pnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qnt.c -o qnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qtukey.c -o qtukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ptukey.c -o ptukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c wilcox.c -o wilcox.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c signrank.c -o signrank.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c toms708.c -o toms708.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o qnbinom_mu.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making Rembedded.d from Rembedded.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making X11.d from X11.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making dynload.d from dynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making system.d from system.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making sys-unix.d from sys-unix.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' making sys-std.d from sys-std.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rembedded.c -o Rembedded.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dynload.c -o dynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c X11.c -o X11.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c system.c -o system.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sys-unix.c -o sys-unix.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sys-std.c -o sys-std.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-4.2.2"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making CommandLineArgs.d from CommandLineArgs.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making Renviron.d from Renviron.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making Rdynload.d from Rdynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making RNG.d from RNG.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making agrep.d from agrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making altrep.d from altrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making apply.d from apply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making altclasses.d from altclasses.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making arithmetic.d from arithmetic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making attrib.d from attrib.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making array.d from array.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making bind.d from bind.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making clippath.d from clippath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making character.d from character.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making builtin.d from builtin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making coerce.d from coerce.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making colors.d from colors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making cum.d from cum.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making complex.d from complex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making context.d from context.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making dcf.d from dcf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making datetime.d from datetime.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making debug.d from debug.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making connections.d from connections.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making deparse.d from deparse.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making devices.d from devices.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making dstruct.d from dstruct.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making duplicate.d from duplicate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making dotcode.d from dotcode.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making dounzip.d from dounzip.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making edit.d from edit.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making engine.d from engine.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making envir.d from envir.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making errors.d from errors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making format.d from format.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making gevents.d from gevents.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making gram-ex.d from gram-ex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making graphics.d from graphics.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making eval.d from eval.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making gram.d from gram.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making identical.d from identical.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making inlined.d from inlined.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making grep.d from grep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making inspect.d from inspect.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making internet.d from internet.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making iosupport.d from iosupport.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making lapack.d from lapack.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making list.d from list.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making localecharset.d from localecharset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making logic.d from logic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making mapply.d from mapply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making mask.d from mask.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making main.d from main.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making match.d from match.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making names.d from names.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making memory.d from memory.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making objects.d from objects.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making options.d from options.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making patterns.d from patterns.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making paste.d from paste.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making plot.d from plot.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making plot3d.d from plot3d.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making plotmath.d from plotmath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making platform.d from platform.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making print.d from print.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making printarray.d from printarray.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making printvector.d from printvector.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making printutils.d from printutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making qsort.d from qsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making radixsort.d from radixsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making random.d from random.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making raw.d from raw.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making registration.d from registration.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making relop.d from relop.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making rlocale.d from rlocale.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making saveload.d from saveload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making scan.d from scan.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making seq.d from seq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making sort.d from sort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making serialize.d from serialize.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making source.d from source.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making split.d from split.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making sprintf.d from sprintf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making startup.d from startup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making subassign.d from subassign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making subscript.d from subscript.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making subset.d from subset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making summary.d from summary.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making times.d from times.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making sysutils.d from sysutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making unique.d from unique.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making version.d from version.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making g_alab_her.d from g_alab_her.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making alloca.d from alloca.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making Rmain.d from Rmain.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making g_cntrlify.d from g_cntrlify.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making g_fontdb.d from g_fontdb.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making util.d from util.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making g_her_glyph.d from g_her_glyph.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making strdup.d from strdup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making strncasecmp.d from strncasecmp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' making mkdtemp.d from mkdtemp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Renviron.c -o Renviron.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c RNG.c -o RNG.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c apply.c -o apply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c altrep.c -o altrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdynload.c -o Rdynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agrep.c -o agrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c altclasses.c -o altclasses.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colors.c -o colors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c builtin.c -o builtin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bind.c -o bind.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c attrib.c -o attrib.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c character.c -o character.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c array.c -o array.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c complex.c -o complex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cum.c -o cum.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c arithmetic.c -o arithmetic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c context.c -o context.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dcf.c -o dcf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c debug.c -o debug.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coerce.c -o coerce.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devices.c -o devices.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dstruct.c -o dstruct.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c datetime.c -o datetime.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dounzip.c -o dounzip.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c edit.c -o edit.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c deparse.c -o deparse.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c duplicate.c -o duplicate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dotcode.c -o dotcode.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gevents.c -o gevents.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gram-ex.c -o gram-ex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graphics.c -o graphics.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c engine.c -o engine.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c connections.c -o connections.o connections.c: In function 'do_readLines': connections.c:4008:21: warning: pointer 'buf_89' may be used after 'realloc' [-Wuse-after-free] 4008 | free(buf); | ^~~~~~~~~ connections.c:4006:38: note: call to 'realloc' here 4006 | char *tmp = (char *) realloc(buf, buf_size); | ^~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c errors.c -o errors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c identical.c -o identical.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c inlined.c -o inlined.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c inspect.c -o inspect.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c internet.c -o internet.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c iosupport.c -o iosupport.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lapack.c -o lapack.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c localecharset.c -o localecharset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c envir.c -o envir.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c list.c -o list.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mask.c -o mask.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mapply.c -o mapply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c logic.c -o logic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c main.c -o main.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c match.c -o match.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gram.c -o gram.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c grep.c -o grep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c names.c -o names.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c patterns.c -o patterns.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c options.c -o options.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c paste.c -o paste.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot.c -o plot.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c objects.c -o objects.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot3d.c -o plot3d.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c printarray.c -o printarray.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c printvector.c -o printvector.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c platform.c -o platform.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c print.c -o print.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c printutils.c -o printutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c memory.c -o memory.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c registration.c -o registration.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plotmath.c -o plotmath.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qsort.c -o qsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c raw.c -o raw.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c random.c -o random.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c eval.c -o eval.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlocale.c -o rlocale.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c radixsort.c -o radixsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c scan.c -o scan.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c relop.c -o relop.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c source.c -o source.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c split.c -o split.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c saveload.c -o saveload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c startup.c -o startup.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c seq.c -o seq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sprintf.c -o sprintf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sort.c -o sort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c serialize.c -o serialize.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c times.c -o times.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c subscript.c -o subscript.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c subset.c -o subset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c summary.c -o summary.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c version.c -o version.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sysutils.c -o sysutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c xxxpr.f -o xxxpr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c subassign.c -o subassign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c util.c -o util.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unique.c -o unique.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o mask.o match.o memory.o names.o objects.o options.o paste.o patterns.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a ../extra/xdr/libxdr.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/bin/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/lib make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rmain.c -o Rmain.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' x86_64-alt-linux-gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o -lR make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making sock.d from sock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making Rsock.d from Rsock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' making rotated.d from rotated.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making Rhttpd.d from Rhttpd.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making internet.d from internet.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' making Lapack.d from Lapack.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making libcurl.d from libcurl.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' making rbitmap.d from rbitmap.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' making sockconn.d from sockconn.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' making devX11.d from devX11.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rbitmap.c -o rbitmap.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rotated.c -o rotated.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Lapack.c -o Lapack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o libcurl.c: In function 'in_do_curlDownload': libcurl.c:637:13: warning: 'CURLOPT_PROGRESSFUNCTION' is deprecated: since 7.32.0. Use CURLOPT_XFERINFOFUNCTION [-Wdeprecated-declarations] 637 | curl_easy_setopt(hnd[i], CURLOPT_PROGRESSFUNCTION, progress); | ^~~~~~~~~~~~~~~~ In file included from libcurl.c:38: /usr/include/curl/curl.h:1291:3: note: declared here 1291 | CURLOPTDEPRECATED(CURLOPT_PROGRESSFUNCTION, CURLOPTTYPE_FUNCTIONPOINT, 56, | ^~~~~~~~~~~~~~~~~ libcurl.c:693:9: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations] 693 | curl_easy_getinfo(hnd[0], CURLINFO_SIZE_DOWNLOAD, &dl); | ^~~~~~~~~~~~~~~~~ /usr/include/curl/curl.h:2862:3: note: declared here 2862 | CURLINFO_SIZE_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~ libcurl.c:702:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 702 | curl_easy_getinfo(hnd[0], CURLINFO_CONTENT_LENGTH_DOWNLOAD, &cl); | ^~~~~~~~~~~~~~~~~ /usr/include/curl/curl.h:2879:3: note: declared here 2879 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libcurl.c:714:13: warning: 'CURLINFO_SIZE_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_SIZE_DOWNLOAD_T [-Wdeprecated-declarations] 714 | curl_easy_getinfo(hnd[i], CURLINFO_SIZE_DOWNLOAD, &dl); | ^~~~~~~~~~~~~~~~~ /usr/include/curl/curl.h:2862:3: note: declared here 2862 | CURLINFO_SIZE_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dataentry.c -o dataentry.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devX11.c -o devX11.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' mkdir -p -- /usr/src/RPM/BUILD/R-4.2.2/modules make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -lcurl -lR make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lpng16 -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/modules/X11' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' mkdir -p -- ../../library make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/profile' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/translations' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' building package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making md5.d from md5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making text.d from text.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making http.d from http.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making Rmd5.d from Rmd5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making signals.d from signals.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making install.d from install.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making getfmts.d from getfmts.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making pdscan.d from pdscan.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making gramLatex.d from gramLatex.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' making gramRd.d from gramRd.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c md5.c -o md5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c text.c -o text.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c http.c -o http.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c signals.c -o signals.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rmd5.c -o Rmd5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c getfmts.c -o getfmts.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pdscan.c -o pdscan.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c install.c -o install.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gramLatex.c -o gramLatex.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gramRd.c -o gramRd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o pdscan.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/compiler' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' mkdir -p -- ../../../library/utils/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making sock.d from sock.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making hashtab.d from hashtab.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making size.d from size.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' making io.d from io.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sock.c -o sock.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c hashtab.c -o hashtab.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c size.c -o size.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c io.c -o io.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o hashtab.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/utils' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making chull.d from chull.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making axis_scales.d from axis_scales.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making devices.d from devices.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making colors.d from colors.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making clippath.d from clippath.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making patterns.d from patterns.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making mask.d from mask.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making group.d from group.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making devCairo.d from devCairo.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making devQuartz.d from devQuartz.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making devPicTeX.d from devPicTeX.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' making devPS.d from devPS.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c axis_scales.c -o axis_scales.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chull.c -o chull.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c patterns.c -o patterns.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devices.c -o devices.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mask.c -o mask.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c group.c -o group.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devCairo.c -o devCairo.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devQuartz.c -o devQuartz.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colors.c -o colors.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c devPS.c -o devPS.o devPS.c: In function 'XFigDeviceDriver': devPS.c:4950:53: warning: pointer 'pd_139' used after 'free' [-Wuse-after-free] 4950 | error(_("invalid page type '%s' (xfig)"), pd->papername); | ~~^~~~~~~~~~~ devPS.c:4949:9: note: call to 'free' here 4949 | free(pd); | ^~~~~~~~ make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src' make[7]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[7]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cairoBM.c -o cairoBM.o make[9]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' x86_64-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lz -lcairo -lpng16 -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices/src/cairo' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grDevices' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making base.d from base.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making graphics.d from graphics.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making par.d from par.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making plot3d.d from plot3d.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making plot.d from plot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' making stem.d from stem.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stem.c -o stem.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c base.c -o base.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c par.c -o par.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graphics.c -o graphics.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot3d.c -o plot3d.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c plot.c -o plot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/graphics' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making bandwidths.d from bandwidths.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making kmeans.d from kmeans.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making ansari.d from ansari.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making chisqsim.d from chisqsim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making d2x2xk.d from d2x2xk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making kendall.d from kendall.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making fexact.d from fexact.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making line.d from line.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making swilk.d from swilk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making prho.d from prho.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making ks.d from ks.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making ksmooth.d from ksmooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making smooth.d from smooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making monoSpl.d from monoSpl.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making loessc.d from loessc.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making dblcen.d from dblcen.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making isoreg.d from isoreg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making Srunmed.d from Srunmed.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making hclust-utils.d from hclust-utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making distance.d from distance.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making nls.d from nls.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making HoltWinters.d from HoltWinters.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making rWishart.d from rWishart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making PPsum.d from PPsum.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making arima.d from arima.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making burg.d from burg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making filter.d from filter.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making mAR.d from mAR.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making pacf.d from pacf.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making port.d from port.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making starma.d from starma.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making family.d from family.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making sbart.d from sbart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making approx.d from approx.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making lowess.d from lowess.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making massdist.d from massdist.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making loglin.d from loglin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making lm.d from lm.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making complete_cases.d from complete_cases.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making fft.d from fft.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making cov.d from cov.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making deriv.d from deriv.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making fourier.d from fourier.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making model.d from model.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making optim.d from optim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making integrate.d from integrate.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making optimize.d from optimize.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making zeroin.d from zeroin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making rcont.d from rcont.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making random.d from random.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making influence.d from influence.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' making distn.d from distn.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ansari.c -o ansari.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bandwidths.c -o bandwidths.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c kmeans.c -o kmeans.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chisqsim.c -o chisqsim.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c kendall.c -o kendall.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c prho.c -o prho.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c line.c -o line.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c swilk.c -o swilk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ksmooth.c -o ksmooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ks.c -o ks.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c smooth.c -o smooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c isoreg.c -o isoreg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c monoSpl.c -o monoSpl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dblcen.c -o dblcen.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fexact.c -o fexact.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c loessc.c -o loessc.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c hclust-utils.c -o hclust-utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Srunmed.c -o Srunmed.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c distance.c -o distance.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c HoltWinters.c -o HoltWinters.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c PPsum.c -o PPsum.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nls.c -o nls.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c burg.c -o burg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rWishart.c -o rWishart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c family.c -o family.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c filter.c -o filter.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sbart.c -o sbart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c port.c -o port.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mAR.c -o mAR.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pacf.c -o pacf.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c starma.c -o starma.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c approx.c -o approx.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c massdist.c -o massdist.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c arima.c -o arima.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lowess.c -o lowess.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c loglin.c -o loglin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lm.c -o lm.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c splines.c -o splines.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c complete_cases.c -o complete_cases.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fft.c -o fft.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fourier.c -o fourier.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c integrate.c -o integrate.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c optim.c -o optim.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c zeroin.c -o zeroin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cov.c -o cov.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bsplvd.f -o bsplvd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c influence.c -o influence.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rcont.c -o rcont.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bvalue.f -o bvalue.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall 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make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qsbart.f -o qsbart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c deriv.c -o deriv.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sinerp.f -o sinerp.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sgram.f -o sgram.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sslvrg.f -o sslvrg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stxwx.f -o stxwx.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c distn.c -o distn.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c eureka.f -o eureka.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c hclust.f -o hclust.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lminfl.f -o lminfl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c kmns.f -o kmns.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stl.f -o stl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c model.c -o model.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ppr.f -o ppr.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c loessf.f -o loessf.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gfortran -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making slot.d from slot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making class_support.d from class_support.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making tests.d from tests.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making methods_list_dispatch.d from methods_list_dispatch.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c slot.c -o slot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c class_support.c -o class_support.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tests.c -o tests.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/methods' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making clippath.d from clippath.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making gpar.d from gpar.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making just.d from just.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making layout.d from layout.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making mask.d from mask.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making matrix.d from matrix.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making path.d from path.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making grid.d from grid.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making register.d from register.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making state.d from state.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making unit.d from unit.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making viewport.d from viewport.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' making util.d from util.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clippath.c -o clippath.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c just.c -o just.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mask.c -o mask.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c path.c -o path.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gpar.c -o gpar.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c layout.c -o layout.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c register.c -o register.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c state.c -o state.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c util.c -o util.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c viewport.c -o viewport.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unit.c -o unit.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c grid.c -o grid.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/grid' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c splines.c -o splines.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/splines' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/stats4' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' making init.d from init.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' making tcltk_unix.d from tcltk_unix.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' making tcltk.d from tcltk.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tcltk.c -o tcltk.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/tcltk/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 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directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' making rngstream.d from rngstream.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' making fork.d from fork.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rngstream.c -o rngstream.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[5]: 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rngstream.o fork.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/parallel' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' installing parsed NAMESPACE files make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[1]: Nothing to be done for 'R'. make: Entering directory '/usr/src/RPM/BUILD/R-4.2.2' you should 'make docs' now ... make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2' configuring Java ... Java interpreter : /usr/lib/jvm/jre/bin/java Java version : 21.0.2 Java home path : /usr/lib/jvm/jre Java compiler : not present Java headers gen.: Java archive tool: trying to compile and link a JNI program detected JNI cpp flags : detected JNI linker flags : -L$(JAVA_HOME)/lib -ljvm make[2]: Entering directory '/usr/src/tmp/Rjavareconf.xlRQm8' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c conftest.c -o conftest.o conftest.c:1:10: fatal error: jni.h: No such file or directory 1 | #include | ^~~~~~~ compilation terminated. make[2]: *** [/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf:169: conftest.o] Error 1 make[2]: Leaving directory '/usr/src/tmp/Rjavareconf.xlRQm8' Unable to compile a JNI program JAVA_HOME : /usr/lib/jvm/jre Java library path: JNI cpp flags : JNI linker flags : Updating Java configuration in /usr/src/RPM/BUILD/R-4.2.2 Done. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc' creating doc/NEWS make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc' creating doc/NEWS.pdf make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/version.texi make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-data.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-FAQ.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-lang.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-ints.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-admin.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-intro.html R-intro.texi:6741: warning: @pxref should not appear on @item line make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' building/updating vignettes for package 'grid' ... building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... building/updating vignettes for package 'stats' ... processing 'reshape.Rnw' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' creating doc/manual/R-exts.html R-exts.texi:3663: warning: @noindent is useless inside of a paragraph R-exts.texi:14773: warning: unexpected argument on @tex line: $\pi :=$ @code{prob[]}, R-exts.texi:14773: warning: unexpected argument on @iftex line: @tex $\pi :=$ @code{prob[]}, @end tex make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' installing parsed Rd make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' grid make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' tcltk make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' splines make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' stats4 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[3]: 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converting help for package 'base' Arithmetic html AsIs html Bessel html CallExternal html Colon html Comparison html Constants html Control html Cstack_info html DateTimeClasses html Dates html Defunct html Deprecated html Encoding html EnvVar html Extract html Extract.data.frame html Extract.factor html Extremes html Foreign-internal html Foreign html Hyperbolic html ISOdatetime html Internal html InternalMethods html La_library html La_version html Last.value html Log html Logic html LongVectors html MathFun html Memory-limits html Memory html NA html NULL html NumericConstants html Ops.Date html Paren html Platform html Primitive html Quotes html Random-user html Random html RdUtils html Recall html Reserved html Rhome html Round html S3method html Special html StackOverflows html Startup html Syntax html Sys.getenv html Sys.getpid html Sys.glob html Sys.info html Sys.localeconv html Sys.readlink html Sys.setFileTime html Sys.setenv html Sys.sleep html Sys.time html Sys.which html Trig html UTF8filepaths html UseMethod html Vectorize html Version html abbreviate html agrep html all html all.equal html allnames html any html aperm html append html apply html args html array html as.Date html as.POSIXlt html as.data.frame html as.environment html as.function html asplit html assign html assignOps html attach html attr html attributes html autoload html backsolve html base-defunct html REDIRECT:topic Previous alias or file overwritten by alias: ../../library/base/help/Version.html REDIRECT:topic Previous alias or file overwritten by alias: ../../library/base/help/Platform.html base-deprecated html base-internal html base-package html basename html bincode html bindenv html bitwise html body html bquote html browser html browserText html builtins html by html c html call html callCC html capabilities html cat html cbind html char.expand html character html charmatch html chartr html chkDots html chol html chol2inv html class html col html colSums html colnames html commandArgs html comment html complex html conditions html conflicts html connections html contributors html copyright html crossprod html cumsum html curlGetHeaders html cut.POSIXt html cut html data.class html data.frame html data.matrix html dataframeHelpers html date html dcf html debug html delayedAssign html deparse html deparseOpts html det html detach html dev html diag html diff html difftime html dim html dimnames html do.call html dontCheck html dots html double html dput html drop html droplevels html dump html duplicated html dynload html eapply html eigen html encodeString html environment html eval html exists html expand.grid html expression html extSoftVersion html factor html file.access html file.choose html file.info html file.path html file.show html files html files2 html find.package html findInterval html force html forceAndCall html formals html format html format.info html format.pval html formatDL html formatc html function html funprog html gc html gc.time html gctorture html get html getCallingDLL html getDLLRegisteredRoutines html getLoadedDLLs html getNativeSymbolInfo html gettext html getwd html gl html grep html grepRaw html groupGeneric html grouping html gzcon html hexmode html iconv html icuSetCollate html identical html identity html ifelse html integer html interaction html interactive html invisible html is.finite html is.function html is.language html is.object html is.recursive html is.single html is.unsorted html isR html isS4 html isSymmetric html jitter html kappa html kronecker html l10n_info html labels html lapply html lazyload html length html lengths html levels html libPaths html libcurlVersion html library html library.dynam html license html list html list.files html list2DF html list2env html load html locales html logical html lower.tri html ls html make.names html make.unique html mapply html marginSums html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memlimits html memory.profile html merge html message html missing html mode html mtfrm html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pcre_config html pipeOp html plot html pmatch html polyroot html pos.to.env html pretty html print html print.dataframe html print.default html prmatrix html proc.time html prod html proportions html pushBack html qr html qraux html quit html range html rank html rapply html raw html rawConnection html rawConversion html readBin html readChar html readLines html readRDS html readRenviron html readline html reg.finalizer html regex html regmatches html rep html replace html rev html rle html rm html round.POSIXt html row html row.names html rowsum html sQuote html sample html save html scale html scan html search html seek html seq.Date html seq.POSIXt html seq html sequence html serialize html setTimeLimit html sets html shQuote html showConnections html sign html sink html slice.index html slotOp html socketSelect html solve html sort html source html split html sprintf html srcfile html standardGeneric html startsWith html stop html stopifnot html strptime html strrep html strsplit html strtoi html strtrim html structure html strwrap html subset html substitute html substr html sum html summary html svd html sweep html switch html sys.parent html sys.source html system html system.file html system.time html system2 html t html table html tabulate html tapply html taskCallback html taskCallbackManager html taskCallbackNames html tempfile html textconnections html tilde html timezones html toString html trace html traceback html tracemem html transform html trimws html try html typeof html unique html unlink html unlist html unname html userhooks html utf8Conversion html validUTF8 html vector html warning html warnings html weekday.POSIXt html which html which.min html with html withVisible html write html writeLines html xtfrm html zMachine html zScript html zapsmall html zpackages html zutils html Signals html converting help for package 'tools' CRANtools html HTMLheader html HTMLlinks html QC html Rcmd html Rd2HTML html Rd2txt_options html RdTextFilter html Rdiff html Rdindex html Rdutils html SweaveTeXFilter html add_datalist html assertCondition html bibstyle html buildVignette html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html find_gs_cmd html getVignetteInfo html loadRdMacros html makeLazyLoading html make_translations_pkg html makevars html md5sum html package_dependencies html package_native_routine_registration_skeleton html parseLatex html parse_Rd html print.via.format html pskill html psnice html read.00Index html showNonASCII html startDynamicHelp html testInstalledPackage html texi2dvi html toHTML html toRd html toTitleCase html tools-defunct html tools-deprecated html tools-package html undoc html updatePACKAGES html update_pkg_po html userdir html vignetteEngine html vignetteInfo html writePACKAGES html xgettext html converting help for package 'utils' BATCH html COMPILE html DLL.version html INSTALL html LINK html PkgUtils html Question html REMOVE html RHOME html RShowDoc html RSiteSearch html Rconsole html Rprof html Rprofmem html Rscript html Rtangle html RweaveLatex html SHLIB html Sweave html SweaveSyntConv html SweaveUtils html URLencode html View html adist html alarm html apropos html aregexec html arrangeWindows html askYesNo html aspell-utils html aspell html available.packages html bibentry html browseEnv html 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converting help for package 'grDevices' Devices html Hershey html Japanese html Type1Font html adjustcolor html as.graphicsAnnot html as.raster html axisTicks html boxplot.stats html bringToTop html cairo html cairoSymbolFont html check.options html chull html cm html col2rgb html colorRamp html colors html contourLines html convertColor html densCols html dev html dev.capabilities html dev.capture html dev.flush html dev.interactive html dev.size html dev2 html dev2bitmap html devAskNewPage html embedFonts html extendrange html getGraphicsEvent html grDevices-package html grSoftVersion html gray html gray.colors html hcl html hsv html make.rgb html msgWindow html n2mfrow html nclass html palette html palettes html pdf html pdf.options html pictex html plotmath html postscript html postscriptFonts html pretty.Date html ps.options html quartz html quartzFonts html recordGraphics html recordplot html rgb html rgb2hsv html trans3d html windows html windows.options html windowsFonts html x11 html x11Fonts html xfig html xy.coords html xyTable html xyz.coords html png html savePlot html converting help for package 'graphics' abline html arrows html assocplot html axTicks html axis.POSIXct html axis html barplot html box html boxplot html boxplot.matrix html bxp html cdplot html clip html contour html convertXY html coplot html curve html dotchart html filled.contour html fourfoldplot html frame html graphics-defunct html graphics-package html grid html hist.POSIXt html hist html identify html image html layout html legend html lines html locator html matplot html mosaicplot html mtext html pairs html panel.smooth html par html persp html pie html plot.dataframe html plot.default html plot.design html plot.factor html plot.formula html plot.raster html plot.table html plot.window html plot.xy html plothistogram html points html polygon html polypath html rasterImage html rect html rug html screen html segments html smoothScatter html spineplot html stars html stem html stripchart html strwidth html sunflowerplot html symbols html text html title html units html xspline html zAxis html converting help for package 'stats' AIC html ARMAacf html ARMAtoMA html Beta html Binomial html Cauchy html Chisquare html Distributions html Exponential html Fdist html GammaDist html Geometric html HoltWinters html Hypergeometric html IQR html KalmanLike html Logistic html Lognormal html Multinom html NLSstAsymptotic html NLSstClosestX html NLSstLfAsymptote html NLSstRtAsymptote html NegBinomial html Normal html Pair html Poisson html SSD html SSasymp html SSasympOff html SSasympOrig html SSbiexp html SSfol html SSfpl html SSgompertz html SSlogis html SSmicmen html SSweibull html SignRank html Smirnov html StructTS html TDist html Tukey html TukeyHSD html Uniform html Weibull html Wilcoxon html acf html acf2AR html add1 html addmargins html aggregate html alias html anova html anova.glm html anova.lm html anova.mlm html ansari.test html aov html approxfun html ar html ar.ols html arima html arima.sim html arima0 html as.hclust html asOneSidedFormula html ave html bandwidth html bartlett.test html binom.test html biplot html biplot.princomp html birthday html box.test html cancor html case.names html checkMFClasses html chisq.test html cmdscale html coef html complete.cases html confint html constrOptim html contrast html contrasts html convolve html cophenetic html cor html cor.test html cov.wt html cpgram html cutree html decompose html delete.response html dendrapply html dendrogram html density html deriv html deviance html df.residual html diffinv html dist html dummy.coef html ecdf html eff.aovlist html effects html embed html expand.model.frame html extractAIC html factanal html factor.scope html family html fft html filter html fisher.test html fitted.values html fivenum html fligner.test html formula html formula.nls html friedman.test html ftable html ftable.formula html getInitial html glm html glm.control html glm.summaries html hclust html heatmap html identify.hclust html influence.measures html integrate html interaction.plot html is.empty html isoreg html kernapply html kernel html kmeans html kruskal.test html ks.test html ksmooth html lag html lag.plot html line html listof html lm html lm.influence html lm.summaries html lmfit html loadings html loess html loess.control html logLik html loglin html lowess html ls.diag html ls.print html lsfit html mad html mahalanobis html make.link html makepredictcall html manova html mantelhaen.test html mauchly.test html mcnemar.test html median html medpolish html model.extract html model.frame html model.matrix html model.tables html monthplot html mood.test html na.action html na.contiguous html na.fail html nafns html naprint html nextn html nlm html nlminb html nls html nls.control html nobs html numericDeriv html offset html oneway.test html optim html optimize html order.dendrogram html p.adjust html pairwise.prop.test html pairwise.t.test html pairwise.table html pairwise.wilcox.test html plot.HoltWinters html plot.acf html plot.density html plot.isoreg html plot.lm html plot.ppr html plot.profile.nls html plot.spec html plot.stepfun html plot.ts html poisson.test html poly html power html power.anova.test html power.prop.test html power.t.test html pp.test html ppoints html ppr html prcomp html predict.HoltWinters html predict html predict.arima html predict.glm html predict.lm html predict.loess html predict.nls html predict.smooth.spline html preplot html princomp html print.power.htest html print.ts html printCoefmat html profile html profile.nls html proj html prop.test html prop.trend.test html qqnorm html quade.test html quantile html r2dtable html rWishart html read.ftable html rect.hclust html relevel html reorder.dendrogram html reorder.factor html replications html reshape html residuals html runmed html scatter.smooth html screeplot html sd html se.contrast html selfStart html setNames html shapiro.test html sigma html simulate html smooth html smooth.spline html smoothEnds html sortedXyData html spec.ar html spec.pgram html spec.taper html spectrum html splinefun html start html stat.anova html stats-defunct html stats-deprecated html stats-package html step html stepfun html stl html stlmethods html summary.aov html summary.glm html summary.lm html summary.manova html summary.nls html summary.princomp html supsmu html symnum html t.test html termplot html terms html terms.formula html terms.object html time html toeplitz html ts-methods html ts html ts.plot html ts.union html tsSmooth html tsdiag html tsp html uniroot html update html update.formula html var.test html varimax html vcov html weighted.mean html weighted.residuals html weights html wilcox.test html window html xtabs html zC html converting help for package 'datasets' AirPassengers html BJsales html BOD html ChickWeight html DNase html EuStockMarkets html Formaldehyde html HairEyeColor html Harman23.cor html Harman74.cor html Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html npk html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Classes_Details html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html Introduction html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html Methods_Details html Methods_for_Nongenerics html Methods_for_S3 html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html removeMethod html representation html selectSuperClasses html setAs html setClass html setClassUnion html setGeneric html setGroupGeneric html setIs html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html as.mask html calcStringMetric html current.viewport html dataViewport html depth html deviceLoc html drawDetails html editDetails html editViewport html explode html gEdit html gPath html getNames html gpar html grid-defunct html grid-internal html grid-package html grid.DLapply html grid.add html grid.bezier html grid.cap html grid.circle html grid.clip html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grep html grid.grill html grid.grob html grid.group html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.stroke html grid.text html grid.xaxis html grid.xspline html grid.yaxis html gridCoords html grobCoords html grobName html grobWidth html grobX html legendGrob html makeContent html patterns html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html unitType html valid.just html validDetails html viewport html viewportTransform html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package MASS make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package lattice make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package codetools make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package foreign make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package KernSmooth make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package nnet make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package rpart make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package spatial make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpqA3vqg/R.INSTALL27eefa515cad29/nnet/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nnet.c -o nnet.o make[3]: Leaving directory '/usr/src/tmp/RtmpqA3vqg/R.INSTALL27eefa515cad29/nnet/src' make[3]: Entering directory '/usr/src/tmp/RtmpqA3vqg/R.INSTALL27eefa515cad29/nnet/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpqA3vqg/R.INSTALL27eefa515cad29/nnet/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html nnet html predict.nnet html which.is.max html ** building package indices ** testing if installed package can be loaded * DONE (nnet) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c krc.c -o krc.o make[3]: Leaving directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pps.c -o pps.o make[3]: Leaving directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpzV8lbs/R.INSTALL27eefe761abfe/spatial/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c blkest.f -o blkest.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cp.f -o cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgedi.f -o dgedi.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgefa.f -o dgefa.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgesl.f -o dgesl.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c linbin.f -o linbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c linbin2D.f -o linbin2D.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c locpoly.f -o locpoly.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rlbin.f -o rlbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sdiag.f -o sdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sstdiag.f -o sstdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpwkQbn9/R.INSTALL27eef61d7fbb93/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html bkfe html dpih html dpik html dpill html locpoly html ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c R_systat.c -o R_systat.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c SASxport.c -o SASxport.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c avl.c -o avl.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dbfopen.c -o dbfopen.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c file-handle.c -o file-handle.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c minitab.c -o minitab.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pfm-read.c -o pfm-read.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sfm-read.c -o sfm-read.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c spss.c -o spss.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c stataread.c -o stataread.o make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' make[3]: Entering directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmpz9osjV/R.INSTALL27eef27ce5be9f/foreign/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c anova.c -o anova.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c anovapred.c -o anovapred.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c branch.c -o branch.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c bsplit.c -o bsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c choose_surg.c -o choose_surg.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fix_cp.c -o fix_cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c free_tree.c -o free_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gini.c -o gini.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c graycode.c -o graycode.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c insert_split.c -o insert_split.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mysort.c -o mysort.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nodesplit.c -o nodesplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c partition.c -o partition.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c poisson.c -o poisson.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c print_tree.c -o print_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpart.c -o rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpartexp.c -o rpartexp.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpcountup.c -o rpcountup.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rundown.c -o rundown.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rundown2.c -o rundown2.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c surrogate.c -o surrogate.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c usersplit.c -o usersplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c xpred.c -o xpred.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c xval.c -o xval.o make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpGGs2LK/R.INSTALL27eefc6eae27ff/rpart/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder.balance html stagec html summary.rpart html text.rpart html xpred.rpart html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c MASS.c -o MASS.o make[3]: Leaving directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lqs.c -o lqs.o make[3]: Leaving directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpTZHnh6/R.INSTALL27eeed534cb75/MASS/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package class make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package cluster make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c threeDplot.c -o threeDplot.o make[3]: Leaving directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpPtWssP/R.INSTALL27eeefa7b76f2/lattice/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' finding HTML links ... done Lattice html Rows html USMortality html axis.default html banking html barchart.table html barley html cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package Matrix make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package nlme make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpVTq2Zw/R.INSTALL28225b31840d99/class/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c class.c -o class.o make[3]: Leaving directory '/usr/src/tmp/RtmpVTq2Zw/R.INSTALL28225b31840d99/class/src' make[3]: Entering directory '/usr/src/tmp/RtmpVTq2Zw/R.INSTALL28225b31840d99/class/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpVTq2Zw/R.INSTALL28225b31840d99/class/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html batchSOM html condense html knn html knn.cv html knn1 html lvq1 html lvq2 html lvq3 html lvqinit html lvqtest html multiedit html olvq1 html reduce.nn html somgrid html ** building package indices ** testing if installed package can be loaded * DONE (class) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dysta.f -o dysta.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c daisy.f -o daisy.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mona.c -o mona.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sildist.c -o sildist.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c fanny.c -o fanny.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c spannel.c -o spannel.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c clara.c -o clara.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c twins.c -o twins.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pam.c -o pam.o make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpnzFIqo/R.INSTALL28225d434ebfff/cluster/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html agnes.object html agriculture html animals html bannerplot html chorSub html clara html clara.object html clusGap html clusplot.default html clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html fanny html fanny.object html flower html lower.to.upper.tri.inds html medoids html mona html mona.object html pam html pam.object html partition.object html plantTraits html plot.agnes html plot.diana html plot.mona html plot.partition html pltree html pluton html predict.ellipsoid html print.agnes html print.clara html print.diana html print.dissimilarity html print.fanny html print.mona html print.pam html ruspini html silhouette html sizeDiss html summary.agnes html summary.clara html summary.diana html summary.mona html summary.pam html twins.object html volume.ellipsoid html votes.repub html xclara html ** building package indices ** testing if installed package can be loaded * DONE (cluster) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chol.f -o chol.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gnls.c -o gnls.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pythag.c -o pythag.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlme.c -o nlme.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pdMat.c -o pdMat.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c corStruct.c -o corStruct.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c rs.f -o rs.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c nlmefit.c -o nlmefit.o make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpRalNZW/R.INSTALL282693f7a20cf/nlme/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls-internal html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html varConstProp html varExp html varFixed html varFunc html varIdent html varPower html varWeights html varWeights.glsStruct html varWeights.lmeStruct html ** building package indices ** testing if installed package can be loaded * DONE (nlme) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Tsparse.c -o Tsparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cs_utils.c -o cs_utils.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chm_common.c -o chm_common.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Csparse.c -o Csparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cs.c -o cs.o cs.c: In function 'cs_realloc': cs.c:1161:26: warning: pointer 'p_11(D)' may be used after 'realloc' [-Wuse-after-free] 1161 | return ((*ok) ? pnew : p) ; /* return original p if failure */ | ~~~~~~~~~~~~~~^~~~ cs.c:1159:12: note: call to 'realloc' here 1159 | pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c Mutils.c -o Mutils.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ldense.c -o ldense.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c factorizations.c -o factorizations.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c abIndex.c -o abIndex.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' ( cd Lib ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparseQR.c -o sparseQR.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' ( cd Source ; make clean ) ( cd Source ; make clean ) ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile ) make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dense.c -o dense.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c unpackedMatrix.c -o unpackedMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o ../Core/cholmod_copy.c: In function 'cholmod_copy': ../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] 275 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ ../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] 275 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o In file included from ../Core/cholmod_change_factor.c:113: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 37 | double *Lx, *Lz ; | ^~ In file included from ../Core/cholmod_change_factor.c:115: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 37 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] 262 | Int nsuper, xsize, ssize ; | ^~~~~ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] 677 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] 677 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 676 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] 676 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] 824 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; | ^ ../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] 823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~~ ../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] 823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o In file included from ../Core/cholmod_dense.c:45: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ In file included from ../Core/cholmod_dense.c:47: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ In file included from ../Core/cholmod_dense.c:49: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/cholmod_dense.c: In function 'cholmod_eye': ../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] 300 | Int i, n, nz ; | ^~ ../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 299 | double *Xx, *Xz ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o ../Core/cholmod_memory.c: In function 'cholmod_malloc': ../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable] 121 | size_t s ; | ^ ../Core/cholmod_memory.c: In function 'cholmod_realloc': ../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable] 311 | size_t s ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c packedMatrix.c -o packedMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_sparse.c -o cholmod_sparse.o ../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse': ../Core/cholmod_sparse.c:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 485 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ; | ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o In file included from ../Core/cholmod_triplet.c:105: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:107: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:109: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse': ../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] 342 | Int i, j, p, k, stype, nrow, ncol, nz, ok ; | ^~ ../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] 341 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Check/cholmod_write.c -o cholmod_write.o ../Check/cholmod_write.c: In function 'cholmod_write_sparse': ../Check/cholmod_write.c:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] 366 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o In file included from ../Core/cholmod_transpose.c:121: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:123: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:125: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:128: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:130: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ In file included from ../Core/cholmod_transpose.c:133: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2': ../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] 419 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, | ^~~~ ../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] 416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ ../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] 416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o ../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p': ../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] 111 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] 204 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; | ^~~~~~~~~~ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] 950 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; | ^~ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] 1497 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; | ^~~ ../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable] 1495 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast, | ^~~~~~~ ../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] 1494 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse.c -o sparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:161: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:163: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:165: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:169: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:171: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:173: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] 562 | Int totsize ; | ^~~~~~~ ../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable] 185 | double max_fraction; | ^~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable] 184 | const char* env_max_fraction; | ^~~~~~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable] 183 | size_t max_bytes; | ^~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable] 182 | const char* env_max_bytes; | ^~~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable] 181 | const char* env_use_gpu; | ^~~~~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:44: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ ../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:46: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ ../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:26: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 30 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 238 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ In file included from ../Supernodal/cholmod_super_solve.c:28: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 30 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 238 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:82: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ ../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ ../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:84: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ ../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ ../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:86: ../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o ../Core/cholmod_add.c:34:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 34 | double alpha [2], /* scale factor for A */ | ~~~~~~~^~~~~~~~~ In file included from ../Core/cholmod_add.c:27: ../Include/cholmod_core.h:1582:68: note: previously declared as 'double *' 1582 | cholmod_sparse *cholmod_l_add (cholmod_sparse *, cholmod_sparse *, double *, | ^~~~~~~~ ../Core/cholmod_add.c:35:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=] 35 | double beta [2], /* scale factor for B */ | ~~~~~~~^~~~~~~~ ../Include/cholmod_core.h:1583:5: note: previously declared as 'double *' 1583 | double *, int, int, cholmod_common *) ; | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o In file included from ../Cholesky/cholmod_solve.c:63: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 61 | double *Lx, *Yx, *Yz ; | ^~ In file included from ../Cholesky/cholmod_solve.c:66: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 61 | double *Lx, *Yx, *Yz ; | ^~ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] 334 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o ../Core/cholmod_copy.c: In function 'cholmod_l_copy': ../Core/cholmod_copy.c:275:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] 275 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ ../Core/cholmod_copy.c:275:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] 275 | Int nrow, ncol, up, lo, values, diag, astype ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o ../Core/cholmod_memory.c: In function 'cholmod_l_malloc': ../Core/cholmod_memory.c:121:12: warning: unused variable 's' [-Wunused-variable] 121 | size_t s ; | ^ ../Core/cholmod_memory.c: In function 'cholmod_l_realloc': ../Core/cholmod_memory.c:311:12: warning: unused variable 's' [-Wunused-variable] 311 | size_t s ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o In file included from ../Core/cholmod_change_factor.c:113: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 37 | double *Lx, *Lz ; | ^~ In file included from ../Core/cholmod_change_factor.c:115: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:37:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 37 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:262:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] 262 | Int nsuper, xsize, ssize ; | ^~~~~ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:677:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] 677 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:677:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] 677 | Int *Lp, *Li, *Lnz ; | ^~ ../Core/cholmod_change_factor.c:676:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 676 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c:676:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] 676 | double *Lx, *Lz ; | ^~ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:824:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] 824 | Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; | ^ ../Core/cholmod_change_factor.c:823:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] 823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~~ ../Core/cholmod_change_factor.c:823:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] 823 | Int *Ls, *Lpi, *Lpx, *Super, *Li ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o In file included from ../Core/cholmod_dense.c:45: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ In file included from ../Core/cholmod_dense.c:47: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ In file included from ../Core/cholmod_dense.c:49: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:27:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c:27:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 27 | double *Ax, *Xx, *Az, *Xz ; | ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:133:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c:133:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 133 | double *Xx, *Cx, *Xz, *Cz ; | ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:226:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/t_cholmod_dense.c:226:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 226 | double *Xx, *Xz, *Yx, *Yz ; | ^~ ../Core/cholmod_dense.c: In function 'cholmod_l_eye': ../Core/cholmod_dense.c:300:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] 300 | Int i, n, nz ; | ^~ ../Core/cholmod_dense.c:299:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 299 | double *Xx, *Xz ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o ../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse': ../Core/cholmod_sparse.c:485:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 485 | Int p, pend, j, ncol, packed, nzmax, nz, xtype ; | ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o In file included from ../Core/cholmod_triplet.c:105: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:107: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ In file included from ../Core/cholmod_triplet.c:109: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] 28 | double *Rx, *Rz, *Tx, *Tz ; | ^~ ../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse': ../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] 342 | Int i, j, p, k, stype, nrow, ncol, nz, ok ; | ^~ ../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] 341 | Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o ../Check/cholmod_write.c: In function 'cholmod_l_write_sparse': ../Check/cholmod_write.c:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] 366 | Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o In file included from ../Core/cholmod_transpose.c:121: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:123: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:125: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:128: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 42 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ ../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 139 | double *Ax, *Az, *Fx, *Fz ; | ^~ In file included from ../Core/cholmod_transpose.c:130: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ In file included from ../Core/cholmod_transpose.c:133: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~~~~ ../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 44 | Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; | ^~~~ ../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~~ ../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 43 | Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; | ^~ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] 140 | Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2': ../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] 419 | Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, | ^~~~ ../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] 416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ ../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] 416 | Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, | ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o ../Cholesky/cholmod_factorize.c:101:12: warning: argument 2 of type 'double[2]' with mismatched bound [-Warray-parameter=] 101 | double beta [2], /* factorize beta*I+A or beta*I+A'*A */ | ~~~~~~~^~~~~~~~ In file included from ../Cholesky/cholmod_factorize.c:58: ../Include/cholmod_cholesky.h:168:46: note: previously declared as 'double *' 168 | int cholmod_l_factorize_p (cholmod_sparse *, double *, SuiteSparse_long *, | ^~~~~~~~ ../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p': ../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] 111 | Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] 204 | Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; | ^~~~~~~~~~ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] 950 | Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; | ^~ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1497:9: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] 1497 | ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; | ^~~ ../Check/cholmod_check.c:1495:16: warning: variable 'precise' set but not used [-Wunused-but-set-variable] 1495 | count, precise, init_print, ilast, lnz, head, tail, jprev, plast, | ^~~~~~~ ../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] 1494 | Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_updown_mask2': ../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] 433 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; | ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:161: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:163: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:165: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:169: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:171: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ ../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 46 | double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; | ^~ In file included from ../Cholesky/cholmod_rowfac.c:173: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:50:53: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] 50 | use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; | ^~~~~ ../Cholesky/cholmod_rowfac.c: At top level: ../Cholesky/cholmod_rowfac.c:577:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 577 | double beta [2], /* factorize beta*I+A or beta*I+AA' */ | ~~~~~~~^~~~~~~~ In file included from ../Cholesky/cholmod_rowfac.c:103: ../Include/cholmod_cholesky.h:387:59: note: previously declared as 'double *' 387 | int cholmod_l_rowfac (cholmod_sparse *, cholmod_sparse *, double *, size_t, | ^~~~~~~~ ../Cholesky/cholmod_rowfac.c:602:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 602 | double beta [2], /* factorize beta*I+A or beta*I+AA' */ | ~~~~~~~^~~~~~~~ ../Include/cholmod_cholesky.h:413:64: note: previously declared as 'double *' 413 | int cholmod_l_rowfac_mask (cholmod_sparse *, cholmod_sparse *, double *, size_t, | ^~~~~~~~ ../Cholesky/cholmod_rowfac.c:629:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 629 | double beta [2], /* factorize beta*I+A or beta*I+AA' */ | ~~~~~~~^~~~~~~~ ../Include/cholmod_cholesky.h:434:65: note: previously declared as 'double *' 434 | int cholmod_l_rowfac_mask2 (cholmod_sparse *, cholmod_sparse *, double *, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o ../Modify/cholmod_rowdel.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 72 | double yk [2], /* kth entry in the solution to A*y=b */ | ~~~~~~~^~~~~~ In file included from ../Modify/cholmod_rowdel.c:25: ../Include/cholmod_modify.h:294:55: note: previously declared as 'double *' 294 | int cholmod_l_rowdel_solve (size_t, cholmod_sparse *, double *, | ^~~~~~~~ ../Modify/cholmod_rowdel.c:104:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 104 | double yk [2], /* kth entry in the solution to A*y=b */ | ~~~~~~~^~~~~~ ../Include/cholmod_modify.h:320:54: note: previously declared as 'double *' 320 | int cholmod_l_rowdel_mark (size_t, cholmod_sparse *, double *, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o ../Modify/cholmod_rowadd.c:72:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 72 | double bk [2], /* kth entry of the right-hand-side b */ | ~~~~~~~^~~~~~ In file included from ../Modify/cholmod_rowadd.c:24: ../Include/cholmod_modify.h:215:55: note: previously declared as 'double *' 215 | int cholmod_l_rowadd_solve (size_t, cholmod_sparse *, double *, | ^~~~~~~~ ../Modify/cholmod_rowadd.c:116:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 116 | double bk [2], /* kth entry of the right hand side, b */ | ~~~~~~~^~~~~~ ../Include/cholmod_modify.h:241:54: note: previously declared as 'double *' 241 | int cholmod_l_rowadd_mark (size_t, cholmod_sparse *, double *, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:562:21: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] 562 | Int totsize ; | ^~~~~~~ ../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable] 185 | double max_fraction; | ^~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable] 184 | const char* env_max_fraction; | ^~~~~~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable] 183 | size_t max_bytes; | ^~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable] 182 | const char* env_max_bytes; | ^~~~~~~~~~~~~ ../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable] 181 | const char* env_use_gpu; | ^~~~~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:44: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ ../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:46: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ ../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ ../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 49 | double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; | ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] 52 | Int packed, nrow, ncol, j, k, p, pend, kcol, i ; | ^~~~ ../MatrixOps/cholmod_sdmult.c: At top level: ../MatrixOps/cholmod_sdmult.c:59:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 59 | double alpha [2], /* scale factor for A */ | ~~~~~~~^~~~~~~~~ In file included from ../MatrixOps/cholmod_sdmult.c:36: ../Include/cholmod_matrixops.h:143:46: note: previously declared as 'double *' 143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *, | ^~~~~~~~ ../MatrixOps/cholmod_sdmult.c:60:12: warning: argument 4 of type 'double[2]' with mismatched bound [-Warray-parameter=] 60 | double beta [2], /* scale factor for Y */ | ~~~~~~~^~~~~~~~ ../Include/cholmod_matrixops.h:143:56: note: previously declared as 'double *' 143 | int cholmod_l_sdmult (cholmod_sparse *, int, double *, double *, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:26: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 30 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 238 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ In file included from ../Supernodal/cholmod_super_solve.c:28: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:30:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 30 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:238:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] 238 | nsrow2, n, ps2, j, i, d, nrhs ; | ^ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:82: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ ../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ ../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:84: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ ../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ ../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] 108 | double *Lx, *Ax, *Fx, *Az, *Fz, *C ; | ^~ In file included from ../Supernodal/cholmod_super_numeric.c:86: ../Supernodal/t_cholmod_super_numeric.c: In function 'z_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:249: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 249 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:311: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 311 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:326: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 326 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:355: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 355 | #pragma omp parallel for private ( p, pend, pfend, pf, i, j, imap, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:743: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 743 | #pragma omp parallel for num_threads(CHOLMOD_OMP_NUM_THREADS) \ | ../Supernodal/t_cholmod_super_numeric.c:756: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 756 | #pragma omp parallel for private ( j, i, px, q ) \ | ../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable] 116 | tail, nscol_new = 0; | ^~~~ ../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable] 113 | pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1, | ^~ ../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable] 111 | *Previous; | ^~~~~~~~ ../Supernodal/cholmod_super_numeric.c: At top level: ../Supernodal/cholmod_super_numeric.c:102:12: warning: argument 3 of type 'double[2]' with mismatched bound [-Warray-parameter=] 102 | double beta [2], /* beta*I is added to diagonal of matrix to factorize */ | ~~~~~~~^~~~~~~~ In file included from ../Supernodal/cholmod_super_numeric.c:60: ../Include/cholmod_supernodal.h:120:66: note: previously declared as 'double *' 120 | int cholmod_l_super_numeric (cholmod_sparse *, cholmod_sparse *, double *, | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o In file included from ../Cholesky/cholmod_solve.c:63: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 61 | double *Lx, *Yx, *Yz ; | ^~ In file included from ../Cholesky/cholmod_solve.c:66: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] 61 | double *Lx, *Yx, *Yz ; | ^~ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] 334 | Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; | ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask2': ../Modify/cholmod_updown.c:433:40: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] 433 | *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; | ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/CHOLMOD/Lib' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c colamd.c -o colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' ar -rucs ../../COLAMD.a colamd.o colamd_l.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/COLAMD/Source' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.2.2/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o ar: `u' modifier ignored since `D' is the default (see `U') make[5]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/AMD/Source' make[4]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/SuiteSparse_config' ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src/SuiteSparse_config' make[3]: Entering directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o packedMatrix.o unpackedMatrix.o sparse.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpNzTI9y/R.INSTALL2826916a83e8d6/Matrix/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csc","RsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.coo","RsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","sparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","sparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","sparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"Matrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"Matrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"Matrix","matrix.coo"': no definition for class "matrix.coo" Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","TsparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","RsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","TsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","sparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"Matrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"Matrix","graph"': no definition for class "graph" Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html KhatriRao html LU-class html Matrix-class html Matrix html MatrixClass html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html abIseq html all-methods html all.equal-methods html atomicVector-class html band html bandSparse html bdiag html boolean-matprod html cBind html chol html chol2inv-methods html colSums html compMatrix-class html condest html dMatrix-class html ddenseMatrix-class html ddiMatrix-class html denseMatrix-class html dgCMatrix-class html dgRMatrix-class html dgTMatrix-class html dgeMatrix-class html diagU2N html diagonalMatrix-class html dmperm html dpoMatrix-class html drop0 html dsCMatrix-class html dsRMatrix-class html dsparseMatrix-class html dsyMatrix-class html dtCMatrix-class html dtRMatrix-class-def html dtpMatrix-class html dtrMatrix-class html expand html expm html externalFormats html facmul html forceSymmetric html formatSparseM html generalMatrix-class html graph2T html image-methods html indMatrix-class html index-class html invPerm html is.na-methods html is.null.DN html isSymmetric-methods html isTriangular html kronecker-methods html ldenseMatrix-class html ldiMatrix-class html lgeMatrix-class html lsparseMatrix-classes html lsyMatrix-class html ltrMatrix-class html lu html mat2triplet html matrix-products html nMatrix-class html ndenseMatrix-class html nearPD html ngeMatrix-class html nnzero html norm html nsparseMatrix-classes html nsyMatrix-class html ntrMatrix-class html number-class html pMatrix-class html packedMatrix-class html printSpMatrix html qr-methods html rankMatrix html rcond html rep2abI html replValue-class html rleDiff-class html rsparsematrix html solve-methods html spMatrix html sparse.model.matrix html sparseLU-class html sparseMatrix-class html sparseMatrix html sparseQR-class html sparseVector-class html sparseVector html symmetricMatrix-class html symmpart html triangularMatrix-class html uniqTsparse html unpack html unpackedMatrix-class html unused-classes html updown html wrld_1deg html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package mgcv make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package survival make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agmart3.c -o agmart3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agscore2.c -o agscore2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agmart.c -o agmart.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agexact.c -o agexact.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv3.c -o agsurv3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv4.c -o agsurv4.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agsurv5.c -o agsurv5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chinv2.c -o chinv2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky3.c -o cholesky3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agfit5.c -o agfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cdecomp.c -o cdecomp.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky2.c -o cholesky2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c agfit4.c -o agfit4.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cholesky5.c -o cholesky5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chinv3.c -o chinv3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve5.c -o chsolve5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c collapse.c -o collapse.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve2.c -o chsolve2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c chsolve3.c -o chsolve3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance1.c -o concordance1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxdetail.c -o coxdetail.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance5.c -o concordance5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxexact.c -o coxexact.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxcount1.c -o coxcount1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c concordance3.c -o concordance3.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxfit5.c -o coxfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxfit6.c -o coxfit6.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxmart.c -o coxmart.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsafe.c -o coxsafe.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxscho.c -o coxscho.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxmart2.c -o coxmart2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxscore2.c -o coxscore2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsurv2.c -o coxsurv2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c dmatrix.c -o dmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c doloop.c -o doloop.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c finegray.c -o finegray.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxsurv1.c -o coxsurv1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gchol.c -o gchol.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c norisk.c -o norisk.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c multicheck.c -o multicheck.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears1.c -o pyears1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pystep.c -o pystep.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears2.c -o pyears2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c pyears3b.c -o pyears3b.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survConcordance.c -o survConcordance.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survdiff2.c -o survdiff2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfit4.c -o survfit4.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitci.c -o survfitci.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survpenal.c -o survpenal.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survreg6.c -o survreg6.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitkm.c -o survfitkm.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survfitresid.c -o survfitresid.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survreg7.c -o survreg7.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survregc2.c -o survregc2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survsplit.c -o survsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tmerge.c -o tmerge.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c survregc1.c -o survregc1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c zph1.c -o zph1.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c zph2.c -o zph2.o make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agsurv3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o dmatrix.o doloop.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpprK4qS/R.INSTALL2aa1a2305afe6f/survival/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'survival' finding HTML links ... done Surv html Surv2 html Surv2data html Survmethods html aareg html aeqSurv html aggregate.survfit html agreg.fit html aml html anova.coxph html attrassign html basehaz html bladder html blogit html cch html cgd html cgd0 html cipoisson html clogit html cluster html colon html concordance html concordancefit html cox.zph html coxph html coxph.control html coxph.detail html coxph.object html coxph.wtest html coxphms.object html coxsurv.fit html diabetic html dsurvreg html finegray html flchain html frailty html gbsg html heart html is.ratetable html kidney html levels.Surv html lines.survfit html logLik.coxph html logan html lung html mgus html mgus2 html model.frame.coxph html model.matrix.coxph html myeloid html myeloma html nafld html neardate html nsk html nwtco html ovarian html pbc html pbcseq html plot.aareg html plot.cox.zph html plot.survfit html predict.coxph html predict.survreg html print.aareg html print.summary.coxph html print.summary.survexp html print.summary.survfit html print.survfit html pseudo html pspline html pyears html quantile.survfit html ratetable html ratetableDate html rats html rats2 html reliability html residuals.coxph html residuals.survfit html residuals.survreg html retinopathy html rhDNase html ridge html rotterdam html royston html rttright html solder html stanford2 html statefig html strata html summary.aareg html summary.coxph html summary.pyears html summary.survexp html summary.survfit html survSplit html survcheck html survdiff html survexp html survexp.fit html survexp.object html survexp.us html survfit html survfit.coxph html survfit.formula html survfit.matrix html survfit.object html survfit0 html survfitcoxph.fit html survival-deprecated html survival-internal html survobrien html survreg html survreg.control html survreg.distributions html survreg.object html survregDtest html tcut html tmerge html tobin html transplant html udca html untangle.specials html uspop2 html vcov.coxph html veteran html xtfrm.Surv html yates html yates_setup html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' begin installing recommended package boot make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'boot' finding HTML links ... done EEF.profile html Imp.Estimates html abc.ci html acme html aids html aircondit html amis html aml html beaver html bigcity html boot-practicals html boot html boot.array html boot.ci html brambles html breslow html calcium html cane html capability html catsM html cav html cd4 html cd4.nested html censboot html channing html claridge html cloth html co.transfer html coal html control html corr html cum3 html cv.glm html darwin html dogs html downs.bc html ducks html empinf html envelope html exp.tilt html fir html freq.array html frets html glm.diag html glm.diag.plots html gravity html hirose html imp.weights html inv.logit html islay html jack.after.boot html k3.linear html linear.approx html lines.saddle.distn html logit html manaus html melanoma html motor html neuro html nitrofen html nodal html norm.ci html nuclear html paulsen html plot.boot html poisons html polar html print.boot html print.bootci html print.saddle.distn html print.simplex html remission html saddle html saddle.distn html saddle.distn.object html salinity html simplex html simplex.object html smooth.f html sunspot html survival html tau html tilt.boot html tsboot html tuna html urine html var.linear html wool html ** building package indices ** testing if installed package can be loaded * DONE (boot) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/src/library/Recommended' * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c coxph.c -o coxph.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c magic.c -o magic.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c davies.c -o davies.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c misc.c -o misc.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mgcv.c -o mgcv.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mvn.c -o mvn.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c mat.c -o mat.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c discrete.c -o discrete.o discrete.c: In function 'XWXijspace': discrete.c:1074:11: warning: unused variable 'kk' [-Wunused-variable] 1074 | jm,im,kk,ddtj, | ^~ make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c soap.c -o soap.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c qp.c -o qp.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c tprs.c -o tprs.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c ncv.c -o ncv.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c gdi.c -o gdi.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.2.2/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c sparse.c -o sparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.2.2/lib -L/usr/local/lib64 -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/usr/src/RPM/BUILD/R-4.2.2/lib -lR /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: warning: type of 'dtrsm_' does not match original declaration [-Wlto-type-mismatch] 216 | F77_NAME(dtrsm)(const char *side, const char *uplo, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: type mismatch in parameter 12 216 | F77_NAME(dtrsm)(const char *side, const char *uplo, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: type 'size_t' should match type 'void' /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:216:1: note: 'dtrsm_' was previously declared here /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: warning: type of 'dsyrk_' does not match original declaration [-Wlto-type-mismatch] 242 | F77_NAME(dsyrk)(const char *uplo, const char *trans, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: type mismatch in parameter 11 242 | F77_NAME(dsyrk)(const char *uplo, const char *trans, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: type 'size_t' should match type 'void' /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:242:1: note: 'dsyrk_' was previously declared here /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: warning: type of 'dtrmm_' does not match original declaration [-Wlto-type-mismatch] 225 | F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: type mismatch in parameter 12 225 | F77_NAME(dtrmm)(const char *side, const char *uplo, const char *transa, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: type 'size_t' should match type 'void' /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:225:1: note: 'dtrmm_' was previously declared here /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: warning: type of 'dgemm_' does not match original declaration [-Wlto-type-mismatch] 207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: type mismatch in parameter 14 207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: type 'size_t' should match type 'void' /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:207:1: note: 'dgemm_' was previously declared here /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: warning: type of 'dgemv_' does not match original declaration [-Wlto-type-mismatch] 107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: type mismatch in parameter 12 107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n, | ^ /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: type 'size_t' should match type 'void' /usr/src/RPM/BUILD/R-4.2.2/include/R_ext/BLAS.h:107:1: note: 'dgemv_' was previously declared here make[3]: Leaving directory '/usr/src/tmp/RtmpFl1Sjn/R.INSTALL2aa1af35ddb986/mgcv/src' installing to /usr/src/RPM/BUILD/R-4.2.2/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mgcv' finding HTML links ... done Beta html FFdes html Predict.matrix html Predict.matrix.cr.smooth html Predict.matrix.soap.film html Rrank html Sl.initial.repara html Sl.repara html Sl.setup html Tweedie html XWXd html anova.gam html bam html bam.update html bandchol html 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Converting parsed Rd's to LaTeX ........................................... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi @setfilename R-admin.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en Underfull \hbox (badness 10000) in paragraph at lines 151--156 []@textrm The tar-balls are avail-able from [][]@texttt https:// stat. ethz. ch/ R/ daily/ [][][]@textrm . Down-load [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1511--1515 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make Chapter 4 [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] Overfull \hbox (56.55324pt too wide) in paragraph at lines 2344--2344 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37] [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3303--3303 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Appendix B [50] [51] [52] [53] [54] Appendix C [55] [56] [57] [58] [59] [60] Overfull \hbox (112.72658pt too wide) in paragraph at lines 5182--5182 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/pcre2-10.39-d arwin.17-x86_64.tar.xz[] Overfull \hbox (95.48051pt too wide) in paragraph at lines 5184--5184 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] [61] Overfull \hbox (17.16873pt too wide) in paragraph at lines 5333--5334 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [62] Underfull \hbox (badness 10000) in paragraph at lines 5361--5365 @textrm Mon-terey there is [][]@texttt https:// github. com/ fxcoudert/ gfo rtran-for-macOS/ releases/ [63] Overfull \hbox (62.30193pt too wide) in paragraph at lines 5426--5426 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/ usr/lib/pkgconfig[] [64] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5532--5532 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @textrm in @texttt src/Makevars[]@textrm . It would also be pos-si-ble to stat ic link the For- Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @texttt /usr/local/gfortran/lib/libquadmath.a[] @textrm should the For-tran co m-piler have Overfull \hbox (22.06111pt too wide) in paragraph at lines 6035--6035 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [69] (Function and variable index) [70] No file R-admin.vrs. (Concept index) [71] No file R-admin.cps. (Environment variable index) [72] No file R-admin.ens. [73] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one < /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb> Output written on R-admin.pdf (76 pages, 470504 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en Underfull \hbox (badness 10000) in paragraph at lines 151--156 []@textrm The tar-balls are avail-able from [][]@texttt https:// stat. ethz. ch/ R/ daily/ [][][]@textrm . Down-load [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 3 [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1511--1515 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make Chapter 4 [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] Overfull \hbox (56.55324pt too wide) in paragraph at lines 2344--2344 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37] [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3303--3303 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Appendix B [50] [51] [52] [53] [54] Appendix C [55] [56] [57] [58] [59] [60] Overfull \hbox (112.72658pt too wide) in paragraph at lines 5182--5182 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/pcre2-10.39-d arwin.17-x86_64.tar.xz[] Overfull \hbox (95.48051pt too wide) in paragraph at lines 5184--5184 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] l.5231: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5231: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5231: Undefined cross reference ` Tcl/Tk headers and libraries-pg'. [61] Overfull \hbox (17.16873pt too wide) in paragraph at lines 5333--5334 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [62] Underfull \hbox (badness 10000) in paragraph at lines 5361--5365 @textrm Mon-terey there is [][]@texttt https:// github. com/ fxcoudert/ gfo rtran-for-macOS/ releases/ [63] Overfull \hbox (62.30193pt too wide) in paragraph at lines 5426--5426 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/ usr/lib/pkgconfig[] [64] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5532--5532 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @textrm in @texttt src/Makevars[]@textrm . It would also be pos-si-ble to stat ic link the For- Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5849--5855 @texttt /usr/local/gfortran/lib/libquadmath.a[] @textrm should the For-tran co m-piler have Overfull \hbox (22.06111pt too wide) in paragraph at lines 6035--6035 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [69] (Function and variable index) [70] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.vrs) (Concept index) [71] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.cps) (Environment variable index) [72] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-admin.ens) [73] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (78 pages, 515285 bytes). Transcript written on R-admin.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi @setfilename R-data.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27] (Function and variable index) [28] No file R-data.vrs. (Concept index) [29] No file R-data.cps. [30] ) (see the transcript file for additional information) Output written on R-data.pdf (33 pages, 265846 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.aux) Chapter 1 [1] Writing index file R-data.cp [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27] (Function and variable index) [28] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.vrs [29]) (Concept index) [30] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 305731 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.aux) Chapter 1 [1] Writing index file R-data.cp [2] [3] [4] Underfull \hbox (badness 10000) in paragraph at lines 445--449 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ Chapter 2 [5] [6] [7] [8] [9] [10] Chapter 3 [11] [12] Chapter 4 [13] [14] [15] [16] [17] [18] Chapter 5 [19] Chapter 6 [20] Chapter 7 [21] [22] [23] [24] Chapter 8 [25] Chapter 9 [26] Appendix A [27] (Function and variable index) [28] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.vrs [29]) (Concept index) [30] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 305737 bytes). Transcript written on R-data.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi @setfilename R-FAQ.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 292--314 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 644--647 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 644--647 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 644--647 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 671--676 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [8] [9] [10] Chapter 3 [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 @texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia l-ized ver-sions of Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] Underfull \hbox (badness 10000) in paragraph at lines 3138--3152 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 354491 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 292--314 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 644--647 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 644--647 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 644--647 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 671--676 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 @texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia l-ized ver-sions of Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] Underfull \hbox (badness 10000) in paragraph at lines 3138--3152 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 370685 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 292--314 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 644--647 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 644--647 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 644--647 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 671--676 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 @texttt Commercialized_versions_of_R[][][] @textrm for point-ers to com-mer-cia l-ized ver-sions of Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] Underfull \hbox (badness 10000) in paragraph at lines 3138--3152 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] [42] Chapter 8 [43] Chapter 9 [44] [45] [46] Chapter 10 [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 370682 bytes). Transcript written on R-FAQ.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi @setfilename R-lang.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4353--4355 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] No file R-lang.vrs. (Concept Index) [52] No file R-lang.cps. Appendix A [53] [54] ) (see the transcript file for additional information) Output written on R-lang.pdf (57 pages, 326959 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4353--4355 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.vrs [52]) (Concept Index) [53] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 375648 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4353--4355 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.vrs [52]) (Concept Index) [53] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 375641 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi @setfilename R-ints.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1503--1503 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1504--1504 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [45] Chapter 8 [46] Underfull \hbox (badness 10000) in paragraph at lines 3955--3959 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [47] Underfull \hbox (badness 10000) in paragraph at lines 3989--3994 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60] Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64] (Function and variable index) [65] No file R-ints.vrs. (Concept index) [66] No file R-ints.cps. [67] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on R-ints.pdf (70 pages, 413028 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1503--1503 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1504--1504 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [45] Chapter 8 [46] Underfull \hbox (badness 10000) in paragraph at lines 3955--3959 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [47] Underfull \hbox (badness 10000) in paragraph at lines 3989--3994 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60] Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64] (Function and variable index) [65] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.vrs [66]) (Concept index) [67] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.cps) [68] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 464617 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1501--1501 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1502--1502 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1503--1503 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1504--1504 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3768--3777 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [45] Chapter 8 [46] Underfull \hbox (badness 10000) in paragraph at lines 3955--3959 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [47] Underfull \hbox (badness 10000) in paragraph at lines 3989--3994 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] Chapter 9 [59] [60] Chapter 10 [61] Chapter 11 [62] Chapter 12 [63] [64] (Function and variable index) [65] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.vrs [66]) (Concept index) [67] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-ints.cps) [68] ) (see the transcript file for additional information) Output written on R-ints.pdf (72 pages, 464600 bytes). Transcript written on R-ints.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' collecting LaTeX docs for package 'mgcv' ... Converting parsed Rd's to LaTeX ............... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi @setfilename R-intro.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] Chapter 9 [38] [39] Chapter 10 [40] [41] [42] [43] [44] [45] [46] [47] [48] Chapter 11 [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] Chapter 12 [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Chapter 13 [74] [75] Chapter 14 [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6644--6649 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6644--6649 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [78] Appendix A [79] [80] [81] Appendix B [82] [83] [84] [85] [86] [87] [88] Appendix C [89] [90] Appendix D [91] No file R-intro.vrs. Appendix E [92] No file R-intro.cps. Appendix F [93] [94] ) (see the transcript file for additional information) Output written on R-intro.pdf (97 pages, 568782 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] Chapter 9 [38] [39] Chapter 10 [40] [41] [42] [43] [44] [45] [46] [47] [48] Chapter 11 [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] Chapter 12 [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Chapter 13 [74] [75] Chapter 14 [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6644--6649 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6644--6649 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [78] Appendix A [79] [80] [81] Appendix B [82] [83] [84] [85] [86] [87] [88] Appendix C [89] [90] Appendix D [91] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.vrs [92] [93]) Appendix E [94] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.cps [95]) Appendix F [96] [97] ) (see the transcript file for additional information) Output written on R-intro.pdf (103 pages, 626129 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] Chapter 9 [38] [39] Chapter 10 [40] [41] [42] [43] [44] [45] [46] [47] [48] Chapter 11 [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] Chapter 12 [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Chapter 13 [74] [75] Chapter 14 [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6644--6649 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6644--6649 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [78] Appendix A [79] [80] [81] Appendix B [82] [83] [84] [85] [86] [87] [88] Appendix C [89] [90] Appendix D [91] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.vrs [92] [93]) Appendix E [94] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.cps [95]) Appendix F [96] [97] ) (see the transcript file for additional information) Output written on R-intro.pdf (103 pages, 626138 bytes). Transcript written on R-intro.log. tar: R-intro.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.toc) (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] Chapter 9 [38] [39] Chapter 10 [40] [41] [42] [43] [44] [45] [46] [47] [48] Chapter 11 [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] Chapter 12 [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Chapter 13 [74] [75] Chapter 14 [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6644--6649 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6644--6649 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [78] Appendix A [79] [80] [81] Appendix B [82] [83] [84] [85] [86] [87] [88] Appendix C [89] [90] Appendix D [91] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.vrs [92] [93]) Appendix E [94] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-intro.cps [95]) Appendix F [96] [97] ) (see the transcript file for additional information) Output written on R-intro.pdf (103 pages, 635097 bytes). Transcript written on R-intro.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi @setfilename R-exts.info This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 500--503 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (73.7993pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1639--1649 @texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt able2. 10. tar. gz[][][]@textrm , but [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2846--2849 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [33] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [34] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 @textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c make-env-variables. 7. html# [35] [36] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [54] [55] [56] [57] [58] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [59] Overfull \hbox (55.2397pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] Underfull \hbox (badness 7558) in paragraph at lines 5301--5305 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [66] [67] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] Underfull \hbox (badness 10000) in paragraph at lines 6092--6093 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 6543--6553 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 7595--7602 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] Underfull \hbox (badness 10000) in paragraph at lines 7774--7780 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4 [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 9059--9068 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 9328--9340 @textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm l# controlling-code-generation[][][]@textrm , Overfull \hbox (27.28387pt too wide) in paragraph at lines 9344--9345 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [108] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9483--9483 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [109] Underfull \hbox (badness 10000) in paragraph at lines 9516--9518 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [110] [111] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9662--9662 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [112] [113] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10032--10034 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [116] Overfull \hbox (102.54274pt too wide) in paragraph at lines 10089--10089 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 10108--10108 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (119.7888pt too wide) in paragraph at lines 10119--10119 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (22.06111pt too wide) in paragraph at lines 10149--10149 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Overfull \hbox (30.03963pt too wide) in paragraph at lines 11002--11002 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11588--11588 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12598--12602 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13694--13694 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [157] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13789--13789 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [158] Chapter 6 [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15835--15841 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [182] [183] Chapter 8 [184] [185] [186] Overfull \hbox (22.06111pt too wide) in paragraph at lines 16253--16253 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [187] Overfull \hbox (33.55849pt too wide) in paragraph at lines 16311--16311 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 16826--16833 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 16961--16965 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [196] No file R-exts.vrs. (Concept index) [197] No file R-exts.cps. [198] ) (see the transcript file for additional information) Output written on R-exts.pdf (201 pages, 957911 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 500--503 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (73.7993pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1639--1649 @texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt able2. 10. tar. gz[][][]@textrm , but [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2846--2849 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [33] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [34] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 @textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c make-env-variables. 7. html# [35] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [54] [55] [56] [57] [58] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [59] Underfull \hbox (badness 7558) in paragraph at lines 5301--5305 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [65] [66] [67] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] Underfull \hbox (badness 10000) in paragraph at lines 6092--6093 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 6543--6553 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 7595--7602 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] Underfull \hbox (badness 10000) in paragraph at lines 7774--7780 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4 [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 9059--9068 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 9328--9340 @textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm l# controlling-code-generation[][][]@textrm , Overfull \hbox (27.28387pt too wide) in paragraph at lines 9344--9345 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [108] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9483--9483 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [109] Underfull \hbox (badness 10000) in paragraph at lines 9516--9518 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [110] [111] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9662--9662 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [112] [113] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10032--10034 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [116] Overfull \hbox (102.54274pt too wide) in paragraph at lines 10089--10089 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 10108--10108 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (119.7888pt too wide) in paragraph at lines 10119--10119 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (22.06111pt too wide) in paragraph at lines 10149--10149 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Overfull \hbox (30.03963pt too wide) in paragraph at lines 11002--11002 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11588--11588 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12598--12602 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13694--13694 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [157] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13789--13789 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [158] Chapter 6 [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15835--15841 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [182] [183] Chapter 8 [184] [185] [186] Overfull \hbox (22.06111pt too wide) in paragraph at lines 16253--16253 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [187] Overfull \hbox (33.55849pt too wide) in paragraph at lines 16311--16311 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 16826--16833 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 16961--16965 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [196] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.vrs [197] [198] [199] [200]) (Concept index) [201] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.cps [202]) [203] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb>< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-exts.pdf (209 pages, 1034423 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 500--503 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (73.7993pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1639--1649 @texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt able2. 10. tar. gz[][][]@textrm , but [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2846--2849 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [33] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [34] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 @textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c make-env-variables. 7. html# [35] [36] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [54] [55] [56] [57] [58] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [59] Overfull \hbox (55.2397pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] Underfull \hbox (badness 7558) in paragraph at lines 5301--5305 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [66] [67] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] Underfull \hbox (badness 10000) in paragraph at lines 6092--6093 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 6543--6553 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 7595--7602 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] Underfull \hbox (badness 10000) in paragraph at lines 7774--7780 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4 [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 9059--9068 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 9328--9340 @textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm l# controlling-code-generation[][][]@textrm , Overfull \hbox (27.28387pt too wide) in paragraph at lines 9344--9345 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [108] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9483--9483 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [109] Underfull \hbox (badness 10000) in paragraph at lines 9516--9518 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [110] [111] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9662--9662 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [112] [113] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10032--10034 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [116] Overfull \hbox (102.54274pt too wide) in paragraph at lines 10089--10089 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 10108--10108 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (119.7888pt too wide) in paragraph at lines 10119--10119 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (22.06111pt too wide) in paragraph at lines 10149--10149 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Overfull \hbox (30.03963pt too wide) in paragraph at lines 11002--11002 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11588--11588 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12598--12602 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13694--13694 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [157] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13789--13789 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [158] Chapter 6 [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15835--15841 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [182] [183] Chapter 8 [184] [185] [186] Overfull \hbox (22.06111pt too wide) in paragraph at lines 16253--16253 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [187] Overfull \hbox (33.55849pt too wide) in paragraph at lines 16311--16311 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 16826--16833 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 16961--16965 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [196] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.vrs [197] [198] [199] [200]) (Concept index) [201] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.cps [202]) [203] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb> Output written on R-exts.pdf (209 pages, 1046222 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 500--503 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (73.7993pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1639--1649 @texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt able2. 10. tar. gz[][][]@textrm , but [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2846--2849 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [33] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [34] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 @textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c make-env-variables. 7. html# [35] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [54] [55] [56] [57] [58] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [59] Underfull \hbox (badness 7558) in paragraph at lines 5301--5305 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [65] [66] [67] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] Underfull \hbox (badness 10000) in paragraph at lines 6092--6093 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 6543--6553 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 7595--7602 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] Underfull \hbox (badness 10000) in paragraph at lines 7774--7780 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4 [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 9059--9068 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 9328--9340 @textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm l# controlling-code-generation[][][]@textrm , Overfull \hbox (27.28387pt too wide) in paragraph at lines 9344--9345 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [108] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9483--9483 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [109] Underfull \hbox (badness 10000) in paragraph at lines 9516--9518 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [110] [111] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9662--9662 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [112] [113] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10032--10034 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [116] Overfull \hbox (102.54274pt too wide) in paragraph at lines 10089--10089 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 10108--10108 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (119.7888pt too wide) in paragraph at lines 10119--10119 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (22.06111pt too wide) in paragraph at lines 10149--10149 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Overfull \hbox (30.03963pt too wide) in paragraph at lines 11002--11002 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11588--11588 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12598--12602 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13694--13694 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [157] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13789--13789 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [158] Chapter 6 [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15835--15841 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [182] [183] Chapter 8 [184] [185] [186] Overfull \hbox (22.06111pt too wide) in paragraph at lines 16253--16253 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [187] Overfull \hbox (33.55849pt too wide) in paragraph at lines 16311--16311 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 16826--16833 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 16961--16965 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [196] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.vrs [197] [198] [199] [200]) (Concept index) [201] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.cps [202]) [203] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb>< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-exts.pdf (209 pages, 1034426 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2022-01-02.12]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 500--503 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] Overfull \hbox (73.7993pt too wide) in paragraph at lines 1539--1539 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1540--1540 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1639--1649 @texttt sourceforge. net/ projects/ tktable/ files/ tktable/ 2. 10/ Tkt able2. 10. tar. gz[][][]@textrm , but [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2603--2603 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2605--2605 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [30] [31] [32] Underfull \hbox (badness 10000) in paragraph at lines 2846--2849 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [33] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2924--2924 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2947--2953 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [34] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 @textrm ([][]@texttt https:// cmake. org/ cmake/ help/ latest/ manual/ c make-env-variables. 7. html# [35] Overfull \hbox (22.06111pt too wide) in paragraph at lines 3138--3138 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4762--4762 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4781--4781 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [54] [55] [56] [57] [58] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5213--5213 []@texttt 1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 (announced 19 20 21)[] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5223--5223 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5225--5225 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5226--5226 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 5241--5241 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [59] Underfull \hbox (badness 7558) in paragraph at lines 5301--5305 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [60] [61] [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 5755--5758 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [65] [66] [67] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5979--5979 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [68] Underfull \hbox (badness 10000) in paragraph at lines 6092--6093 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [69] [70] [71] [72] [73] Underfull \hbox (badness 10000) in paragraph at lines 6543--6553 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] Underfull \hbox (badness 10000) in paragraph at lines 7595--7602 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [87] Underfull \hbox (badness 10000) in paragraph at lines 7774--7780 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [88] [89] [90] [91] Chapter 3 [92] [93] [94] [95] [96] [97] [98] Chapter 4 [99] [100] [101] [102] [103] [104] Underfull \hbox (badness 10000) in paragraph at lines 9059--9068 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [105] [106] [107] Underfull \hbox (badness 10000) in paragraph at lines 9328--9340 @textrm See [][]@texttt https:// clang. llvm. org/ docs/ UsersManual. htm l# controlling-code-generation[][][]@textrm , Overfull \hbox (27.28387pt too wide) in paragraph at lines 9344--9345 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [108] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9483--9483 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [109] Underfull \hbox (badness 10000) in paragraph at lines 9516--9518 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [110] [111] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9662--9662 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [112] [113] [114] [115] Underfull \hbox (badness 10000) in paragraph at lines 10032--10034 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [116] Overfull \hbox (102.54274pt too wide) in paragraph at lines 10089--10089 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 10108--10108 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] Overfull \hbox (119.7888pt too wide) in paragraph at lines 10119--10119 []@texttt reg.f:78:33: warning: type of 'dqrdc' does not match original declar ation [-Wlto-type-mismatch][] Overfull \hbox (22.06111pt too wide) in paragraph at lines 10149--10149 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Overfull \hbox (30.03963pt too wide) in paragraph at lines 11002--11002 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [127] [128] [129] [130] [131] [132] [133] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11588--11588 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] Underfull \hbox (badness 10000) in paragraph at lines 12598--12602 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13694--13694 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [157] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13789--13789 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [158] Chapter 6 [159] [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 [][]@texttt https:// www. intel. com/ content/ www/ us/ en/ develop/ d ocumentation/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14542--14547 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] Warning: unbalanced parentheses in @def... [176] [177] [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 15835--15841 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [182] [183] Chapter 8 [184] [185] [186] Overfull \hbox (22.06111pt too wide) in paragraph at lines 16253--16253 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [187] Overfull \hbox (33.55849pt too wide) in paragraph at lines 16311--16311 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 16826--16833 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [194] [195] Underfull \hbox (badness 10000) in paragraph at lines 16961--16965 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [196] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.vrs [197] [198] [199] [200]) (Concept index) [201] (/usr/src/RPM/BUILD/R-4.2.2/doc/manual/R-exts.cps [202]) [203] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb>< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-exts.pdf (209 pages, 1034401 bytes). 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(/usr/share/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texmf-dist/fon ts/map/pdftex/updmap/pdftex.map}] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/share/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texmf-dist/tex/latex/jknapltx/ursfs.fd) [3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 137--143 \T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/ n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 137--143 \T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth -er-wise, it is []\T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 4454) in paragraph at lines 143--151 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 3009) in paragraph at lines 228--240 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 371--374 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 569--575 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 638--638 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 914--914 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 935--935 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [17] [18] [19] [20] [21] [22] [23] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1581--1587 Underfull \hbox (badness 10000) in paragraph at lines 1594--1596 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [26] [27] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1773--1773 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [28] Underfull \hbox (badness 1303) in paragraph at lines 1802--1805 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [29] [30] [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2059--2059 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 2097--2099 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [33] [34] [35] [36] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2362--2362 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2404--2404 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] [39] Underfull \hbox (badness 1107) in paragraph at lines 2566--2568 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2733--2733 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3437--3437 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3438--3438 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3445--3445 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3449--3449 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 3897--3899 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [59] [60] [61] [62] [63] [64] [65] [66] Underfull \hbox (badness 4927) in paragraph at lines 4395--4399 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4395--4399 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4479--4479 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4555--4558 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [69] [70] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4718--4718 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [71] Underfull \hbox (badness 1199) in paragraph at lines 4749--4755 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4760--4763 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4936--4936 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] [77] Underfull \hbox (badness 2521) in paragraph at lines 5192--5194 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [78] [79] [80] [81] [82] [83] Underfull \hbox (badness 1270) in paragraph at lines 5615--5623 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6184--6192 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [93] [94] [95] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6381--6381 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6383--6383 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6384--6384 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [96] [97] Underfull \hbox (badness 1635) in paragraph at lines 6586--6589 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6590--6593 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [98] Underfull \hbox (badness 1308) in paragraph at lines 6633--6641 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [99] [100] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6797--6797 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Underfull \hbox (badness 4505) in paragraph at lines 6849--6852 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6986--6991 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 7234--7236 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7276--7283 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [107] [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7480--7480 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7814--7816 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [115] [116] [117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7973--7973 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7975--7975 []\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo rt is vanishing[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [122] Underfull \hbox (badness 10000) in paragraph at lines 8322--8332 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8322--8332 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [123] [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8490--8490 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8842--8854 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9291--9295 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9382--9382 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9384--9384 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9412--9412 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9413--9413 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] [139] Underfull \hbox (badness 5403) in paragraph at lines 9544--9546 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 9563--9565 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [140] [141] [142] Underfull \hbox (badness 1603) in paragraph at lines 9794--9797 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [143] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 1917) in paragraph at lines 10410--10415 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [152] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10465--10465 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10466--10466 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [153] [154] Underfull \hbox (badness 1168) in paragraph at lines 10568--10573 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10670--10670 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10672--10672 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10791--10796 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 10822--10822 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10896--10896 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [159] [160] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11044--11044 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [161] [162] [163] Underfull \hbox (badness 6396) in paragraph at lines 11242--11250 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11251--11253 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11468--11471 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] Underfull \hbox (badness 2744) in paragraph at lines 11904--11906 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11927--11927 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [174] [175] [176] Underfull \hbox (badness 5288) in paragraph at lines 12179--12181 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12189--12194 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12246--12249 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12264--12266 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12514--12516 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 12557--12559 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13375--13375 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14100--14102 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14135--14138 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14268--14270 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 14427--14429 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14548--14552 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14559--14562 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 14580--14580 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [210] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14605--14605 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [211] Underfull \hbox (badness 10000) in paragraph at lines 14702--14705 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14712--14712 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [212] Underfull \hbox (badness 10000) in paragraph at lines 14778--14781 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14795--14795 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14824--14824 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 14856--14860 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [214] [215] [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15020--15020 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15021--15021 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] [220] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15263--15263 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15266--15266 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [221] Underfull \hbox (badness 1168) in paragraph at lines 15352--15356 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15352--15356 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [222] Underfull \hbox (badness 6944) in paragraph at lines 15449--15452 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [223] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15474--15474 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [224] [225] Underfull \hbox (badness 10000) in paragraph at lines 15612--15614 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15632--15632 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15638--15638 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 15645--15648 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [226] Underfull \hbox (badness 1024) in paragraph at lines 15676--15683 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [227] Underfull \hbox (badness 10000) in paragraph at lines 15751--15753 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 15773--15778 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 15779--15781 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 15790--15798 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [228] [229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15898--15898 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] [243] Underfull \hbox (badness 2418) in paragraph at lines 16863--16867 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16870--16873 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16905--16912 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [244] [245] Underfull \hbox (badness 10000) in paragraph at lines 17012--17016 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17012--17016 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [246] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17075--17075 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17078--17078 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [247] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17109--17109 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [248] [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17246--17246 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17274--17281 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [250] [251] [252] [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17575--17575 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] [254] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17604--17604 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [255] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17660--17660 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [256] [257] [258] [259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18033--18033 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18098--18098 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [261] [262] [263] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18307--18307 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [264] [265] [266] [267] [268] Underfull \hbox (badness 1163) in paragraph at lines 18653--18655 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18661--18661 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] [269] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18691--18691 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [270] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18785--18785 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18786--18786 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [271] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18845--18845 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18848--18848 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18854--18854 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [272] [273] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18981--18981 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18989--18989 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [274] [275] [276] Underfull \hbox (badness 10000) in paragraph at lines 19194--19196 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [277] [278] [279] [280] [281] Underfull \hbox (badness 10000) in paragraph at lines 19532--19538 Underfull \hbox (badness 10000) in paragraph at lines 19545--19547 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [282] [283] [284] Underfull \hbox (badness 4699) in paragraph at lines 19777--19780 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [285] [286] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19905--19905 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [287] [288] [289] Underfull \hbox (badness 4739) in paragraph at lines 20040--20042 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [290] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20089--20089 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20090--20090 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [291] [292] [293] [294] [295] [296] [297] [298] [299] Underfull \hbox (badness 1975) in paragraph at lines 20709--20712 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [300] [301] [302] [303] [304] [305] Underfull \hbox (badness 1077) in paragraph at lines 21124--21129 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21138--21145 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [306] Underfull \hbox (badness 1112) in paragraph at lines 21212--21221 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [307] Underfull \hbox (badness 2970) in paragraph at lines 21272--21275 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21272--21275 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21385--21389 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21385--21389 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21390--21397 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [310] [311] Underfull \hbox (badness 10000) in paragraph at lines 21521--21528 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [312] Underfull \hbox (badness 10000) in paragraph at lines 21642--21646 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [313] Underfull \hbox (badness 5161) in paragraph at lines 21712--21717 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [314] [315] [316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21880--21880 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21884--21884 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [317] Underfull \hbox (badness 3343) in paragraph at lines 21945--21949 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [318] [319] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22083--22083 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22094--22094 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [320] [321] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22205--22205 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22208--22208 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22255--22263 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [322] [323] Underfull \hbox (badness 2564) in paragraph at lines 22358--22361 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22395--22395 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22406--22406 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22414--22414 [] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[ 1]], "=")), nrow=2)[] [324] [325] Underfull \hbox (badness 1400) in paragraph at lines 22575--22579 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23419--23419 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23420--23420 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 23423--23423 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [339] Overfull \hbox (20.58041pt too wide) in paragraph at lines 23520--23520 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] [340] Underfull \hbox (badness 1655) in paragraph at lines 23554--23558 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [341] [342] [343] Underfull \hbox (badness 2277) in paragraph at lines 23803--23806 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [344] [345] [346] [347] [348] [349] [350] [351] [352] Underfull \hbox (badness 1484) in paragraph at lines 24392--24400 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 24392--24400 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [353] [354] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24466--24466 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [355] [356] [357] [358] [359] [360] [361] [362] Underfull \hbox (badness 1448) in paragraph at lines 25014--25022 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [363] Underfull \hbox (badness 3849) in paragraph at lines 25129--25134 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [364] Underfull \hbox (badness 2165) in paragraph at lines 25206--25212 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25206--25212 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25206--25212 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [365] [366] [367] Underfull \hbox (badness 2237) in paragraph at lines 25369--25371 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [368] [369] [370] Underfull \hbox (badness 6188) in paragraph at lines 25596--25599 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [371] [372] [373] Underfull \hbox (badness 1521) in paragraph at lines 25781--25795 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [374] [375] [376] [377] Underfull \hbox (badness 2197) in paragraph at lines 26095--26099 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26095--26099 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use [378] Underfull \hbox (badness 2846) in paragraph at lines 26109--26113 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26109--26113 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26151--26151 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 26155--26155 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [379] Underfull \hbox (badness 10000) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26217--26219 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [380] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26284--26284 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [381] [382] [383] Underfull \hbox (badness 8189) in paragraph at lines 26479--26485 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [384] [385] [386] Underfull \hbox (badness 1694) in paragraph at lines 26704--26707 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [387] [388] [389] [390] Underfull \hbox (badness 1603) in paragraph at lines 26976--26978 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [391] [392] Underfull \hbox (badness 1210) in paragraph at lines 27103--27111 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [393] [394] Underfull \hbox (badness 3271) in paragraph at lines 27323--27326 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [395] [396] [397] [398] Underfull \hbox (badness 3138) in paragraph at lines 27629--27635 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 27642--27645 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27668--27670 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 27695--27701 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27710--27715 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [399] Underfull \hbox (badness 1009) in paragraph at lines 27728--27731 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 27744--27747 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up date.packages[][][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27767--27774 []\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut il-i-ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27767--27774 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke []\T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; [400] [401] [402] [403] [404] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 28128--28132 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [405] [406] Underfull \hbox (badness 1210) in paragraph at lines 28275--28278 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [407] [408] [409] [410] Underfull \hbox (badness 7133) in paragraph at lines 28557--28563 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 28579--28579 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28591--28591 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [411] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28604--28604 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling : [] Overfull \hbox (63.78036pt too wide) in paragraph at lines 28608--28608 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [412] [413] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] [414] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28806--28806 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] Underfull \hbox (badness 1360) in paragraph at lines 28861--28865 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [415] [416] [417] [418] [419] Underfull \hbox (badness 2277) in paragraph at lines 29173--29178 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [420] [421] Underfull \hbox (badness 1701) in paragraph at lines 29289--29293 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [422] Underfull \hbox (badness 1796) in paragraph at lines 29357--29360 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [423] [424] [425] Underfull \hbox (badness 10000) in paragraph at lines 29561--29564 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [436] [437] [438] [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30560--30560 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30566--30566 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30572--30572 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [441] Underfull \hbox (badness 7415) in paragraph at lines 30662--30666 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [442] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30683--30683 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30729--30729 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [443] [444] Underfull \hbox (badness 3713) in paragraph at lines 30874--30885 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [445] [446] Underfull \hbox (badness 1248) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [447] Underfull \hbox (badness 1533) in paragraph at lines 31144--31147 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [448] [449] [450] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31289--31289 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 31307--31318 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [451] [452] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 31453--31453 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31454--31454 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31456--31456 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [453] [454] [455] [456] [457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31773--31773 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31783--31783 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] Underfull \vbox (badness 10000) has occurred while \output is active [458] [459] Underfull \hbox (badness 4048) in paragraph at lines 31879--31884 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 2080) in paragraph at lines 32417--32427 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 32451--32451 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [468] [469] [470] [471] [472] [473] [474] Underfull \hbox (badness 7558) in paragraph at lines 32971--32975 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32981--32983 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [475] Underfull \hbox (badness 10000) in paragraph at lines 32992--32994 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 32995--32999 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [476] [477] [478] [479] [480] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33366--33366 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [481] Underfull \hbox (badness 10000) in paragraph at lines 33437--33441 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [482] [483] [484] Underfull \hbox (badness 2302) in paragraph at lines 33663--33668 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 33663--33668 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [485] [486] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33796--33796 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33799--33799 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33806--33806 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [487] [488] [489] [490] [491] [492] [493] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34254--34254 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [494] [495] [496] [497] [498] [499] [500] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34691--34691 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [501] Underfull \hbox (badness 1158) in paragraph at lines 34795--34800 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [502] [503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34981--34981 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [504] [505] [506] [507] Underfull \hbox (badness 4752) in paragraph at lines 35241--35244 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35245--35251 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as Underfull \hbox (badness 3271) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru les for the C run- Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso ft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 35915--35926 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [518] [519] [520] [521] [522] [523] [524] [525] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [526] [527] [528] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36709--36709 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [529] Underfull \hbox (badness 4954) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [530] [531] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36863--36863 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [532] [533] [534] [535] [536] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37206--37206 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37221--37221 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [537] [538] [539] Underfull \hbox (badness 10000) in paragraph at lines 37446--37448 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [540] [541] [542] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37673--37673 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37674--37674 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [543] [544] [545] [546] [547] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [548] Underfull \hbox (badness 6110) in paragraph at lines 38101--38111 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38101--38111 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [549] Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38172--38179 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [550] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38234--38234 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [551] [552] [553] Underfull \hbox (badness 1484) in paragraph at lines 38407--38411 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 38469--38469 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [554] [555] [556] [557] [558] [559] [560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955 []\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is still NA (not "NA")[] [561] [562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [563] [564] [565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 39314--39314 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39358--39358 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [567] [568] [569] [570] [571] [572] [573] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39805--39805 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39808--39808 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [575] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39912--39912 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [576] [577] [578] [579] Overfull \hbox (31.3804pt too wide) in paragraph at lines 40223--40223 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [580] [581] [582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [583] Overfull \hbox (20.58041pt too wide) in paragraph at lines 40427--40427 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 40457--40463 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 40457--40463 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 40476--40481 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 40476--40481 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [584] [585] [586] [587] Underfull \hbox (badness 10000) in paragraph at lines 40764--40768 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 40779--40782 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [588] [589] [590] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [591] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40998--40998 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [592] [593] Underfull \hbox (badness 1082) in paragraph at lines 41143--41146 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41170--41172 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [594] [595] [596] Underfull \hbox (badness 1038) in paragraph at lines 41336--41339 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [597] [598] [599] [600] [601] Underfull \hbox (badness 1442) in paragraph at lines 41701--41705 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [602] [603] [604] [605] Underfull \hbox (badness 4096) in paragraph at lines 41955--41958 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [606] Underfull \hbox (badness 7888) in paragraph at lines 42069--42073 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [607] [608] [609] Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 42225--42225 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 42240--42242 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [610] Underfull \hbox (badness 10000) in paragraph at lines 42320--42323 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [611] [612] Underfull \hbox (badness 3872) in paragraph at lines 42438--42441 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [613] Underfull \hbox (badness 5475) in paragraph at lines 42504--42508 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [614] [615] [616] [617] [618] [619] Underfull \hbox (badness 1655) in paragraph at lines 42927--42934 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 42935--42940 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 42935--42940 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing Underfull \hbox (badness 4467) in paragraph at lines 42985--42994 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42985--42994 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [620] Underfull \hbox (badness 1082) in paragraph at lines 42995--43007 []\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1 0 ' in that di-rec-tory states the ver-sion. That op-tion is [621] Underfull \hbox (badness 1337) in paragraph at lines 43080--43088 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43089--43092 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 43143--43146 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43147--43149 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- [622] Overfull \hbox (31.3804pt too wide) in paragraph at lines 43156--43156 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [623] [624] [625] [626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43499--43499 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43501--43501 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [627] Underfull \vbox (badness 10000) has occurred while \output is active [628] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43604--43604 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [629] [630] [631] [632] Underfull \hbox (badness 6542) in paragraph at lines 43878--43880 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [633] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43997--43997 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [634] Underfull \hbox (badness 1708) in paragraph at lines 44065--44073 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44065--44073 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [635] Underfull \hbox (badness 4859) in paragraph at lines 44105--44110 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [636] Underfull \hbox (badness 3895) in paragraph at lines 44167--44179 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44167--44179 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [637] [638] [639] [640] [641] Overfull \hbox (9.78043pt too wide) in paragraph at lines 44490--44490 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [642] [643] [644] [645] [646] [647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44959--44959 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44968--44968 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] Underfull \hbox (badness 2057) in paragraph at lines 45034--45040 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [649] Underfull \hbox (badness 3861) in paragraph at lines 45043--45048 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [650] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45136--45136 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [651] Underfull \hbox (badness 1803) in paragraph at lines 45199--45202 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 45203--45209 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [652] [653] [654] Underfull \hbox (badness 3668) in paragraph at lines 45432--45434 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [655] Overfull \hbox (36.78088pt too wide) in paragraph at lines 45538--45538 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [656] [657] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45621--45621 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [658] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45715--45715 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 45719--45719 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings AsFactors = FALSE) {[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720 [] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa ctors=stringsAsFactors)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45727--45727 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 45730--45730 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [659] Underfull \hbox (badness 10000) in paragraph at lines 45791--45796 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 45791--45796 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [660] [661] Underfull \hbox (badness 2818) in paragraph at lines 45887--45893 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 45922--45922 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [662] [663] [664] [665] [666] [667] [668] Underfull \hbox (badness 2846) in paragraph at lines 46381--46385 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46421--46421 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 46442--46446 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [670]) (./compiler-pkg.tex Chapter 2. [671] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [672] [673] [674]) (./datasets-pkg.tex Chapter 3. [675] [676] [677] [678] [679] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [680] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [681] [682] [683] [684] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [685] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [686] [687] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [688] [689] [690] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [691] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [692] [693] [694] [695] [696] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [697] [698] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [699] [700] [701] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [702] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [703] [704] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [705] [706] [707] [708] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [709] [710] [711] [712] [713] [714] [715] [716] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [717] [718] [719] [720] [721] [722] [723] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [724] [725] [726] [727] [728] [729] [730] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [731] [732] [733] Underfull \hbox (badness 4779) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [734] [735] [736] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3968--3968 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]) (./grDevices-pkg.tex Chapter 4. [751] [752] [753] [754] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [755] [756] [757] [758] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [769] [770] [771] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [772] [773] [774] Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1624--1628 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [775] [776] [777] [778] [779] Underfull \hbox (badness 1565) in paragraph at lines 1914--1919 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1914--1919 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [780] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1997--1997 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [781] Underfull \hbox (badness 1184) in paragraph at lines 2038--2048 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2038--2048 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [782] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [783] [784] [785] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [786] [787] Underfull \hbox (badness 2326) in paragraph at lines 2447--2457 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2447--2457 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2447--2457 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2447--2457 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [788] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2550--2550 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] [789] [790] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2666--2666 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2667--2667 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [791] [792] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [795] [796] [797] [798] [799] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3273--3273 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [800] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3358--3358 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 3516--3522 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3591--3591 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [805] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3675--3675 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3695--3695 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3702--3702 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [806] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3758--3758 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [807] Underfull \hbox (badness 8170) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [808] Underfull \hbox (badness 2189) in paragraph at lines 3848--3853 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3886--3890 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [809] Underfull \vbox (badness 10000) has occurred while \output is active [810] Underfull \hbox (badness 5260) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [811] [812] [813] [814] [815] Underfull \hbox (badness 5939) in paragraph at lines 4349--4354 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [816] [817] [818] [819] [820] [821] [822] [823] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [824] [825] Underfull \hbox (badness 1348) in paragraph at lines 5074--5077 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [826] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5098--5098 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5139--5145 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [827] Underfull \hbox (badness 1112) in paragraph at lines 5172--5176 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [828] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [829] [830] [831] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5505--5509 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [832] [833] Underfull \hbox (badness 1552) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5642--5644 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5674--5680 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [834] Underfull \hbox (badness 5388) in paragraph at lines 5700--5702 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [835] [836] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5915--5915 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 6001--6003 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [840] [841] [842] [843] [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [845] [846] [847] [848] [849] [850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [851] [852] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6990--6995 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [855] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7096--7096 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [856] Underfull \hbox (badness 3590) in paragraph at lines 7135--7138 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7135--7138 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7146--7146 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [857] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [858] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [859] Underfull \hbox (badness 10000) in paragraph at lines 7362--7369 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7362--7369 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [860] Underfull \hbox (badness 5607) in paragraph at lines 7446--7450 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [861] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7498--7498 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [862] [863] Underfull \hbox (badness 5637) in paragraph at lines 7630--7636 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7663--7666 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [864] [865] [866] Underfull \hbox (badness 1231) in paragraph at lines 7832--7834 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [867] [868]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [869] [870] [871] [872] [873] [874] [875] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [876] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [878] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [879] [880] Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770 []\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0: 1e-2 1e0 1e2 .. 1e10[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [881] [882] [883] Underfull \hbox (badness 10000) in paragraph at lines 966--970 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [884] [885] [886] [887] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [888] [889] [890] Underfull \hbox (badness 2503) in paragraph at lines 1433--1442 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1468--1470 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [891] [892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1543--1543 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1549--1549 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1550--1550 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [893] [894] [895] [896] [897] Underfull \hbox (badness 10000) in paragraph at lines 1853--1859 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and Overfull \hbox (9.78043pt too wide) in paragraph at lines 1873--1873 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1910--1910 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [898] [899] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1995--1995 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [900] [901] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2124--2124 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2129--2129 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [902] [903] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2303--2303 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2304--2304 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [904] Underfull \hbox (badness 1430) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [905] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2416--2416 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [906] Underfull \hbox (badness 7273) in paragraph at lines 2510--2514 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [907] [908] [909] [910] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2758--2758 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [911] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2795--2795 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [912] [913] Underfull \hbox (badness 1226) in paragraph at lines 2923--2927 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [914] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2980--2980 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [915] Underfull \hbox (badness 10000) in paragraph at lines 3042--3045 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3093--3093 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [916] [917] [918] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3262--3262 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is [921] [922] [923] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3590--3590 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3613--3613 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [924] [925] [926] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3798--3798 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3799--3799 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3803--3803 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3844--3844 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3870--3870 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3872--3872 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3883--3883 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3898--3898 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [928] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3908--3908 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3916--3916 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3926--3926 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [929] Underfull \hbox (badness 10000) in paragraph at lines 3988--3992 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [930] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4100--4100 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [931] [932] [933] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4254--4254 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [934] Underfull \hbox (badness 3930) in paragraph at lines 4333--4335 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [935] [936] [937] [938] [939] Underfull \hbox (badness 1286) in paragraph at lines 4644--4647 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [940] [941] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4748--4748 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [942] Underfull \hbox (badness 1264) in paragraph at lines 4944--4957 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [943] [944] [945] [946] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [947 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 [948 ] [949] [950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5517--5517 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5518--5518 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5884--5884 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [957] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [958] [959] [960] [961] [962] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6275--6275 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [963] [964] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6405--6405 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 6711--6713 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [969] [970] Underfull \hbox (badness 1028) in paragraph at lines 6805--6807 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [971 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6942--6942 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [972] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6973--6973 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [973] [974] Underfull \hbox (badness 10000) in paragraph at lines 7095--7097 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7122--7122 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7128--7128 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [975] Underfull \hbox (badness 2600) in paragraph at lines 7185--7187 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [976] [977] [978] [979] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7417--7417 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [980] [981] [982] [983] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7804--7804 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7808--7808 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [986] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7820--7820 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [987] [988] [989] [990] [991] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8169--8169 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8172--8172 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8176--8176 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [992] [993] [994] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8347--8347 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8348--8348 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [995] [996] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [997] Underfull \hbox (badness 1112) in paragraph at lines 8511--8515 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [998] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8586--8586 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [999] [1000] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8723--8723 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8908--8908 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [1003] Underfull \hbox (badness 1215) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 8970--8976 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1004] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1005] Underfull \hbox (badness 1205) in paragraph at lines 9083--9085 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9202--9202 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1008]) (./grid-pkg.tex Chapter 6. [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1019] [1020] [1021] [1022] [1023] [1024] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1025] [1026] [1027] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1028] [1029] [1030] [1031] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1032] [1033] [1034] [1035] [1036] [1037] [1038] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1039] [1040] [1041] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1042] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1043] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1044] [1045] [1046] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1047] [1048] [1049] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1050] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2664--2664 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1051] [1052] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2826--2826 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1053] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2858--2858 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1054] [1055] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1056] [1057] [1058] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3228--3228 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1059] [1060] [1061] [1062] [1063] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3543--3543 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1064] [1065] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3639--3639 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3676--3682 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1068] [1069] [1070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3976--3976 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3991--3991 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4012--4012 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1084] [1085] [1086] [1087] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4977--4977 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1088] [1089] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1090] [1091] [1092] [1093] [1094] [1095] Underfull \hbox (badness 2726) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5561--5565 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1096] [1097] Underfull \hbox (badness 2080) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1098] [1099] [1100] Underfull \hbox (badness 10000) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6900--6900 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1118] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7020--7020 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1119] [1120] Underfull \hbox (badness 1867) in paragraph at lines 7122--7124 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1121] Underfull \hbox (badness 10000) in paragraph at lines 7159--7165 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1122] [1123] [1124] [1125] [1126] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7495--7495 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1131] [1132] [1133] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1134] [1135] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1137] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1153] [1154] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1155] [1156] [1157] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1160] [1161] [1162] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1163] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1164] [1165] [1166] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1167] [1168] [1169] [1170] [1171] [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1174] [1175] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1176] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1177] [1178] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1179] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1180] [1181] [1182] [1183] [1184] [1185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1186] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1187] [1188] [1189] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1190] [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1193] [1194] [1195] [1196] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1197] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1198] [1199] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1200] [1201] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1202] [1203] [1204] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1205] [1206] [1207] [1208] [1209] [1210] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1211] [1212] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1213] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1214] [1215] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] [1218] [1219] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1220] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1221] [1222] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1223] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1224] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1225] [1226] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1227] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1241] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1242] [1243] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1246] [1247] [1248] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1249] [1250] [1251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1252] [1253] [1254] [1255] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1256] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1267] [1268] [1269]) (./parallel-pkg.tex [1270] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1271] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1272] [1273] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1274] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 445--447 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1277] [1278] [1279] [1280] [1281] Underfull \hbox (badness 1917) in paragraph at lines 779--788 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 779--788 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1282] [1283] Overfull \hbox (60.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1284] [1285] [1286] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1063--1063 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1067--1067 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1287] Underfull \hbox (badness 5388) in paragraph at lines 1182--1187 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from [1288] Underfull \hbox (badness 10000) in paragraph at lines 1206--1214 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1289] [1290] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1373--1373 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1291] Underfull \hbox (badness 1577) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1449--1451 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1292] [1293]) (./splines-pkg.tex [1294] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1303] Underfull \hbox (badness 1043) in paragraph at lines 597--599 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1304] [1305] Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1306] [1307] [1308]) (./stats-pkg.tex Chapter 10. [1309] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1310] [1311] [1312] [1313] [1314] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1315] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1024) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1628--1628 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1333] [1334] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1335] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2805--2805 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1350] [1351] [1352] [1353] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3053--3053 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1354] [1355] [1356] Underfull \hbox (badness 10000) in paragraph at lines 3264--3266 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1357] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3313--3313 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3314--3314 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1358] [1359] [1360] [1361] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1362] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1363] [1364] [1365] [1366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1367] [1368] [1369] [1370] [1371] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4277--4277 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1372] [1373] [1374] [1375] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1376] [1377] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1378] [1379] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1380] [1381] [1382] [1383] [1384] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5174--5174 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1385] [1386] [1387] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5414--5414 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1388] [1389] [1390] [1391] Underfull \hbox (badness 1436) in paragraph at lines 5624--5629 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1392] [1393] [1394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1395] [1396] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5994--5994 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1397] [1398] [1399] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1400] [1401] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1402] [1403] [1404] [1405] Underfull \hbox (badness 5954) in paragraph at lines 6550--6552 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1406] Underfull \hbox (badness 2503) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6636--6638 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6639--6644 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1407] Underfull \hbox (badness 7238) in paragraph at lines 6675--6678 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6687--6687 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6710--6710 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6725--6725 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6740--6740 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1409] [1410] [1411] Underfull \vbox (badness 10000) has occurred while \output is active [1412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 7394--7398 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1419] Underfull \hbox (badness 6493) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1420] [1421] Underfull \hbox (badness 10000) in paragraph at lines 7630--7633 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1422] [1423] [1424] [1425] [1426] [1427] Underfull \hbox (badness 10000) in paragraph at lines 8042--8047 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 1210) in paragraph at lines 8397--8399 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1434] [1435] [1436] [1437] [1438] [1439] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1440] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8905--8905 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8908--8908 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1449] [1450] [1451] Underfull \hbox (badness 7291) in paragraph at lines 9668--9670 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 6944) in paragraph at lines 10160--10166 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1459] [1460] [1461] Underfull \hbox (badness 3758) in paragraph at lines 10374--10377 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1462] [1463] [1464] [1465] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1466] Underfull \hbox (badness 4132) in paragraph at lines 10683--10687 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10737--10743 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1467] Underfull \hbox (badness 10000) in paragraph at lines 10788--10791 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1468] [1469] [1470] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1471] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1472] Underfull \hbox (badness 10000) in paragraph at lines 11128--11134 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11166--11171 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1473] [1474] Underfull \hbox (badness 2635) in paragraph at lines 11299--11302 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1475] [1476] [1477] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1478] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1479] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11613--11613 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11626--11630 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1480] [1481] [1482] [1483] [1484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1485] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1486] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12088--12093 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1487] [1488] [1489] [1490] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12730--12732 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1497] [1498] [1499] [1500] [1501] Underfull \hbox (badness 3417) in paragraph at lines 13037--13039 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13043--13047 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1502] [1503] [1504] [1505] [1506] [1507] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1508] [1509] [1510] [1511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1512] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1513] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1514] [1515] [1516] Underfull \hbox (badness 10000) in paragraph at lines 14062--14066 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 1163) in paragraph at lines 14402--14410 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1522] [1523] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1524] [1525] [1526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1527] [1528] [1529] [1530] [1531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15055--15055 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1533] [1534] [1535] [1536] [1537] [1538] [1539] Underfull \hbox (badness 2726) in paragraph at lines 15557--15560 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1551] [1552] Underfull \hbox (badness 1490) in paragraph at lines 16425--16430 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1553] Underfull \hbox (badness 1648) in paragraph at lines 16491--16493 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1554] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1564] [1565] [1566] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] Underfull \vbox (badness 10000) has occurred while \output is active [1577] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1578] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1579] [1580] [1581] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1582] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18417--18417 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1583] [1584] [1585] [1586] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 1248) in paragraph at lines 18938--18941 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 18959--18963 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1592] Underfull \hbox (badness 2042) in paragraph at lines 19017--19019 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1593] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1595] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19210--19210 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19245--19256 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19245--19256 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1597] [1598] [1599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1600] [1601] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1602] [1603] [1604] [1605] [1606] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1607] [1608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20055--20055 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1609] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20125--20131 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20136--20139 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1610] [1611] [1612] [1613] [1614] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1615] Underfull \hbox (badness 1107) in paragraph at lines 20505--20507 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1616] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1617] [1618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1619] [1620] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1621] Underfull \hbox (badness 7740) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1622] Underfull \hbox (badness 10000) in paragraph at lines 20957--20959 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1623] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1637] Underfull \hbox (badness 6859) in paragraph at lines 21921--21928 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1650] [1651] [1652] [1653] [1654] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1655] [1656] [1657] [1658] [1659] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1668] [1669] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1670] Underfull \hbox (badness 1028) in paragraph at lines 24024--24027 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1671] [1672] Underfull \hbox (badness 10000) in paragraph at lines 24139--24142 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7099) in paragraph at lines 24194--24196 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1673] Underfull \hbox (badness 7099) in paragraph at lines 24258--24260 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1674] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24488--24488 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to [1680] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1681] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1682] Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1683] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1684] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 6268) in paragraph at lines 25429--25434 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1692] [1693] [1694] [1695] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 25689--25689 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1696] [1697] [1698] Underfull \hbox (badness 2495) in paragraph at lines 25879--25888 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1699] [1700] Underfull \hbox (badness 2197) in paragraph at lines 26021--26024 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and [1701] Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26048--26050 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1702] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26160--26160 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26163--26163 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1703] [1704] [1705] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26396--26402 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1706] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1707] [1708] [1709] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1710] [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1717] [1718] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27232--27232 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1719] Underfull \hbox (badness 2922) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1720] Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1721] Underfull \hbox (badness 3240) in paragraph at lines 27409--27412 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1722] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27430--27430 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27433--27433 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1723] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27520--27520 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27530--27530 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1724] Underfull \hbox (badness 2922) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1725] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27623--27623 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27625--27625 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27628--27628 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27630--27630 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1726] [1727] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27742--27742 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1728] Underfull \hbox (badness 2922) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (69.18036pt too wide) in paragraph at lines 27842--27842 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1729] Underfull \hbox (badness 2922) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1730] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27922--27922 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27981--27981 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27985--27985 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28005--28005 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28015--28015 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] [1732] Underfull \hbox (badness 2922) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28072--28072 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1733] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28090--28090 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28173--28173 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28176--28176 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28179--28179 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 3396) in paragraph at lines 29062--29064 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1749] [1750] Underfull \hbox (badness 2237) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1751] [1752] [1753] Underfull \hbox (badness 2591) in paragraph at lines 29403--29405 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1754] Underfull \hbox (badness 2237) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1755] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29522--29522 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1756] Underfull \hbox (badness 3407) in paragraph at lines 29631--29635 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1757] [1758] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29701--29701 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1759] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1760] [1761] [1762] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30028--30028 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1763] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30056--30056 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1764] [1765] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30161--30161 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30239--30239 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1767] Underfull \hbox (badness 2205) in paragraph at lines 30328--30333 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30927--30927 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30928--30928 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1777] [1778] [1779] [1780] [1781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31228--31228 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31229--31229 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1782] [1783] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31355--31355 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31364--31364 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1784] [1785] [1786] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1795] [1796] [1797] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32317--32317 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32319--32319 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1798] [1799] [1800] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32478--32478 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32563--32563 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1802] [1803] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32696--32696 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1804]) (./stats4-pkg.tex Chapter 11. [1805] [1806] [1807] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1808] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1809] [1810] [1811] [1812] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1813] [1814] [1815]) (./tcltk-pkg.tex [1816] Chapter 12. [1817] [1818] [1819] [1820] Overfull \hbox (36.7804pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1821] [1822] [1823] Underfull \vbox (badness 10000) has occurred while \output is active [1824] Underfull \hbox (badness 1292) in paragraph at lines 666--673 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1825] [1826] [1827] [1828] [1829] [1830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1079--1079 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1831] [1832] [1833] [1834] [1835] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1836]) (./tools-pkg.tex Chapter 13. [1837] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1838] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1839] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1840] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1841] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1842] [1843] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1844] [1845] [1846] [1847] [1848] [1849] [1850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 911--911 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 966--966 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1851] [1852] [1853] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1134--1134 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1135--1135 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1854] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and [1855] Underfull \hbox (badness 10000) in paragraph at lines 1225--1228 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1856] [1857] Underfull \hbox (badness 10000) in paragraph at lines 1374--1377 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1858] [1859] Underfull \hbox (badness 4647) in paragraph at lines 1543--1548 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1860] Underfull \hbox (badness 2762) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1861] [1862] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1707--1707 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1714--1722 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1714--1722 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1714--1722 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1863] [1864] [1865] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1866] [1867] [1868] [1869] Underfull \hbox (badness 1142) in paragraph at lines 2196--2202 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1870] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2230--2230 [] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] Underfull \hbox (badness 2359) in paragraph at lines 2258--2265 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1871] Underfull \hbox (badness 1342) in paragraph at lines 2310--2316 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1872] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2384--2384 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2399--2407 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2399--2407 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2399--2407 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2435--2435 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2468--2468 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2752--2752 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1878] Underfull \hbox (badness 2486) in paragraph at lines 2797--2805 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1879] [1880] [1881] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3009--3009 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3013--3013 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1882] [1883] [1884] Underfull \hbox (badness 1072) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1885] [1886] [1887] [1888] [1889] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3534--3534 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1890] Underfull \hbox (badness 5417) in paragraph at lines 3572--3582 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1891] [1892] [1893] Underfull \hbox (badness 4108) in paragraph at lines 3782--3789 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1894] [1895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3882--3882 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3885--3885 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3919--3925 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1896] [1897] Underfull \hbox (badness 7832) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1898] [1899] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4276--4276 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1902] [1903] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4438--4438 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4453--4456 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1904] Underfull \hbox (badness 6859) in paragraph at lines 4469--4474 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 4703--4705 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1908] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4746--4749 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4750--4760 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4788--4794 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4788--4794 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1909] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4842--4847 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1910] [1911] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1912]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1913] [1914] [1915] [1916] Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1917] Underfull \hbox (badness 10000) in paragraph at lines 378--383 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", [1918] Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 452--452 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1920] [1921] [1922] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 689--689 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 690--690 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 726--732 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1923] [1924] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1928] Underfull \hbox (badness 1748) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/ 10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1092) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1 ) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1929] Underfull \hbox (badness 10000) in paragraph at lines 1235--1238 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1930] [1931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 1859) in paragraph at lines 1721--1730 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1721--1730 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1937] [1938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1826--1826 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1939] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1861--1861 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1940] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1941] Underfull \hbox (badness 2277) in paragraph at lines 2076--2081 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1942] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2109--2109 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1943] [1944] [1945] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2319--2319 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1947] [1948] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1949] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2512--2512 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1950] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2632--2632 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1951] Underfull \hbox (badness 1082) in paragraph at lines 2706--2710 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [1952] Underfull \hbox (badness 1163) in paragraph at lines 2742--2744 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1953] Underfull \hbox (badness 10000) in paragraph at lines 2835--2837 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 3053--3055 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1958] [1959] [1960] [1961] Underfull \hbox (badness 1762) in paragraph at lines 3346--3349 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1962] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1963] Underfull \hbox (badness 2452) in paragraph at lines 3515--3518 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1964] [1965] [1966] [1967] [1968] [1969] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1970] Underfull \hbox (badness 4779) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1971] Underfull \hbox (badness 1072) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1972] Underfull \hbox (badness 7238) in paragraph at lines 4129--4134 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4129--4134 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1973] Underfull \hbox (badness 4660) in paragraph at lines 4261--4264 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [1974] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 1565) in paragraph at lines 4470--4474 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1977] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1978] Underfull \hbox (badness 1910) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4587--4594 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4594--4601 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1979] [1980] [1981] [1982] Underfull \hbox (badness 5939) in paragraph at lines 4840--4842 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [1983] [1984] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1985] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1994] [1995] [1996] [1997] [1998] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [1999] [2000] [2001] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2002] [2003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2004] [2005] [2006] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2007] Underfull \hbox (badness 10000) in paragraph at lines 6546--6548 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2008] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2011] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2012] Underfull \hbox (badness 5175) in paragraph at lines 6848--6851 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2013] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2014] [2015] [2016] Underfull \hbox (badness 5091) in paragraph at lines 7146--7148 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages Underfull \hbox (badness 1270) in paragraph at lines 7191--7201 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If [2017] Underfull \hbox (badness 4441) in paragraph at lines 7234--7237 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7234--7237 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2018] Underfull \hbox (badness 2376) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2019] Underfull \hbox (badness 1314) in paragraph at lines 7401--7408 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2020] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7504--7504 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2021] Underfull \hbox (badness 5133) in paragraph at lines 7540--7544 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7554--7557 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2022] [2023] Underfull \hbox (badness 4132) in paragraph at lines 7725--7727 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2024] [2025] [2026] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2027] [2028] [2029] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) Underfull \hbox (badness 10000) in paragraph at lines 8075--8077 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2030] [2031] Underfull \hbox (badness 10000) in paragraph at lines 8180--8182 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2032] [2033] [2034] [2035] Underfull \hbox (badness 1859) in paragraph at lines 8413--8416 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8432--8442 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2036] Underfull \hbox (badness 1655) in paragraph at lines 8507--8510 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8518--8518 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8534--8534 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2037] [2038] Underfull \hbox (badness 1917) in paragraph at lines 8621--8623 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2039] [2040] [2041] [2042] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8893--8893 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2043] Underfull \hbox (badness 10000) in paragraph at lines 8923--8925 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 8937--8939 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2044] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8992--8992 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2045] [2046] Underfull \hbox (badness 10000) in paragraph at lines 9121--9126 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9128--9131 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2047] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9244--9244 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9245--9245 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2048] [2049] [2050] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418 [] \T1/pcr/m/n/9 "S original, "),[] [2051] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] Underfull \hbox (badness 5203) in paragraph at lines 10124--10127 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the []\T1/pcr/m/n/10 $ []\T1/ptm/m/ n/10 ex-trac-tor are de-ter-mined by the generic func-tion [2061] [2062] [2063] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2064] [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2066] [2067] [2068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2069] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10802--10802 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10805--10805 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10810--10810 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2070] Underfull \hbox (badness 2027) in paragraph at lines 10882--10885 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2071] [2072] [2073] [2074] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11161--11161 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11162--11162 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2075] [2076] [2077] [2078] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2079] [2080] [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11681--11681 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11686--11686 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11819--11819 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2085] [2086] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11955--11955 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2087] [2088] Underfull \hbox (badness 1917) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12087--12090 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12110--12110 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2089] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12202--12202 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12203--12203 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12205--12205 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12206--12206 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] [2090] Underfull \hbox (badness 6725) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or Overfull \hbox (9.78043pt too wide) in paragraph at lines 12274--12274 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2091] Underfull \hbox (badness 1377) in paragraph at lines 12330--12333 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style [2092] Underfull \hbox (badness 3646) in paragraph at lines 12365--12367 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / Overfull \hbox (30.78088pt too wide) in paragraph at lines 12403--12403 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2093] [2094] [2095] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12633--12641 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2096] [2097] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12794--12794 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2098] Underfull \hbox (badness 1009) in paragraph at lines 12812--12824 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 2600) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2099] Underfull \hbox (badness 1043) in paragraph at lines 12895--12900 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2100] [2101] [2102] [2103] Underfull \hbox (badness 1888) in paragraph at lines 13188--13191 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13205--13208 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2104] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2105] Underfull \hbox (badness 2158) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13354--13354 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2106] [2107] [2108] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2109] Underfull \hbox (badness 3333) in paragraph at lines 13619--13621 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2110] [2111] [2112] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13786--13786 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13819--13822 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13830--13839 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2113] Underfull \hbox (badness 1442) in paragraph at lines 13846--13850 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 13892--13892 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2114] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13919--13919 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13926--13926 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13928--13928 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2115] [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 14094--14096 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2118] Underfull \hbox (badness 10000) in paragraph at lines 14204--14207 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14204--14207 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2119] Underfull \hbox (badness 6300) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2120] [2121] Underfull \hbox (badness 2020) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2122] Underfull \hbox (badness 1622) in paragraph at lines 14426--14433 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 5022) in paragraph at lines 14567--14571 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2124] [2125] [2126] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14740--14740 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2127] [2128] [2129] [2130] [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15181--15181 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15187--15187 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 15208--15210 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15223--15227 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [2133] Underfull \hbox (badness 1694) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15249--15251 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15279--15284 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15279--15284 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15300--15305 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with [2134] Underfull \hbox (badness 10000) in paragraph at lines 15308--15311 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (15.18042pt too wide) in paragraph at lines 15362--15362 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2135] [2136] [2137] Underfull \hbox (badness 2293) in paragraph at lines 15569--15572 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2138] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15585--15585 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2139] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15652--15652 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15674--15674 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2140] [2141] Underfull \hbox (badness 1297) in paragraph at lines 15805--15807 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2142] Underfull \hbox (badness 4036) in paragraph at lines 15852--15854 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2143] [2144] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15972--15972 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2145] Underfull \hbox (badness 1715) in paragraph at lines 16024--16027 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16069--16071 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex Chapter 15. [2151] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2152] [2153] [2154] [2155] [2156] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2157] [2158] [2159] [2160]) (./MASS-pkg.tex Chapter 16. [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2418--2418 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2195] [2196] [2197] [2198] Underfull \hbox (badness 6559) in paragraph at lines 2701--2704 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2199] [2200] [2201] Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2202] [2203] Underfull \hbox (badness 4686) in paragraph at lines 3039--3041 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2204] [2205] [2206] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3234--3234 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2207] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3364--3364 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] Underfull \hbox (badness 1845) in paragraph at lines 4164--4166 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2220] [2221] [2222] [2223] [2224] [2225] [2226] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2227] [2228] [2229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5930--5930 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2244] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5991--5991 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2245] [2246] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} [2247] [2248] [2249] [2250] [2251] [2252] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6571--6571 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2253] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6659--6659 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2254] [2255] [2256] [2257] [2258] [2259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7098--7098 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7115--7115 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2260] Underfull \hbox (badness 3138) in paragraph at lines 7193--7199 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2261] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7263--7263 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2262] [2263] Underfull \hbox (badness 1389) in paragraph at lines 7372--7375 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2264] [2265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7502--7502 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2266] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2267] [2268] [2269] [2270] [2271] [2272] Underfull \hbox (badness 4686) in paragraph at lines 8005--8007 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2273] [2274] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8124--8124 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8148--8152 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9529--9529 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2295] Underfull \hbox (badness 2035) in paragraph at lines 9641--9643 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9656--9659 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2296] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9738--9738 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9743--9743 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308] [2309]) (./Matrix-pkg.tex [2310] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2311] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2312] Underfull \hbox (badness 2229) in paragraph at lines 153--156 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 153--156 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new [2313] Underfull \hbox (badness 10000) in paragraph at lines 256--259 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2314] [2315] Overfull \hbox (15.18042pt too wide) in paragraph at lines 445--445 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2316] Underfull \hbox (badness 5119) in paragraph at lines 488--492 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 492--497 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 522--522 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 524--524 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 533--533 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2318] Overfull \hbox (52.98038pt too wide) in paragraph at lines 647--647 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 648--648 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 649--649 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2319] Overfull \hbox (31.3804pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 663--663 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2320] Underfull \hbox (badness 1874) in paragraph at lines 737--740 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 https : / / netlib . org / [2321] [2322] Underfull \hbox (badness 1107) in paragraph at lines 860--865 \T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/ 10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in [] \T1/pcr/m/n/10 selectMethod(cbind2, Underfull \hbox (badness 10000) in paragraph at lines 903--908 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: [2323] Overfull \hbox (72.78088pt too wide) in paragraph at lines 967--967 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2324] Underfull \hbox (badness 3612) in paragraph at lines 1054--1057 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10 re-turns the per-mu-ta-tion [2325] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol.1}) has been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} [2326] [2327] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1301--1301 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2328] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1396--1396 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2329] Underfull \hbox (badness 2277) in paragraph at lines 1424--1427 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2330] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1498--1498 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1520--1520 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529 []\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[] [2331] Underfull \hbox (badness 10000) in paragraph at lines 1565--1572 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 4673) in paragraph at lines 1565--1572 []\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1600--1604 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2332] Underfull \hbox (badness 1221) in paragraph at lines 1616--1622 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][][]\T1/pcr/m/n/10 matrix[][][][]\T1/ptm/m/n/10 . Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10 and pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums.1 }) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.1658 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.1681 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.1694 \aliasA{rowSums}{colSums}{rowSums} [2333 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans, diagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums,d iagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' ] Underfull \hbox (badness 2922) in paragraph at lines 1750--1754 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1750--1754 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 1761--1764 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2334] [2335] Underfull \hbox (badness 3547) in paragraph at lines 1915--1918 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2336] [2337] [2338] [2339] [2340] [2341] Underfull \hbox (badness 7379) in paragraph at lines 2445--2447 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2342] [2343] [2344] Underfull \hbox (badness 10000) in paragraph at lines 2696--2699 []\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 , and typ-i-cally co-er-cion Underfull \hbox (badness 4846) in paragraph at lines 2721--2725 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2726--2730 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 dgCMatrix[][][] []\T1/ptm/m/n/10 or the su-per-classes [][][]\T1/pcr/m/n/10 dsparseMatrix[][][] []\T1/ptm/m/n/10 a nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ; [2345] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2780--2780 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2789--2791 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2793--2798 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 .symDiagonal []\T1/ptm/m/n/10 ([]\T1/pcr/ m/n/10 .trDiagonal[]\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2793--2798 [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 (or [][][]\T1/pcr/m /n/10 triangularMatrix[][][][]\T1/ptm/m/n/10 ) will have slot []\T1/pcr/m/n/10 uplo [2346] Underfull \hbox (badness 1097) in paragraph at lines 2816--2819 []\T1/pcr/m/n/10 Diagonal() []\T1/ptm/m/n/10 re-turns an ob-ject of class [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 or [][][]\T1/pcr/m/n/10 ldiMat rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2829--2834 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of [2347] Underfull \hbox (badness 3646) in paragraph at lines 2925--2928 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 2960--2964 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 2969--2975 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2348 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,di agonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.2975 ] Underfull \hbox (badness 10000) in paragraph at lines 2976--2980 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 2986--2990 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 3166--3168 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2351] [2352] Overfull \hbox (69.18036pt too wide) in paragraph at lines 3312--3312 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2353] Underfull \hbox (badness 2469) in paragraph at lines 3422--3425 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via Underfull \hbox (badness 10000) in paragraph at lines 3445--3450 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 3445--3450 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 3451--3460 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 3451--3460 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", [2354] [2355] Underfull \hbox (badness 10000) in paragraph at lines 3599--3603 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 3599--3603 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , [2356] Underfull \hbox (badness 1571) in paragraph at lines 3649--3652 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 3813--3818 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3813--3818 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 3825--3828 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2359] Underfull \hbox (badness 10000) in paragraph at lines 3896--3898 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 3938--3941 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3983--3983 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2362] Underfull \hbox (badness 3635) in paragraph at lines 4179--4183 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 4188--4191 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; [2363] Underfull \hbox (badness 10000) in paragraph at lines 4193--4197 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2364] [2365 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,dt rMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.4347 \item[\code{diag}:] Object of class \code{"character"}. Must be] Underfull \hbox (badness 2065) in paragraph at lines 4378--4382 []\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie ntely use a ``for-ward-solve'' or [2366] [2367] [2368] [2369] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe ll-Boeing/counterx/counterx.html[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4642--4642 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4649--4649 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4659--4659 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2370] [2371] [2372] [2373] Underfull \hbox (badness 10000) in paragraph at lines 4937--4942 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2374] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 5020--5020 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5024--5024 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2375] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5031--5031 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2376] [2377] Underfull \hbox (badness 4120) in paragraph at lines 5170--5173 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5214--5214 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5230--5230 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2379] Underfull \hbox (badness 1817) in paragraph at lines 5326--5335 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing []\T1/pcr/m/n/10 drop=FALSE[]\T1/ptm/m/n/10 ) stays wit hin the Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 7081) in paragraph at lines 5370--5373 []\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10 : This en-ables typ-i-cal Underfull \hbox (badness 4556) in paragraph at lines 5376--5383 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T he list must have two [2380] Underfull \hbox (badness 3302) in paragraph at lines 5401--5404 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : re-turn the kro-necker [2381] [2382] [2383] [2384] Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8 * tol, checkDN = TRUE, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN = TRUE, ...)[] [2385] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2386] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5962--5962 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2387] [2388] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6043--6043 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6050--6050 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2389] [2390] Underfull \hbox (badness 1062) in paragraph at lines 6204--6207 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 6233--6236 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2391] Underfull \hbox (badness 2635) in paragraph at lines 6402--6407 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6402--6407 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class [2392] Underfull \hbox (badness 10000) in paragraph at lines 6410--6413 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6566--6576 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6566--6576 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2393] Underfull \hbox (badness 3179) in paragraph at lines 6648--6651 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2394] Underfull \hbox (badness 10000) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2395] Underfull \hbox (badness 10000) in paragraph at lines 6830--6833 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2396] Underfull \hbox (badness 1430) in paragraph at lines 6904--6910 \T1/ptm/m/n/10 should be sig-nalled when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar. When []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar, []\T1/pcr/ m/n/10 lu(x, [2397] Underfull \hbox (badness 1675) in paragraph at lines 6929--6932 []\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met h-ods for dif-fer-ent types of ma-tri-ces. Use Overfull \hbox (9.78043pt too wide) in paragraph at lines 7001--7001 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2398] [2399] Underfull \hbox (badness 10000) in paragraph at lines 7141--7144 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , [2400] Underfull \hbox (badness 1490) in paragraph at lines 7163--7165 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2401] [2402] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.7358 \aliasA{det}{Matrix-class}{det} [2403 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,Ma trix,denseMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7439 \item[dim] \code{signature(x = "Matrix")}: extract matrix dimensions] Underfull \hbox (badness 1337) in paragraph at lines 7446--7449 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 7459--7462 Underfull \hbox (badness 10000) in paragraph at lines 7469--7471 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2404] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.7629 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.7723 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7816--7822 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2405] Underfull \hbox (badness 10000) in paragraph at lines 7889--7892 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 7897--7901 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 7907--7908 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2406] [2407] [2408] Underfull \hbox (badness 1062) in paragraph at lines 8087--8090 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 8121--8124 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2409] Underfull \hbox (badness 3312) in paragraph at lines 8177--8179 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2410] [2411] Overfull \hbox (85.38034pt too wide) in paragraph at lines 8279--8279 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8319--8319 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2412] Underfull \hbox (badness 2635) in paragraph at lines 8386--8391 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8386--8391 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8394--8397 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2413] Underfull \hbox (badness 2521) in paragraph at lines 8464--8470 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2414] Underfull \hbox (badness 1867) in paragraph at lines 8586--8588 []\T1/ptm/m/n/10 fast sim- [2415] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} [2416] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8720--8720 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8721--8721 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8867--8877 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2417] Underfull \hbox (badness 3179) in paragraph at lines 8938--8941 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2418] Underfull \hbox (badness 10000) in paragraph at lines 9036--9039 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2419] Underfull \hbox (badness 10000) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2420] [2421] Underfull \hbox (badness 10000) in paragraph at lines 9213--9214 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9214--9215 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9215--9216 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9216--9217 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9217--9218 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9218--9219 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9219--9220 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9220--9221 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9221--9222 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9222--9223 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9223--9224 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9224--9225 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9225--9226 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9226--9227 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9227--9228 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9228--9229 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9229--9230 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = [2422] Underfull \hbox (badness 10000) in paragraph at lines 9230--9231 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9231--9232 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9232--9233 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9233--9234 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9234--9235 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9235--9236 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9236--9237 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9237--9238 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9238--9239 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9239--9240 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9240--9241 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9241--9242 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9242--9243 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = [2423] Underfull \hbox (badness 10000) in paragraph at lines 9332--9334 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 5008) in paragraph at lines 9334--9337 []\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 : This is en-ables typ-i-cal [2424] Underfull \hbox (badness 4954) in paragraph at lines 9340--9347 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional Underfull \hbox (badness 1558) in paragraph at lines 9350--9354 []\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10 : Since per-mu-ta- Underfull \hbox (badness 3229) in paragraph at lines 9354--9358 \T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c es. See [2425] Overfull \hbox (36.78088pt too wide) in paragraph at lines 9433--9433 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9436--9436 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9438--9438 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9442--9442 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9443--9443 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] [2426] Underfull \hbox (badness 3989) in paragraph at lines 9468--9478 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9468--9478 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2427] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.9569 \aliasA{qr}{qr-methods}{qr} [2428] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9641--9641 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9652--9652 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] [2429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9671--9671 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9679--9679 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2430] Underfull \hbox (badness 2005) in paragraph at lines 9736--9742 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 9753--9756 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2431] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9852--9852 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9868--9868 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9874--9874 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9875--9875 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2432] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9893 ... the Reciprocal Condition Number}{rcond} [2433] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10011--10011 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2434] [2435] [2436] Underfull \hbox (badness 2150) in paragraph at lines 10202--10210 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2437] [2438] Underfull \hbox (badness 1558) in paragraph at lines 10342--10345 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n /10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional [2439] Overfull \hbox (52.98038pt too wide) in paragraph at lines 10404--10404 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10408--10408 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.10470 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (48.78088pt too wide) in paragraph at lines 10572--10572 []\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always preferred to [2441] Overfull \hbox (90.78088pt too wide) in paragraph at lines 10584--10584 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1616) in paragraph at lines 10619--10631 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 10636--10639 []\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p cr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10645--10652 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( [2442] Underfull \hbox (badness 10000) in paragraph at lines 10658--10668 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( Underfull \hbox (badness 3657) in paragraph at lines 10658--10668 \T1/pcr/m/n/10 sparse=FALSE, tol = .Machine$double.eps ) []\T1/ptm/m/n/10 : Che cks if []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10685--10689 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10692--10694 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10715--10716 []\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b, Underfull \hbox (badness 10000) in paragraph at lines 10721--10723 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10725--10726 []\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10733--10736 [][][]\T1/pcr/m/n/10 solve[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lu[][][ ][]\T1/ptm/m/n/10 , and class doc-u-men-ta-tions [][][]\T1/pcr/m/n/10 CHMfactor [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 , and [2443] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10751--10751 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10755--10755 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] Underfull \hbox (badness 10000) in paragraph at lines 10776--10779 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 10793--10793 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10795--10795 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] [2444] Underfull \hbox (badness 1648) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10812--10815 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10812--10815 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10823--10827 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10823--10827 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 1668) in paragraph at lines 10838--10843 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10918--10918 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10919--10919 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10920--10920 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2446] [2447] [2448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11107--11107 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Underfull \hbox (badness 1668) in paragraph at lines 11149--11154 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2449] Underfull \hbox (badness 10000) in paragraph at lines 11234--11237 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and [2450] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11246--11246 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11250--11250 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11251--11251 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11256--11256 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11259--11259 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11282--11282 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Underfull \vbox (badness 10000) has occurred while \output is active [2451] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11309--11309 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 11311--11311 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11313--11313 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2452] Underfull \hbox (badness 6842) in paragraph at lines 11411--11414 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 11446--11450 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2453] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2454] Underfull \hbox (badness 10000) in paragraph at lines 11616--11618 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\ T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11644--11644 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2455] Underfull \hbox (badness 5036) in paragraph at lines 11672--11674 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2456] Underfull \hbox (badness 2970) in paragraph at lines 11783--11789 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11783--11789 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11834--11837 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2457] Underfull \hbox (badness 10000) in paragraph at lines 11874--11879 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11889--11891 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2458] Underfull \vbox (badness 10000) has occurred while \output is active [2459] Underfull \hbox (badness 2310) in paragraph at lines 12014--12020 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2460] [2461] Underfull \hbox (badness 6188) in paragraph at lines 12105--12107 []\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm /m/n/10 : and many Underfull \hbox (badness 2591) in paragraph at lines 12131--12136 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2462] Underfull \hbox (badness 2057) in paragraph at lines 12207--12209 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2463] Underfull \hbox (badness 6641) in paragraph at lines 12294--12297 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2464] Underfull \hbox (badness 5133) in paragraph at lines 12338--12342 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 12338--12342 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2465] Underfull \hbox (badness 7649) in paragraph at lines 12445--12447 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2466] [2467] Underfull \hbox (badness 10000) in paragraph at lines 12563--12565 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2468] Underfull \hbox (badness 1668) in paragraph at lines 12692--12695 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2469] Underfull \hbox (badness 7362) in paragraph at lines 12743--12745 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2470] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12781--12781 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12782--12782 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2471] [2472] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12936--12936 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/ x))$modulus))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12941--12941 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2473] Underfull \hbox (badness 6910) in paragraph at lines 13147--13149 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2474] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. [2475] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2476] [2477]) (./boot-pkg.tex [2478] Chapter 18. [2479] [2480] [2481] [2482] [2483] [2484] [2485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2486] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2487] [2488] [2489] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2491] [2492] [2493] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2494] [2495] [2496] [2497] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2498] [2499] [2500] [2501] [2502] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2503] [2504] [2505] Underfull \vbox (badness 10000) has occurred while \output is active [2506] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2507] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2508] [2509] [2510] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2511] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2512] [2513] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2514] [2515] [2516] [2517] [2518] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2519] [2520] [2521] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2522] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2523] [2524] [2525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2526] [2527] [2528] [2529] [2530] [2531] [2532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2533] [2534] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2535] [2536] [2537] [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2550] [2551] [2552] [2553] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2563] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2564] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2565] [2566] [2567] [2568] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2569] [2570] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2571] [2572] [2573] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2574] [2575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2576] [2577] [2578] [2579] [2580] [2581] [2582] [2583]) (./class-pkg.tex [2584] Chapter 19. [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600]) (./cluster-pkg.tex Chapter 20. [2601] [2602] [2603] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2604] [2605] [2606] [2607] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2608] [2609] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2610] Underfull \hbox (badness 3078) in paragraph at lines 691--694 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2611] [2612] Underfull \hbox (badness 2941) in paragraph at lines 791--794 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 881--883 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2614] Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2615] Underfull \hbox (badness 4872) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1208--1212 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2619] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2620] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1477--1480 Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1528--1528 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2623] Underfull \hbox (badness 5741) in paragraph at lines 1568--1571 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2624] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2625] Underfull \hbox (badness 1552) in paragraph at lines 1686--1688 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1699--1703 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1699--1703 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2626] Underfull \hbox (badness 1540) in paragraph at lines 1775--1783 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2628] [2629] [2630] [2631] [2632] Underfull \hbox (badness 10000) in paragraph at lines 2207--2210 Underfull \hbox (badness 3179) in paragraph at lines 2221--2227 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2633] [2634] Underfull \hbox (badness 10000) in paragraph at lines 2379--2382 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2635] Underfull \hbox (badness 1292) in paragraph at lines 2447--2450 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2636] Underfull \hbox (badness 6675) in paragraph at lines 2456--2458 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2479--2482 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2637] [2638] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2639] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2640] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2641] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2642] [2643] [2644] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2645] [2646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2647] [2648] [2649] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2650] Underfull \hbox (badness 10000) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2651] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2652] [2653] [2654] Underfull \hbox (badness 10000) in paragraph at lines 3671--3674 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3671--3674 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2655] Underfull \hbox (badness 10000) in paragraph at lines 3734--3739 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2656] Underfull \hbox (badness 1748) in paragraph at lines 3796--3801 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3808--3811 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2657] [2658] [2659] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2661] Underfull \hbox (badness 2035) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2662] [2663] [2664] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2665] [2666] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4435--4435 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4437--4437 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4440--4440 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4442--4442 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2667] [2668] [2669] [2670] [2671] [2672] [2673] Underfull \hbox (badness 10000) in paragraph at lines 4823--4829 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4839--4841 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2674] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2675]) (./codetools-pkg.tex [2676] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2677] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2678] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2679] [2680] [2681]) (./foreign-pkg.tex [2682] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2683] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2684] [2685] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2686] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2687] [2688] [2689] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2691] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 568--574 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2693] Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2694] [2695] Underfull \hbox (badness 10000) in paragraph at lines 812--813 Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2696] Underfull \hbox (badness 10000) in paragraph at lines 869--873 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 869--873 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2697] Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2698] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2699] [2700] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2703] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2704]) (./lattice-pkg.tex Chapter 23. [2705] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2706] [2707] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2708] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2709] [2710] [2711] [2712] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2713] [2714] [2715] [2716] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2717] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2718] [2719] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2720] [2721] [2722] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2723] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to [2726] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2727] [2728] [2729] [2730] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2731] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2732] [2733] [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2740] [2741] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2742] Underfull \hbox (badness 6758) in paragraph at lines 2919--2923 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2919--2923 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2925--2927 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 2977--2983 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from [2743] Underfull \hbox (badness 2486) in paragraph at lines 3001--3005 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2744] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3104--3104 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3106--3106 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] [2745] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3117--3117 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2746] Underfull \hbox (badness 2913) in paragraph at lines 3187--3194 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3187--3194 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2747] [2748] [2749] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3475 \aliasA{parallel}{B\_08\_splom}{parallel} [2750] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2751] [2752] [2753] [2754] [2755] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2756] [2757] Underfull \hbox (badness 2277) in paragraph at lines 3970--3974 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 3970--3974 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2758] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in [2759] Underfull \hbox (badness 3219) in paragraph at lines 4136--4138 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4153--4157 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2760] Underfull \hbox (badness 5161) in paragraph at lines 4218--4222 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4218--4222 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2761] [2762] Underfull \hbox (badness 1067) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4361--4364 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4364--4366 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2763] [2764] [2765] [2766] [2767] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2768] [2769] Underfull \vbox (badness 1092) has occurred while \output is active [2770] Underfull \hbox (badness 10000) in paragraph at lines 4955--4958 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2771] [2772] Underfull \hbox (badness 1442) in paragraph at lines 5087--5090 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2773] [2774] [2775] [2776] [2777] Underfull \hbox (badness 3646) in paragraph at lines 5426--5429 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5456--5456 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5457--5457 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2778] Underfull \hbox (badness 10000) in paragraph at lines 5545--5548 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5545--5548 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2779] Underfull \hbox (badness 1635) in paragraph at lines 5571--5576 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2780] [2781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5736--5736 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5737--5737 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5740--5740 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5743--5743 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5745--5745 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5751--5751 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5752--5752 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5753--5753 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] [2782] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5754--5754 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5755--5755 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5771--5773 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5782--5784 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2783] Underfull \hbox (badness 2538) in paragraph at lines 5907--5911 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2784] [2785] Underfull \hbox (badness 10000) in paragraph at lines 6071--6075 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2786] Underfull \vbox (badness 10000) has occurred while \output is active [2787] [2788] Underfull \hbox (badness 4242) in paragraph at lines 6218--6223 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2789] [2790] Underfull \hbox (badness 3601) in paragraph at lines 6334--6339 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6334--6339 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2791] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6421--6421 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2792] [2793] Underfull \hbox (badness 1888) in paragraph at lines 6553--6560 []\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1 0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and [2794] Underfull \hbox (badness 10000) in paragraph at lines 6610--6613 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6610--6613 []\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn a valid color. The [2795] [2796] [2797] [2798] [2799] Underfull \hbox (badness 1320) in paragraph at lines 7016--7023 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7016--7023 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2800] [2801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7086--7086 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] Underfull \hbox (badness 10000) in paragraph at lines 7116--7120 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7116--7120 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2802] [2803] Underfull \hbox (badness 10000) in paragraph at lines 7221--7224 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by [2804] [2805] Underfull \hbox (badness 2012) in paragraph at lines 7387--7390 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7433--7433 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2807] [2808] Underfull \hbox (badness 2644) in paragraph at lines 7574--7578 []\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o n to Underfull \hbox (badness 2772) in paragraph at lines 7587--7590 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2809] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7657--7657 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2810] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7728--7728 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7733--7733 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2811] [2812] [2813] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7918--7918 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] Underfull \hbox (badness 1436) in paragraph at lines 7973--7979 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2822] [2823] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8706--8706 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8707--8707 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2824] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 8738--8741 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2825] Underfull \hbox (badness 1515) in paragraph at lines 8814--8818 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2826] [2827] Underfull \hbox (badness 6316) in paragraph at lines 8920--8925 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2828] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9030--9030 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2829] [2830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9169--9169 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2831] Underfull \hbox (badness 1028) in paragraph at lines 9228--9232 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2832] [2833] [2834] [2835] [2836] [2837] [2838] Underfull \hbox (badness 7238) in paragraph at lines 9692--9696 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9692--9696 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2839] [2840] [2841] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma} [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 10085--10090 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10158--10158 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2845] [2846]) (./mgcv-pkg.tex Chapter 24. [2847] [2848] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2849] Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 184--188 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 209--214 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2850] [2851] [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2854] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2855] [2856] [2857] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2858] [2859] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2860] [2861] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2862] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2873] [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2875] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2876] [2877] [2878] [2879] [2880] [2881] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1937--1937 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2882] [2883] [2884] [2885] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2162--2162 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2886] [2887] [2888] [2889] [2890] [2891] [2892] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2579--2582 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2592--2596 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2618--2624 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2893] [2894] [2895] Underfull \hbox (badness 1043) in paragraph at lines 2787--2793 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2896] [2897] Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2898] Underfull \vbox (badness 10000) has occurred while \output is active [2899] Underfull \vbox (badness 10000) has occurred while \output is active [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] [2902] [2903] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3240--3240 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, maxit = 200, [2904] [2905] [2906] [2907] [2908] [2909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3581--3581 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3584--3584 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 5189) in paragraph at lines 4063--4067 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2918] [2919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4180--4180 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2920] [2921] [2922] Underfull \hbox (badness 1184) in paragraph at lines 4350--4354 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2923] [2924] [2925] [2926] [2927] [2928] [2929] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4796--4796 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2930] [2931] [2932] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2933] [2934] Underfull \hbox (badness 1142) in paragraph at lines 5073--5077 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2935] Underfull \hbox (badness 10000) in paragraph at lines 5145--5154 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2936] [2937] Underfull \hbox (badness 5970) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2938] Underfull \vbox (badness 10000) has occurred while \output is active [2939] [2940] [2941] [2942] Underfull \hbox (badness 1577) in paragraph at lines 5614--5617 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5621--5622 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 6708) in paragraph at lines 6010--6011 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [2950] [2951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 6059--6059 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6084--6084 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6113--6113 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2953] [2954] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6235--6235 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2955] [2956] [2957] [2958] [2959] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6572--6572 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2960] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6574--6574 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6595--6599 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2961] [2962] [2963] Underfull \vbox (badness 10000) has occurred while \output is active [2964] [2965] [2966] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6914--6914 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Underfull \vbox (badness 10000) has occurred while \output is active [2972] [2973] [2974] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7346--7346 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7373--7373 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2975] [2976] [2977] [2978] [2979] [2980] [2981] [2982] [2983] Underfull \hbox (badness 1242) in paragraph at lines 7916--7917 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8003--8003 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2986] [2987] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8085--8085 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Underfull \vbox (badness 10000) has occurred while \output is active [3006] [3007] Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3008] Underfull \hbox (badness 10000) in paragraph at lines 9366--9369 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9366--9369 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3009] [3010] [3011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9587--9587 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9590--9590 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3012] [3013] [3014] Underfull \hbox (badness 1629) in paragraph at lines 9748--9753 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3015] [3016] [3017] [3018] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9960--9960 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 9997--10001 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3019] [3020] [3021] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10130--10130 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3022] [3023] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10291--10291 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3024] Underfull \vbox (badness 10000) has occurred while \output is active [3025] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10411--10411 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [3026] Underfull \hbox (badness 1205) in paragraph at lines 10449--10451 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10449--10451 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10455--10460 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3027] Underfull \hbox (badness 1205) in paragraph at lines 10539--10541 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10539--10541 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3028] Underfull \hbox (badness 10000) in paragraph at lines 10608--10611 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10608--10611 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3029] [3030] [3031] Underfull \hbox (badness 1253) in paragraph at lines 10738--10740 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 1946) in paragraph at lines 10991--10998 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 10999--11002 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10999--11002 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11065--11065 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11075--11075 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3038] Underfull \hbox (badness 10000) in paragraph at lines 11106--11109 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3039] [3040] [3041] [3042] [3043] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11408--11408 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3044] [3045] [3046] [3047] [3048] [3049] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11782--11782 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11796--11796 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3050] [3051] Underfull \hbox (badness 3861) in paragraph at lines 11898--11901 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 11907--11907 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3052] Underfull \hbox (badness 10000) in paragraph at lines 11924--11928 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 11964--11968 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12108--12108 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12119--12124 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3056] Underfull \hbox (badness 1803) in paragraph at lines 12196--12200 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12208--12220 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3057] Underfull \hbox (badness 2401) in paragraph at lines 12225--12229 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12225--12229 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3058] [3059] [3060] Underfull \hbox (badness 6876) in paragraph at lines 12420--12426 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3061] Underfull \hbox (badness 10000) in paragraph at lines 12461--12462 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 12579--12580 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3064] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12633--12633 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12645--12645 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3065] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12657--12657 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12662--12662 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12668--12668 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12669--12669 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3066] Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3067] [3068] Underfull \hbox (badness 10000) in paragraph at lines 12868--12869 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3069] [3070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12949--12949 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12950--12950 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3071] [3072] Underfull \hbox (badness 10000) in paragraph at lines 13103--13104 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3073] [3074] [3075] [3076] [3077] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13353--13353 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3078] Underfull \hbox (badness 10000) in paragraph at lines 13414--13416 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3079] [3080] Underfull \hbox (badness 10000) in paragraph at lines 13573--13576 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13573--13576 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13573--13576 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3081] [3082] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13659--13659 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3083] Underfull \hbox (badness 10000) in paragraph at lines 13704--13710 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13704--13710 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3084] [3085] [3086] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13918--13918 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3087] Underfull \vbox (badness 10000) has occurred while \output is active [3088] Underfull \hbox (badness 10000) in paragraph at lines 14021--14029 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14047--14048 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3089] [3090] [3091] Underfull \hbox (badness 7613) in paragraph at lines 14192--14195 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3092] Underfull \hbox (badness 1546) in paragraph at lines 14213--14214 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14259--14259 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3093] [3094] [3095] Underfull \hbox (badness 3396) in paragraph at lines 14405--14408 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14450--14452 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 10000) in paragraph at lines 14741--14743 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][][]\T1/ptm/m/n/10 ,[ ][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 p.spline[][ ][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 2158) in paragraph at lines 15061--15061 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3107] [3108] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3109] [3110] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3111] [3112] Underfull \hbox (badness 4846) in paragraph at lines 15405--15408 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3133] Underfull \hbox (badness 1715) in paragraph at lines 16645--16646 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3134] [3135] [3136] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 16859--16860 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16859--16860 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3138] Underfull \vbox (badness 10000) has occurred while \output is active [3139] [3140] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3141] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3142] [3143] [3144]) (./nlme-pkg.tex Chapter 25. [3145] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3146] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3147] [3148] [3149] [3150] [3151] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3152] [3153] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3162] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3170] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3171] [3172] [3173] [3174] [3175] Underfull \hbox (badness 2042) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3176] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3177] Underfull \hbox (badness 1132) in paragraph at lines 2147--2149 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3178] [3179] Underfull \hbox (badness 4168) in paragraph at lines 2258--2264 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 2849--2853 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3189] [3190] [3191] [3192] [3193] [3194 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3195] [3196] [3197] [3198] [3199] [3200] Underfull \hbox (badness 6493) in paragraph at lines 3585--3593 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3225] [3226] [3227] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 5597--5600 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3232] [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 2799) in paragraph at lines 6103--6109 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3241] Underfull \hbox (badness 7133) in paragraph at lines 6164--6168 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3242] Underfull \hbox (badness 2057) in paragraph at lines 6253--6264 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3243] Underfull \hbox (badness 10000) in paragraph at lines 6317--6319 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3244] [3245] [3246] [3247] Underfull \hbox (badness 7133) in paragraph at lines 6566--6570 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3248] Underfull \hbox (badness 10000) in paragraph at lines 6665--6671 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3249] Underfull \hbox (badness 10000) in paragraph at lines 6730--6732 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3250] [3251] [3252] [3253] Underfull \hbox (badness 10000) in paragraph at lines 7002--7009 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7025--7025 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7047--7049 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3255] [3256] [3257] Underfull \hbox (badness 10000) in paragraph at lines 7262--7267 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3258] [3259] [3260] Underfull \hbox (badness 1997) in paragraph at lines 7414--7422 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7414--7422 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7437--7440 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3261] [3262] [3263] Underfull \hbox (badness 3354) in paragraph at lines 7653--7655 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8213--8213 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] [3272] Underfull \hbox (badness 1642) in paragraph at lines 8222--8244 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3273] [3274] [3275] [3276] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8535--8537 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3277] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8579--8579 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] Underfull \hbox (badness 10000) in paragraph at lines 9336--9343 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3290] [3291] [3292] [3293] [3294] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3295] Underfull \hbox (badness 10000) in paragraph at lines 9718--9721 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9762--9765 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9762--9765 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304] [3305] [3306] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3307] Underfull \hbox (badness 1596) in paragraph at lines 10471--10497 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3308] [3309] [3310] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3311] [3312] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10809--10814 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] [3313] Underfull \hbox (badness 6961) in paragraph at lines 10831--10835 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= Underfull \hbox (badness 10000) in paragraph at lines 10850--10852 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3314] [3315] [3316] [3317] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3318] [3319] [3320] [3321] [3322] [3323] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11532--11532 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3324] [3325] [3326] [3327] [3328] [3329] Underfull \hbox (badness 6268) in paragraph at lines 11919--11929 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3330] [3331] [3332] [3333] Underfull \hbox (badness 10000) in paragraph at lines 12180--12186 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3334] [3335] [3336] [3337] [3338] Underfull \hbox (badness 6876) in paragraph at lines 12502--12504 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3339] [3340] Underfull \hbox (badness 2452) in paragraph at lines 12658--12665 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3341] Underfull \hbox (badness 10000) in paragraph at lines 12723--12729 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3351] [3352] [3353] [3354] [3355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13704--13707 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3357] Underfull \hbox (badness 1838) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3358] Underfull \hbox (badness 10000) in paragraph at lines 13811--13814 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13811--13814 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3359] Underfull \hbox (badness 10000) in paragraph at lines 13919--13922 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3360] [3361] Underfull \hbox (badness 10000) in paragraph at lines 14013--14015 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3362] [3363] [3364] [3365] [3366] [3367] [3368] [3369] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] Underfull \hbox (badness 2126) in paragraph at lines 15830--15834 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3389] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3390] Underfull \hbox (badness 1009) in paragraph at lines 15888--15897 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3391] [3392] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3393] [3394] [3395] [3396] [3397] Underfull \hbox (badness 10000) in paragraph at lines 16370--16376 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3398] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3399] [3400] [3401] [3402] [3403] [3404] [3405] Underfull \hbox (badness 1728) in paragraph at lines 16889--16892 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3406] [3407] [3408] [3409] [3410] Underfull \hbox (badness 1803) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3411] Underfull \hbox (badness 10000) in paragraph at lines 17294--17295 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17295--17296 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3412] [3413] [3414] [3415] Underfull \hbox (badness 10000) in paragraph at lines 17545--17553 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3416] [3417] [3418] [3419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3420] [3421] [3422] [3423] [3424] [3425] Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3426] Underfull \hbox (badness 3579) in paragraph at lines 18293--18298 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3427] Underfull \hbox (badness 3579) in paragraph at lines 18357--18362 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3428] Underfull \hbox (badness 3579) in paragraph at lines 18420--18425 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3429] Underfull \hbox (badness 1577) in paragraph at lines 18481--18483 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18483--18488 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3430] Underfull \hbox (badness 3579) in paragraph at lines 18546--18551 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3431] Underfull \hbox (badness 3579) in paragraph at lines 18618--18623 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3432] [3433] Underfull \hbox (badness 1009) in paragraph at lines 18764--18773 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3434] [3435] Underfull \hbox (badness 1009) in paragraph at lines 18896--18905 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3445] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3446] [3447] [3448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3450] [3451] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3452]) (./rpart-pkg.tex Chapter 27. [3453] [3454] [3455] [3456] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3457] [3458] [3459] [3460] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3461] [3462] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3463] [3464] [3465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3466] [3467] [3468] [3469] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3470] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3471] [3472] [3473] [3474] [3475] [3476] [3477] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3478] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3479] [3480] [3481]) (./spatial-pkg.tex [3482] Chapter 28. [3483] [3484] [3485] [3486] [3487] [3488] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501]) (./survival-pkg.tex [3502] Chapter 29. [3503] [3504] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3505] [3506] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3507] [3508] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3510] Overfull \hbox (6.78088pt too wide) in paragraph at lines 524--524 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3511] [3512] [3513] Overfull \hbox (20.58041pt too wide) in paragraph at lines 769--769 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival [3514] Overfull \hbox (48.78088pt too wide) in paragraph at lines 792--792 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3515] [3516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3517] [3518] [3519] Underfull \hbox (badness 1097) in paragraph at lines 1106--1108 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3520] [3521] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1241--1241 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3522] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1308 ...erapy for Stage B/C colon cancer}{colon} [3523] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1407--1407 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1408--1408 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3524] [3525] [3526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1598--1598 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1647--1647 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3527] [3528] [3529] [3530] [3531] Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3532] Underfull \hbox (badness 3861) in paragraph at lines 2048--2052 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3533] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2103--2103 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3534] [3535] [3536] [3537] [3538] [3539] [3540] [3541] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3542] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2744--2744 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3543] [3544] [3545] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3546] [3547] [3548] [3549] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3317--3317 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3551] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3352--3352 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3366--3368 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3377--3377 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3552] [3553] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3554] [3555] Overfull \hbox (467.89665pt too wide) in alignment at lines 3652--3652 [] [] [3556] [3557] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3774--3774 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3558] [3559] [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3565] [3566] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4360--4360 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4365--4365 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3568] [3569] [3570] [3571] [3572] [3573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4786--4786 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3574] [3575] [3576] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5016--5016 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5142--5142 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5150--5150 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3579] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5236--5236 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3580] [3581] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3582] Underfull \hbox (badness 1852) in paragraph at lines 5386--5388 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3583] [3584] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3585] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5615--5615 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5627--5627 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5629--5629 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] [3586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5653--5653 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3587] [3588] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3589] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5941--5941 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5943--5943 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3590] [3591] [3592] [3593] [3594] [3595] [3596] [3597] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3598] [3599] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6642--6642 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] [3600] Underfull \hbox (badness 1043) in paragraph at lines 6654--6657 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6962--6962 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6963--6963 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3605] [3606] [3607] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7135--7135 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3608] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7216--7216 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7220--7220 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7224 ...ata from a soldering experiment}{solder} [3609] [3610] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7330--7330 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3611] [3612] [3613] [3614] [3615] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7694--7694 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7695--7695 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3616] [3617] [3618] [3619] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8013--8013 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3620] [3621] [3622] [3623] Underfull \hbox (badness 1253) in paragraph at lines 8302--8305 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3624] [3625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8432--8432 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3626] [3627] [3628] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8662--8662 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8680--8680 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3629] Underfull \hbox (badness 1038) in paragraph at lines 8722--8728 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8774--8774 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3632] [3633] [3634] Underfull \hbox (badness 10000) in paragraph at lines 9080--9085 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9100--9100 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9107--9107 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3635] [3636] [3637] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9321--9321 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3638] Underfull \hbox (badness 2653) in paragraph at lines 9454--9459 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3639] [3640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9594--9594 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3641] [3642] [3643] [3644] [3645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9979--9979 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3646] Underfull \hbox (badness 1354) in paragraph at lines 10020--10024 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3647] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10066--10066 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3648] [3649] Underfull \hbox (badness 2035) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10230--10237 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3650] [3651] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10320--10320 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3652] [3653] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10477--10477 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3654] [3655] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10609--10609 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10612--10612 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3656] [3657] [3658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10772--10772 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3659] [3660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10930--10930 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10931--10931 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10937--10937 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10939--10939 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3661] [3662] [3663] [3664] [3665] [3666] [3667] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11380--11380 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3668] [3669] [3670]) No file fullrefman.ind. 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This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-02-24> (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2021/10/04 v1.4n Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf-dist/tex/latex/url/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 137--143 \T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/ n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 137--143 \T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth -er-wise, it is []\T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 4454) in paragraph at lines 143--151 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 3009) in paragraph at lines 228--240 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 371--374 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 569--575 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 638--638 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 914--914 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 935--935 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [17] [18] [19] [20] [21] [22] [23] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1581--1587 Underfull \hbox (badness 10000) in paragraph at lines 1594--1596 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [26] [27] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1773--1773 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [28] Underfull \hbox (badness 1303) in paragraph at lines 1802--1805 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [29] [30] [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2059--2059 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 2097--2099 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [33] [34] [35] [36] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2362--2362 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2404--2404 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] [39] Underfull \hbox (badness 1107) in paragraph at lines 2566--2568 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2733--2733 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3437--3437 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3438--3438 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3445--3445 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3449--3449 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 3897--3899 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [59] [60] [61] [62] [63] [64] [65] [66] Underfull \hbox (badness 4927) in paragraph at lines 4395--4399 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4395--4399 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4479--4479 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4555--4558 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [69] [70] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4718--4718 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [71] Underfull \hbox (badness 1199) in paragraph at lines 4749--4755 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4760--4763 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4936--4936 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] [77] Underfull \hbox (badness 2521) in paragraph at lines 5192--5194 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [78] [79] [80] [81] [82] [83] Underfull \hbox (badness 1270) in paragraph at lines 5615--5623 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6184--6192 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [93] [94] [95] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6381--6381 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6383--6383 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6384--6384 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [96] [97] Underfull \hbox (badness 1635) in paragraph at lines 6586--6589 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6590--6593 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [98] Underfull \hbox (badness 1308) in paragraph at lines 6633--6641 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [99] [100] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6797--6797 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Underfull \hbox (badness 4505) in paragraph at lines 6849--6852 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6986--6991 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 7234--7236 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7276--7283 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [107] [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7480--7480 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7814--7816 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [115] [116] [117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7973--7973 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7975--7975 []\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo rt is vanishing[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [122] Underfull \hbox (badness 10000) in paragraph at lines 8322--8332 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8322--8332 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [123] [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8490--8490 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8842--8854 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9291--9295 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9382--9382 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9384--9384 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9412--9412 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9413--9413 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] [139] Underfull \hbox (badness 5403) in paragraph at lines 9544--9546 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 9563--9565 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [140] [141] [142] Underfull \hbox (badness 1603) in paragraph at lines 9794--9797 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [143] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 1917) in paragraph at lines 10410--10415 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [152] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10465--10465 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10466--10466 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [153] [154] Underfull \hbox (badness 1168) in paragraph at lines 10568--10573 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10670--10670 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10672--10672 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10791--10796 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 10822--10822 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10896--10896 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [159] [160] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11044--11044 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [161] [162] [163] Underfull \hbox (badness 6396) in paragraph at lines 11242--11250 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11251--11253 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11468--11471 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] Underfull \hbox (badness 2744) in paragraph at lines 11904--11906 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11927--11927 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [174] [175] [176] Underfull \hbox (badness 5288) in paragraph at lines 12179--12181 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12189--12194 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12246--12249 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12264--12266 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12514--12516 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 12557--12559 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13375--13375 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14100--14102 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14135--14138 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14268--14270 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 14427--14429 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14548--14552 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14559--14562 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 14580--14580 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [210] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14605--14605 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [211] Underfull \hbox (badness 10000) in paragraph at lines 14702--14705 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14712--14712 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [212] Underfull \hbox (badness 10000) in paragraph at lines 14778--14781 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14795--14795 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14824--14824 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 14856--14860 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [214] [215] [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15020--15020 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15021--15021 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] [220] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15263--15263 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15266--15266 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [221] Underfull \hbox (badness 1168) in paragraph at lines 15352--15356 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15352--15356 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [222] Underfull \hbox (badness 6944) in paragraph at lines 15449--15452 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [223] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15474--15474 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [224] [225] Underfull \hbox (badness 10000) in paragraph at lines 15612--15614 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15632--15632 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15638--15638 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 15645--15648 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [226] Underfull \hbox (badness 1024) in paragraph at lines 15676--15683 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [227] Underfull \hbox (badness 10000) in paragraph at lines 15751--15753 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 15773--15778 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 15779--15781 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 15790--15798 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [228] [229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15898--15898 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] [243] Underfull \hbox (badness 2418) in paragraph at lines 16863--16867 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16870--16873 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16905--16912 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [244] [245] Underfull \hbox (badness 10000) in paragraph at lines 17012--17016 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17012--17016 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [246] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17075--17075 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17078--17078 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [247] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17109--17109 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [248] [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17246--17246 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17274--17281 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [250] [251] [252] [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17575--17575 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] [254] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17604--17604 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [255] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17660--17660 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [256] [257] [258] [259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18033--18033 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18098--18098 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [261] [262] [263] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18307--18307 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [264] [265] [266] [267] [268] Underfull \hbox (badness 1163) in paragraph at lines 18653--18655 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18661--18661 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] [269] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18691--18691 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [270] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18785--18785 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18786--18786 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [271] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18845--18845 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18848--18848 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18854--18854 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [272] [273] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18981--18981 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18989--18989 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [274] [275] [276] Underfull \hbox (badness 10000) in paragraph at lines 19194--19196 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [277] [278] [279] [280] [281] Underfull \hbox (badness 10000) in paragraph at lines 19532--19538 Underfull \hbox (badness 10000) in paragraph at lines 19545--19547 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [282] [283] [284] Underfull \hbox (badness 4699) in paragraph at lines 19777--19780 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [285] [286] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19905--19905 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [287] [288] [289] Underfull \hbox (badness 4739) in paragraph at lines 20040--20042 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [290] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20089--20089 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20090--20090 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [291] [292] [293] [294] [295] [296] [297] [298] [299] Underfull \hbox (badness 1975) in paragraph at lines 20709--20712 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [300] [301] [302] [303] [304] [305] Underfull \hbox (badness 1077) in paragraph at lines 21124--21129 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21138--21145 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [306] Underfull \hbox (badness 1112) in paragraph at lines 21212--21221 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [307] Underfull \hbox (badness 2970) in paragraph at lines 21272--21275 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21272--21275 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21385--21389 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21385--21389 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21390--21397 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [310] [311] Underfull \hbox (badness 10000) in paragraph at lines 21521--21528 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [312] Underfull \hbox (badness 10000) in paragraph at lines 21642--21646 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [313] Underfull \hbox (badness 5161) in paragraph at lines 21712--21717 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [314] [315] [316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21880--21880 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21884--21884 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [317] Underfull \hbox (badness 3343) in paragraph at lines 21945--21949 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [318] [319] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22083--22083 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22094--22094 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [320] [321] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22205--22205 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22208--22208 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22255--22263 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [322] [323] Underfull \hbox (badness 2564) in paragraph at lines 22358--22361 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22395--22395 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22406--22406 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22414--22414 [] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[ 1]], "=")), nrow=2)[] [324] [325] Underfull \hbox (badness 1400) in paragraph at lines 22575--22579 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23419--23419 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23420--23420 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 23423--23423 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [339] Overfull \hbox (20.58041pt too wide) in paragraph at lines 23520--23520 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] [340] Underfull \hbox (badness 1655) in paragraph at lines 23554--23558 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [341] [342] [343] Underfull \hbox (badness 2277) in paragraph at lines 23803--23806 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [344] [345] [346] [347] [348] [349] [350] [351] [352] Underfull \hbox (badness 1484) in paragraph at lines 24392--24400 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 24392--24400 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [353] [354] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24466--24466 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [355] [356] [357] [358] [359] [360] [361] [362] Underfull \hbox (badness 1448) in paragraph at lines 25014--25022 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [363] Underfull \hbox (badness 3849) in paragraph at lines 25129--25134 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [364] Underfull \hbox (badness 2165) in paragraph at lines 25206--25212 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25206--25212 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25206--25212 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [365] [366] [367] Underfull \hbox (badness 2237) in paragraph at lines 25369--25371 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [368] [369] [370] Underfull \hbox (badness 6188) in paragraph at lines 25596--25599 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [371] [372] [373] Underfull \hbox (badness 1521) in paragraph at lines 25781--25795 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [374] [375] [376] [377] Underfull \hbox (badness 2197) in paragraph at lines 26095--26099 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26095--26099 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use [378] Underfull \hbox (badness 2846) in paragraph at lines 26109--26113 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26109--26113 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26151--26151 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 26155--26155 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [379] Underfull \hbox (badness 10000) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26217--26219 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [380] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26284--26284 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [381] [382] [383] Underfull \hbox (badness 8189) in paragraph at lines 26479--26485 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [384] [385] [386] Underfull \hbox (badness 1694) in paragraph at lines 26704--26707 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [387] [388] [389] [390] Underfull \hbox (badness 1603) in paragraph at lines 26976--26978 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [391] [392] Underfull \hbox (badness 1210) in paragraph at lines 27103--27111 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [393] [394] Underfull \hbox (badness 3271) in paragraph at lines 27323--27326 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [395] [396] [397] [398] Underfull \hbox (badness 3138) in paragraph at lines 27629--27635 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 27642--27645 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27668--27670 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 27695--27701 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27710--27715 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [399] Underfull \hbox (badness 1009) in paragraph at lines 27728--27731 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 27744--27747 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up date.packages[][][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27767--27774 []\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut il-i-ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27767--27774 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke []\T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; [400] [401] [402] [403] [404] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 28128--28132 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [405] [406] Underfull \hbox (badness 1210) in paragraph at lines 28275--28278 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [407] [408] [409] [410] Underfull \hbox (badness 7133) in paragraph at lines 28557--28563 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 28579--28579 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28591--28591 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [411] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28604--28604 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling : [] Overfull \hbox (63.78036pt too wide) in paragraph at lines 28608--28608 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [412] [413] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] [414] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28806--28806 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] Underfull \hbox (badness 1360) in paragraph at lines 28861--28865 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [415] [416] [417] [418] [419] Underfull \hbox (badness 2277) in paragraph at lines 29173--29178 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [420] [421] Underfull \hbox (badness 1701) in paragraph at lines 29289--29293 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [422] Underfull \hbox (badness 1796) in paragraph at lines 29357--29360 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [423] [424] [425] Underfull \hbox (badness 10000) in paragraph at lines 29561--29564 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [436] [437] [438] [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30560--30560 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30566--30566 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30572--30572 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [441] Underfull \hbox (badness 7415) in paragraph at lines 30662--30666 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [442] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30683--30683 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30729--30729 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [443] [444] Underfull \hbox (badness 3713) in paragraph at lines 30874--30885 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [445] [446] Underfull \hbox (badness 1248) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [447] Underfull \hbox (badness 1533) in paragraph at lines 31144--31147 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [448] [449] [450] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31289--31289 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 31307--31318 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [451] [452] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 31453--31453 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31454--31454 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31456--31456 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [453] [454] [455] [456] [457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31773--31773 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31783--31783 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] Underfull \vbox (badness 10000) has occurred while \output is active [458] [459] Underfull \hbox (badness 4048) in paragraph at lines 31879--31884 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 2080) in paragraph at lines 32417--32427 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 32451--32451 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [468] [469] [470] [471] [472] [473] [474] Underfull \hbox (badness 7558) in paragraph at lines 32971--32975 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32981--32983 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [475] Underfull \hbox (badness 10000) in paragraph at lines 32992--32994 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 32995--32999 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [476] [477] [478] [479] [480] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33366--33366 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [481] Underfull \hbox (badness 10000) in paragraph at lines 33437--33441 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [482] [483] [484] Underfull \hbox (badness 2302) in paragraph at lines 33663--33668 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 33663--33668 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [485] [486] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33796--33796 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33799--33799 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33806--33806 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [487] [488] [489] [490] [491] [492] [493] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34254--34254 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [494] [495] [496] [497] [498] [499] [500] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34691--34691 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [501] Underfull \hbox (badness 1158) in paragraph at lines 34795--34800 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [502] [503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34981--34981 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [504] [505] [506] [507] Underfull \hbox (badness 4752) in paragraph at lines 35241--35244 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35245--35251 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as Underfull \hbox (badness 3271) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru les for the C run- Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso ft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 35915--35926 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [518] [519] [520] [521] [522] [523] [524] [525] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [526] [527] [528] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36709--36709 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [529] Underfull \hbox (badness 4954) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [530] [531] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36863--36863 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [532] [533] [534] [535] [536] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37206--37206 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37221--37221 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [537] [538] [539] Underfull \hbox (badness 10000) in paragraph at lines 37446--37448 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [540] [541] [542] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37673--37673 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37674--37674 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [543] [544] [545] [546] [547] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [548] Underfull \hbox (badness 6110) in paragraph at lines 38101--38111 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38101--38111 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [549] Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38172--38179 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [550] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38234--38234 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [551] [552] [553] Underfull \hbox (badness 1484) in paragraph at lines 38407--38411 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 38469--38469 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [554] [555] [556] [557] [558] [559] [560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955 []\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is still NA (not "NA")[] [561] [562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [563] [564] [565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 39314--39314 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39358--39358 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [567] [568] [569] [570] [571] [572] [573] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39805--39805 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39808--39808 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [575] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39912--39912 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [576] [577] [578] [579] Overfull \hbox (31.3804pt too wide) in paragraph at lines 40223--40223 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [580] [581] [582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [583] Overfull \hbox (20.58041pt too wide) in paragraph at lines 40427--40427 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 40457--40463 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 40457--40463 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 40476--40481 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 40476--40481 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [584] [585] [586] [587] Underfull \hbox (badness 10000) in paragraph at lines 40764--40768 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 40779--40782 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [588] [589] [590] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [591] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40998--40998 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [592] [593] Underfull \hbox (badness 1082) in paragraph at lines 41143--41146 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41170--41172 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [594] [595] [596] Underfull \hbox (badness 1038) in paragraph at lines 41336--41339 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [597] [598] [599] [600] [601] Underfull \hbox (badness 1442) in paragraph at lines 41701--41705 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [602] [603] [604] [605] Underfull \hbox (badness 4096) in paragraph at lines 41955--41958 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [606] Underfull \hbox (badness 7888) in paragraph at lines 42069--42073 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [607] [608] [609] Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 42225--42225 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 42240--42242 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [610] Underfull \hbox (badness 10000) in paragraph at lines 42320--42323 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [611] [612] Underfull \hbox (badness 3872) in paragraph at lines 42438--42441 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [613] Underfull \hbox (badness 5475) in paragraph at lines 42504--42508 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [614] [615] [616] [617] [618] [619] Underfull \hbox (badness 1655) in paragraph at lines 42927--42934 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 42935--42940 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 42935--42940 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing Underfull \hbox (badness 4467) in paragraph at lines 42985--42994 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42985--42994 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [620] Underfull \hbox (badness 1082) in paragraph at lines 42995--43007 []\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1 0 ' in that di-rec-tory states the ver-sion. That op-tion is [621] Underfull \hbox (badness 1337) in paragraph at lines 43080--43088 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43089--43092 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 43143--43146 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43147--43149 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- [622] Overfull \hbox (31.3804pt too wide) in paragraph at lines 43156--43156 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [623] [624] [625] [626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43499--43499 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43501--43501 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [627] Underfull \vbox (badness 10000) has occurred while \output is active [628] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43604--43604 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [629] [630] [631] [632] Underfull \hbox (badness 6542) in paragraph at lines 43878--43880 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [633] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43997--43997 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [634] Underfull \hbox (badness 1708) in paragraph at lines 44065--44073 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44065--44073 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [635] Underfull \hbox (badness 4859) in paragraph at lines 44105--44110 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [636] Underfull \hbox (badness 3895) in paragraph at lines 44167--44179 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44167--44179 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [637] [638] [639] [640] [641] Overfull \hbox (9.78043pt too wide) in paragraph at lines 44490--44490 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [642] [643] [644] [645] [646] [647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44959--44959 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44968--44968 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] Underfull \hbox (badness 2057) in paragraph at lines 45034--45040 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [649] Underfull \hbox (badness 3861) in paragraph at lines 45043--45048 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [650] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45136--45136 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [651] Underfull \hbox (badness 1803) in paragraph at lines 45199--45202 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 45203--45209 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [652] [653] [654] Underfull \hbox (badness 3668) in paragraph at lines 45432--45434 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [655] Overfull \hbox (36.78088pt too wide) in paragraph at lines 45538--45538 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [656] [657] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45621--45621 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [658] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45715--45715 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 45719--45719 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings AsFactors = FALSE) {[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720 [] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa ctors=stringsAsFactors)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45727--45727 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 45730--45730 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [659] Underfull \hbox (badness 10000) in paragraph at lines 45791--45796 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 45791--45796 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [660] [661] Underfull \hbox (badness 2818) in paragraph at lines 45887--45893 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 45922--45922 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [662] [663] [664] [665] [666] [667] [668] Underfull \hbox (badness 2846) in paragraph at lines 46381--46385 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46421--46421 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 46442--46446 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [670]) (./compiler-pkg.tex Chapter 2. [671] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [672] [673] [674]) (./datasets-pkg.tex Chapter 3. [675] [676] [677] [678] [679] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [680] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [681] [682] [683] [684] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [685] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [686] [687] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [688] [689] [690] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [691] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [692] [693] [694] [695] [696] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [697] [698] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [699] [700] [701] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [702] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [703] [704] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [705] [706] [707] [708] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [709] [710] [711] [712] [713] [714] [715] [716] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [717] [718] [719] [720] [721] [722] [723] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [724] [725] [726] [727] [728] [729] [730] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [731] [732] [733] Underfull \hbox (badness 4779) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [734] [735] [736] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3968--3968 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]) (./grDevices-pkg.tex Chapter 4. [751] [752] [753] [754] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [755] [756] [757] [758] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [769] [770] [771] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [772] [773] [774] Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1624--1628 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [775] [776] [777] [778] [779] Underfull \hbox (badness 1565) in paragraph at lines 1914--1919 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1914--1919 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [780] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1997--1997 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [781] Underfull \hbox (badness 1184) in paragraph at lines 2038--2048 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2038--2048 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [782] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [783] [784] [785] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [786] [787] Underfull \hbox (badness 2326) in paragraph at lines 2447--2457 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2447--2457 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2447--2457 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2447--2457 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [788] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2550--2550 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] [789] [790] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2666--2666 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2667--2667 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [791] [792] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [795] [796] [797] [798] [799] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3273--3273 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [800] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3358--3358 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 3516--3522 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3591--3591 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [805] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3675--3675 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3695--3695 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3702--3702 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [806] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3758--3758 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [807] Underfull \hbox (badness 8170) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [808] Underfull \hbox (badness 2189) in paragraph at lines 3848--3853 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3886--3890 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [809] Underfull \vbox (badness 10000) has occurred while \output is active [810] Underfull \hbox (badness 5260) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [811] [812] [813] [814] [815] Underfull \hbox (badness 5939) in paragraph at lines 4349--4354 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [816] [817] [818] [819] [820] [821] [822] [823] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [824] [825] Underfull \hbox (badness 1348) in paragraph at lines 5074--5077 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [826] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5098--5098 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5139--5145 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [827] Underfull \hbox (badness 1112) in paragraph at lines 5172--5176 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [828] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [829] [830] [831] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5505--5509 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [832] [833] Underfull \hbox (badness 1552) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5642--5644 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5674--5680 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [834] Underfull \hbox (badness 5388) in paragraph at lines 5700--5702 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [835] [836] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5915--5915 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 6001--6003 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [840] [841] [842] [843] [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [845] [846] [847] [848] [849] [850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [851] [852] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6990--6995 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [855] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7096--7096 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [856] Underfull \hbox (badness 3590) in paragraph at lines 7135--7138 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7135--7138 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7146--7146 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [857] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [858] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [859] Underfull \hbox (badness 10000) in paragraph at lines 7362--7369 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7362--7369 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [860] Underfull \hbox (badness 5607) in paragraph at lines 7446--7450 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [861] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7498--7498 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [862] [863] Underfull \hbox (badness 5637) in paragraph at lines 7630--7636 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7663--7666 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [864] [865] [866] Underfull \hbox (badness 1231) in paragraph at lines 7832--7834 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [867] [868]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [869] [870] [871] [872] [873] [874] [875] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [876] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [878] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [879] [880] Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770 []\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0: 1e-2 1e0 1e2 .. 1e10[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [881] [882] [883] Underfull \hbox (badness 10000) in paragraph at lines 966--970 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [884] [885] [886] [887] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [888] [889] [890] Underfull \hbox (badness 2503) in paragraph at lines 1433--1442 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1468--1470 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [891] [892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1543--1543 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1549--1549 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1550--1550 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [893] [894] [895] [896] [897] Underfull \hbox (badness 10000) in paragraph at lines 1853--1859 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and Overfull \hbox (9.78043pt too wide) in paragraph at lines 1873--1873 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1910--1910 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [898] [899] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1995--1995 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [900] [901] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2124--2124 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2129--2129 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [902] [903] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2303--2303 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2304--2304 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [904] Underfull \hbox (badness 1430) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [905] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2416--2416 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [906] Underfull \hbox (badness 7273) in paragraph at lines 2510--2514 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [907] [908] [909] [910] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2758--2758 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [911] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2795--2795 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [912] [913] Underfull \hbox (badness 1226) in paragraph at lines 2923--2927 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [914] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2980--2980 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [915] Underfull \hbox (badness 10000) in paragraph at lines 3042--3045 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3093--3093 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [916] [917] [918] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3262--3262 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is [921] [922] [923] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3590--3590 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3613--3613 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [924] [925] [926] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3798--3798 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3799--3799 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3803--3803 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3844--3844 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3870--3870 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3872--3872 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3883--3883 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3898--3898 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [928] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3908--3908 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3916--3916 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3926--3926 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [929] Underfull \hbox (badness 10000) in paragraph at lines 3988--3992 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [930] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4100--4100 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [931] [932] [933] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4254--4254 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [934] Underfull \hbox (badness 3930) in paragraph at lines 4333--4335 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [935] [936] [937] [938] [939] Underfull \hbox (badness 1286) in paragraph at lines 4644--4647 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [940] [941] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4748--4748 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [942] Underfull \hbox (badness 1264) in paragraph at lines 4944--4957 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [943] [944] [945] [946] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [947 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 [948 ] [949] [950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5517--5517 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5518--5518 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5884--5884 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [957] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [958] [959] [960] [961] [962] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6275--6275 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [963] [964] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6405--6405 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 6711--6713 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [969] [970] Underfull \hbox (badness 1028) in paragraph at lines 6805--6807 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [971 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6942--6942 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [972] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6973--6973 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [973] [974] Underfull \hbox (badness 10000) in paragraph at lines 7095--7097 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7122--7122 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7128--7128 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [975] Underfull \hbox (badness 2600) in paragraph at lines 7185--7187 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [976] [977] [978] [979] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7417--7417 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [980] [981] [982] [983] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7804--7804 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7808--7808 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [986] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7820--7820 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [987] [988] [989] [990] [991] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8169--8169 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8172--8172 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8176--8176 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [992] [993] [994] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8347--8347 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8348--8348 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [995] [996] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [997] Underfull \hbox (badness 1112) in paragraph at lines 8511--8515 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [998] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8586--8586 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [999] [1000] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8723--8723 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8908--8908 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [1003] Underfull \hbox (badness 1215) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 8970--8976 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1004] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1005] Underfull \hbox (badness 1205) in paragraph at lines 9083--9085 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9202--9202 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1008]) (./grid-pkg.tex Chapter 6. [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1019] [1020] [1021] [1022] [1023] [1024] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1025] [1026] [1027] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1028] [1029] [1030] [1031] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1032] [1033] [1034] [1035] [1036] [1037] [1038] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1039] [1040] [1041] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1042] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1043] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1044] [1045] [1046] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1047] [1048] [1049] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1050] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2664--2664 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1051] [1052] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2826--2826 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1053] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2858--2858 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1054] [1055] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1056] [1057] [1058] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3228--3228 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1059] [1060] [1061] [1062] [1063] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3543--3543 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1064] [1065] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3639--3639 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3676--3682 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1068] [1069] [1070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3976--3976 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3991--3991 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4012--4012 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1084] [1085] [1086] [1087] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4977--4977 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1088] [1089] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1090] [1091] [1092] [1093] [1094] [1095] Underfull \hbox (badness 2726) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5561--5565 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1096] [1097] Underfull \hbox (badness 2080) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1098] [1099] [1100] Underfull \hbox (badness 10000) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6900--6900 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1118] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7020--7020 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1119] [1120] Underfull \hbox (badness 1867) in paragraph at lines 7122--7124 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1121] Underfull \hbox (badness 10000) in paragraph at lines 7159--7165 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1122] [1123] [1124] [1125] [1126] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7495--7495 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1131] [1132] [1133] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1134] [1135] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1137] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1153] [1154] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1155] [1156] [1157] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1160] [1161] [1162] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1163] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1164] [1165] [1166] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1167] [1168] [1169] [1170] [1171] [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1174] [1175] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1176] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1177] [1178] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1179] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1180] [1181] [1182] [1183] [1184] [1185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1186] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1187] [1188] [1189] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1190] [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1193] [1194] [1195] [1196] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1197] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1198] [1199] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1200] [1201] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1202] [1203] [1204] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1205] [1206] [1207] [1208] [1209] [1210] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1211] [1212] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1213] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1214] [1215] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] [1218] [1219] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1220] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1221] [1222] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1223] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1224] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1225] [1226] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1227] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1241] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1242] [1243] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1246] [1247] [1248] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1249] [1250] [1251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1252] [1253] [1254] [1255] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1256] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1267] [1268] [1269]) (./parallel-pkg.tex [1270] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1271] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1272] [1273] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1274] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 445--447 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1277] [1278] [1279] [1280] [1281] Underfull \hbox (badness 1917) in paragraph at lines 779--788 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 779--788 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1282] [1283] Overfull \hbox (60.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1284] [1285] [1286] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1063--1063 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1067--1067 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1287] Underfull \hbox (badness 5388) in paragraph at lines 1182--1187 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from [1288] Underfull \hbox (badness 10000) in paragraph at lines 1206--1214 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1289] [1290] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1373--1373 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1291] Underfull \hbox (badness 1577) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1449--1451 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1292] [1293]) (./splines-pkg.tex [1294] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1303] Underfull \hbox (badness 1043) in paragraph at lines 597--599 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1304] [1305] Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1306] [1307] [1308]) (./stats-pkg.tex Chapter 10. [1309] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1310] [1311] [1312] [1313] [1314] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1315] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1024) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1628--1628 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1333] [1334] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1335] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2805--2805 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1350] [1351] [1352] [1353] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3053--3053 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1354] [1355] [1356] Underfull \hbox (badness 10000) in paragraph at lines 3264--3266 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1357] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3313--3313 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3314--3314 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1358] [1359] [1360] [1361] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1362] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1363] [1364] [1365] [1366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1367] [1368] [1369] [1370] [1371] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4277--4277 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1372] [1373] [1374] [1375] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1376] [1377] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1378] [1379] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1380] [1381] [1382] [1383] [1384] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5174--5174 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1385] [1386] [1387] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5414--5414 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1388] [1389] [1390] [1391] Underfull \hbox (badness 1436) in paragraph at lines 5624--5629 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1392] [1393] [1394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1395] [1396] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5994--5994 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1397] [1398] [1399] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1400] [1401] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1402] [1403] [1404] [1405] Underfull \hbox (badness 5954) in paragraph at lines 6550--6552 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1406] Underfull \hbox (badness 2503) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6636--6638 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6639--6644 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1407] Underfull \hbox (badness 7238) in paragraph at lines 6675--6678 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6687--6687 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6710--6710 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6725--6725 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6740--6740 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1409] [1410] [1411] Underfull \vbox (badness 10000) has occurred while \output is active [1412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 7394--7398 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1419] Underfull \hbox (badness 6493) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1420] [1421] Underfull \hbox (badness 10000) in paragraph at lines 7630--7633 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1422] [1423] [1424] [1425] [1426] [1427] Underfull \hbox (badness 10000) in paragraph at lines 8042--8047 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 1210) in paragraph at lines 8397--8399 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1434] [1435] [1436] [1437] [1438] [1439] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1440] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8905--8905 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8908--8908 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1449] [1450] [1451] Underfull \hbox (badness 7291) in paragraph at lines 9668--9670 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 6944) in paragraph at lines 10160--10166 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1459] [1460] [1461] Underfull \hbox (badness 3758) in paragraph at lines 10374--10377 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1462] [1463] [1464] [1465] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1466] Underfull \hbox (badness 4132) in paragraph at lines 10683--10687 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10737--10743 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1467] Underfull \hbox (badness 10000) in paragraph at lines 10788--10791 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1468] [1469] [1470] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1471] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1472] Underfull \hbox (badness 10000) in paragraph at lines 11128--11134 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11166--11171 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1473] [1474] Underfull \hbox (badness 2635) in paragraph at lines 11299--11302 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1475] [1476] [1477] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1478] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1479] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11613--11613 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11626--11630 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1480] [1481] [1482] [1483] [1484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1485] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1486] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12088--12093 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1487] [1488] [1489] [1490] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12730--12732 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1497] [1498] [1499] [1500] [1501] Underfull \hbox (badness 3417) in paragraph at lines 13037--13039 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13043--13047 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1502] [1503] [1504] [1505] [1506] [1507] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1508] [1509] [1510] [1511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1512] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1513] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1514] [1515] [1516] Underfull \hbox (badness 10000) in paragraph at lines 14062--14066 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 1163) in paragraph at lines 14402--14410 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1522] [1523] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1524] [1525] [1526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1527] [1528] [1529] [1530] [1531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15055--15055 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1533] [1534] [1535] [1536] [1537] [1538] [1539] Underfull \hbox (badness 2726) in paragraph at lines 15557--15560 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1551] [1552] Underfull \hbox (badness 1490) in paragraph at lines 16425--16430 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1553] Underfull \hbox (badness 1648) in paragraph at lines 16491--16493 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1554] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1564] [1565] [1566] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] Underfull \vbox (badness 10000) has occurred while \output is active [1577] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1578] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1579] [1580] [1581] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1582] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18417--18417 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1583] [1584] [1585] [1586] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 1248) in paragraph at lines 18938--18941 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 18959--18963 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1592] Underfull \hbox (badness 2042) in paragraph at lines 19017--19019 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1593] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1595] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19210--19210 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19245--19256 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19245--19256 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1597] [1598] [1599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1600] [1601] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1602] [1603] [1604] [1605] [1606] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1607] [1608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20055--20055 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1609] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20125--20131 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20136--20139 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1610] [1611] [1612] [1613] [1614] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1615] Underfull \hbox (badness 1107) in paragraph at lines 20505--20507 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1616] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1617] [1618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1619] [1620] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1621] Underfull \hbox (badness 7740) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1622] Underfull \hbox (badness 10000) in paragraph at lines 20957--20959 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1623] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1637] Underfull \hbox (badness 6859) in paragraph at lines 21921--21928 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1650] [1651] [1652] [1653] [1654] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1655] [1656] [1657] [1658] [1659] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1668] [1669] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1670] Underfull \hbox (badness 1028) in paragraph at lines 24024--24027 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1671] [1672] Underfull \hbox (badness 10000) in paragraph at lines 24139--24142 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7099) in paragraph at lines 24194--24196 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1673] Underfull \hbox (badness 7099) in paragraph at lines 24258--24260 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1674] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24488--24488 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to [1680] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1681] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1682] Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1683] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1684] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 6268) in paragraph at lines 25429--25434 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1692] [1693] [1694] [1695] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 25689--25689 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1696] [1697] [1698] Underfull \hbox (badness 2495) in paragraph at lines 25879--25888 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1699] [1700] Underfull \hbox (badness 2197) in paragraph at lines 26021--26024 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and [1701] Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26048--26050 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1702] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26160--26160 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26163--26163 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1703] [1704] [1705] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26396--26402 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1706] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1707] [1708] [1709] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1710] [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1717] [1718] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27232--27232 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1719] Underfull \hbox (badness 2922) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1720] Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1721] Underfull \hbox (badness 3240) in paragraph at lines 27409--27412 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1722] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27430--27430 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27433--27433 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1723] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27520--27520 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27530--27530 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1724] Underfull \hbox (badness 2922) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1725] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27623--27623 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27625--27625 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27628--27628 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27630--27630 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1726] [1727] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27742--27742 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1728] Underfull \hbox (badness 2922) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (69.18036pt too wide) in paragraph at lines 27842--27842 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1729] Underfull \hbox (badness 2922) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1730] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27922--27922 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27981--27981 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27985--27985 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28005--28005 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28015--28015 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] [1732] Underfull \hbox (badness 2922) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28072--28072 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1733] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28090--28090 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28173--28173 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28176--28176 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28179--28179 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 3396) in paragraph at lines 29062--29064 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1749] [1750] Underfull \hbox (badness 2237) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1751] [1752] [1753] Underfull \hbox (badness 2591) in paragraph at lines 29403--29405 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1754] Underfull \hbox (badness 2237) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1755] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29522--29522 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1756] Underfull \hbox (badness 3407) in paragraph at lines 29631--29635 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1757] [1758] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29701--29701 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1759] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1760] [1761] [1762] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30028--30028 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1763] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30056--30056 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1764] [1765] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30161--30161 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30239--30239 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1767] Underfull \hbox (badness 2205) in paragraph at lines 30328--30333 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30927--30927 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30928--30928 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1777] [1778] [1779] [1780] [1781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31228--31228 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31229--31229 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1782] [1783] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31355--31355 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31364--31364 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1784] [1785] [1786] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1795] [1796] [1797] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32317--32317 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32319--32319 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1798] [1799] [1800] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32478--32478 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32563--32563 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1802] [1803] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32696--32696 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1804]) (./stats4-pkg.tex Chapter 11. [1805] [1806] [1807] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1808] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1809] [1810] [1811] [1812] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1813] [1814] [1815]) (./tcltk-pkg.tex [1816] Chapter 12. [1817] [1818] [1819] [1820] Overfull \hbox (36.7804pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1821] [1822] [1823] Underfull \vbox (badness 10000) has occurred while \output is active [1824] Underfull \hbox (badness 1292) in paragraph at lines 666--673 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1825] [1826] [1827] [1828] [1829] [1830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1079--1079 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1831] [1832] [1833] [1834] [1835] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1836]) (./tools-pkg.tex Chapter 13. [1837] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1838] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1839] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1840] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1841] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1842] [1843] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1844] [1845] [1846] [1847] [1848] [1849] [1850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 911--911 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 966--966 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1851] [1852] [1853] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1134--1134 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1135--1135 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1854] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and [1855] Underfull \hbox (badness 10000) in paragraph at lines 1225--1228 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1856] [1857] Underfull \hbox (badness 10000) in paragraph at lines 1374--1377 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1858] [1859] Underfull \hbox (badness 4647) in paragraph at lines 1543--1548 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1860] Underfull \hbox (badness 2762) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1861] [1862] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1707--1707 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1714--1722 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1714--1722 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1714--1722 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1863] [1864] [1865] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1866] [1867] [1868] [1869] Underfull \hbox (badness 1142) in paragraph at lines 2196--2202 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1870] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2230--2230 [] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] Underfull \hbox (badness 2359) in paragraph at lines 2258--2265 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1871] Underfull \hbox (badness 1342) in paragraph at lines 2310--2316 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1872] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2384--2384 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2399--2407 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2399--2407 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2399--2407 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2435--2435 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2468--2468 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2752--2752 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1878] Underfull \hbox (badness 2486) in paragraph at lines 2797--2805 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1879] [1880] [1881] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3009--3009 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3013--3013 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1882] [1883] [1884] Underfull \hbox (badness 1072) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1885] [1886] [1887] [1888] [1889] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3534--3534 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1890] Underfull \hbox (badness 5417) in paragraph at lines 3572--3582 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1891] [1892] [1893] Underfull \hbox (badness 4108) in paragraph at lines 3782--3789 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1894] [1895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3882--3882 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3885--3885 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3919--3925 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1896] [1897] Underfull \hbox (badness 7832) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1898] [1899] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4276--4276 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1902] [1903] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4438--4438 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4453--4456 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1904] Underfull \hbox (badness 6859) in paragraph at lines 4469--4474 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 4703--4705 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1908] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4746--4749 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4750--4760 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4788--4794 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4788--4794 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1909] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4842--4847 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1910] [1911] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1912]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1913] [1914] [1915] [1916] Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1917] Underfull \hbox (badness 10000) in paragraph at lines 378--383 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", [1918] Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 452--452 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1920] [1921] [1922] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 689--689 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 690--690 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 726--732 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1923] [1924] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1928] Underfull \hbox (badness 1748) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/ 10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1092) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1 ) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1929] Underfull \hbox (badness 10000) in paragraph at lines 1235--1238 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1930] [1931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 1859) in paragraph at lines 1721--1730 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1721--1730 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1937] [1938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1826--1826 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1939] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1861--1861 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1940] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1941] Underfull \hbox (badness 2277) in paragraph at lines 2076--2081 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1942] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2109--2109 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1943] [1944] [1945] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2319--2319 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1947] [1948] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1949] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2512--2512 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1950] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2632--2632 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1951] Underfull \hbox (badness 1082) in paragraph at lines 2706--2710 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [1952] Underfull \hbox (badness 1163) in paragraph at lines 2742--2744 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1953] Underfull \hbox (badness 10000) in paragraph at lines 2835--2837 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 3053--3055 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1958] [1959] [1960] [1961] Underfull \hbox (badness 1762) in paragraph at lines 3346--3349 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1962] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1963] Underfull \hbox (badness 2452) in paragraph at lines 3515--3518 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1964] [1965] [1966] [1967] [1968] [1969] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1970] Underfull \hbox (badness 4779) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1971] Underfull \hbox (badness 1072) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1972] Underfull \hbox (badness 7238) in paragraph at lines 4129--4134 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4129--4134 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1973] Underfull \hbox (badness 4660) in paragraph at lines 4261--4264 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [1974] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 1565) in paragraph at lines 4470--4474 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1977] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1978] Underfull \hbox (badness 1910) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4587--4594 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4594--4601 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1979] [1980] [1981] [1982] Underfull \hbox (badness 5939) in paragraph at lines 4840--4842 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [1983] [1984] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1985] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1994] [1995] [1996] [1997] [1998] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [1999] [2000] [2001] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2002] [2003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2004] [2005] [2006] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2007] Underfull \hbox (badness 10000) in paragraph at lines 6546--6548 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2008] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2011] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2012] Underfull \hbox (badness 5175) in paragraph at lines 6848--6851 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2013] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2014] [2015] [2016] Underfull \hbox (badness 5091) in paragraph at lines 7146--7148 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages Underfull \hbox (badness 1270) in paragraph at lines 7191--7201 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If [2017] Underfull \hbox (badness 4441) in paragraph at lines 7234--7237 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7234--7237 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2018] Underfull \hbox (badness 2376) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2019] Underfull \hbox (badness 1314) in paragraph at lines 7401--7408 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2020] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7504--7504 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2021] Underfull \hbox (badness 5133) in paragraph at lines 7540--7544 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7554--7557 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2022] [2023] Underfull \hbox (badness 4132) in paragraph at lines 7725--7727 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2024] [2025] [2026] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2027] [2028] [2029] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) Underfull \hbox (badness 10000) in paragraph at lines 8075--8077 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2030] [2031] Underfull \hbox (badness 10000) in paragraph at lines 8180--8182 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2032] [2033] [2034] [2035] Underfull \hbox (badness 1859) in paragraph at lines 8413--8416 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8432--8442 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2036] Underfull \hbox (badness 1655) in paragraph at lines 8507--8510 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8518--8518 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8534--8534 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2037] [2038] Underfull \hbox (badness 1917) in paragraph at lines 8621--8623 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2039] [2040] [2041] [2042] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8893--8893 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2043] Underfull \hbox (badness 10000) in paragraph at lines 8923--8925 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 8937--8939 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2044] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8992--8992 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2045] [2046] Underfull \hbox (badness 10000) in paragraph at lines 9121--9126 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9128--9131 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2047] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9244--9244 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9245--9245 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2048] [2049] [2050] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418 [] \T1/pcr/m/n/9 "S original, "),[] [2051] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] Underfull \hbox (badness 5203) in paragraph at lines 10124--10127 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the []\T1/pcr/m/n/10 $ []\T1/ptm/m/ n/10 ex-trac-tor are de-ter-mined by the generic func-tion [2061] [2062] [2063] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2064] [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2066] [2067] [2068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2069] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10802--10802 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10805--10805 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10810--10810 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2070] Underfull \hbox (badness 2027) in paragraph at lines 10882--10885 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2071] [2072] [2073] [2074] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11161--11161 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11162--11162 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2075] [2076] [2077] [2078] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2079] [2080] [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11681--11681 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11686--11686 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11819--11819 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2085] [2086] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11955--11955 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2087] [2088] Underfull \hbox (badness 1917) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12087--12090 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12110--12110 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2089] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12202--12202 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12203--12203 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12205--12205 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12206--12206 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] [2090] Underfull \hbox (badness 6725) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or Overfull \hbox (9.78043pt too wide) in paragraph at lines 12274--12274 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2091] Underfull \hbox (badness 1377) in paragraph at lines 12330--12333 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style [2092] Underfull \hbox (badness 3646) in paragraph at lines 12365--12367 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / Overfull \hbox (30.78088pt too wide) in paragraph at lines 12403--12403 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2093] [2094] [2095] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12633--12641 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2096] [2097] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12794--12794 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2098] Underfull \hbox (badness 1009) in paragraph at lines 12812--12824 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 2600) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2099] Underfull \hbox (badness 1043) in paragraph at lines 12895--12900 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2100] [2101] [2102] [2103] Underfull \hbox (badness 1888) in paragraph at lines 13188--13191 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13205--13208 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2104] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2105] Underfull \hbox (badness 2158) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13354--13354 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2106] [2107] [2108] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2109] Underfull \hbox (badness 3333) in paragraph at lines 13619--13621 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2110] [2111] [2112] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13786--13786 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13819--13822 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13830--13839 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2113] Underfull \hbox (badness 1442) in paragraph at lines 13846--13850 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 13892--13892 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2114] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13919--13919 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13926--13926 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13928--13928 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2115] [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 14094--14096 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2118] Underfull \hbox (badness 10000) in paragraph at lines 14204--14207 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14204--14207 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2119] Underfull \hbox (badness 6300) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2120] [2121] Underfull \hbox (badness 2020) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2122] Underfull \hbox (badness 1622) in paragraph at lines 14426--14433 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 5022) in paragraph at lines 14567--14571 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2124] [2125] [2126] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14740--14740 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2127] [2128] [2129] [2130] [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15181--15181 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15187--15187 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 15208--15210 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15223--15227 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [2133] Underfull \hbox (badness 1694) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15249--15251 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15279--15284 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15279--15284 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15300--15305 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with [2134] Underfull \hbox (badness 10000) in paragraph at lines 15308--15311 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (15.18042pt too wide) in paragraph at lines 15362--15362 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2135] [2136] [2137] Underfull \hbox (badness 2293) in paragraph at lines 15569--15572 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2138] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15585--15585 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2139] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15652--15652 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15674--15674 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2140] [2141] Underfull \hbox (badness 1297) in paragraph at lines 15805--15807 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2142] Underfull \hbox (badness 4036) in paragraph at lines 15852--15854 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2143] [2144] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15972--15972 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2145] Underfull \hbox (badness 1715) in paragraph at lines 16024--16027 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16069--16071 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex Chapter 15. [2151] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2152] [2153] [2154] [2155] [2156] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2157] [2158] [2159] [2160]) (./MASS-pkg.tex Chapter 16. [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2418--2418 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2195] [2196] [2197] [2198] Underfull \hbox (badness 6559) in paragraph at lines 2701--2704 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2199] [2200] [2201] Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2202] [2203] Underfull \hbox (badness 4686) in paragraph at lines 3039--3041 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2204] [2205] [2206] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3234--3234 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2207] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3364--3364 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] Underfull \hbox (badness 1845) in paragraph at lines 4164--4166 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2220] [2221] [2222] [2223] [2224] [2225] [2226] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2227] [2228] [2229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5930--5930 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2244] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5991--5991 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2245] [2246] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} [2247] [2248] [2249] [2250] [2251] [2252] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6571--6571 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2253] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6659--6659 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2254] [2255] [2256] [2257] [2258] [2259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7098--7098 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7115--7115 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2260] Underfull \hbox (badness 3138) in paragraph at lines 7193--7199 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2261] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7263--7263 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2262] [2263] Underfull \hbox (badness 1389) in paragraph at lines 7372--7375 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2264] [2265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7502--7502 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2266] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2267] [2268] [2269] [2270] [2271] [2272] Underfull \hbox (badness 4686) in paragraph at lines 8005--8007 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2273] [2274] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8124--8124 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8148--8152 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9529--9529 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2295] Underfull \hbox (badness 2035) in paragraph at lines 9641--9643 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9656--9659 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2296] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9738--9738 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9743--9743 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308] [2309]) (./Matrix-pkg.tex [2310] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2311] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2312] Underfull \hbox (badness 2229) in paragraph at lines 153--156 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 153--156 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new [2313] Underfull \hbox (badness 10000) in paragraph at lines 256--259 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2314] [2315] Overfull \hbox (15.18042pt too wide) in paragraph at lines 445--445 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2316] Underfull \hbox (badness 5119) in paragraph at lines 488--492 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 492--497 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 522--522 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 524--524 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 533--533 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2318] Overfull \hbox (52.98038pt too wide) in paragraph at lines 647--647 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 648--648 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 649--649 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2319] Overfull \hbox (31.3804pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 663--663 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2320] Underfull \hbox (badness 1874) in paragraph at lines 737--740 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 https : / / netlib . org / [2321] [2322] Underfull \hbox (badness 1107) in paragraph at lines 860--865 \T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/ 10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in [] \T1/pcr/m/n/10 selectMethod(cbind2, Underfull \hbox (badness 10000) in paragraph at lines 903--908 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: [2323] Overfull \hbox (72.78088pt too wide) in paragraph at lines 967--967 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2324] Underfull \hbox (badness 3612) in paragraph at lines 1054--1057 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10 re-turns the per-mu-ta-tion [2325] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol.1}) has been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} [2326] [2327] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1301--1301 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2328] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1396--1396 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2329] Underfull \hbox (badness 2277) in paragraph at lines 1424--1427 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2330] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1498--1498 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1520--1520 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529 []\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[] [2331] Underfull \hbox (badness 10000) in paragraph at lines 1565--1572 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 4673) in paragraph at lines 1565--1572 []\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1600--1604 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2332] Underfull \hbox (badness 1221) in paragraph at lines 1616--1622 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][][]\T1/pcr/m/n/10 matrix[][][][]\T1/ptm/m/n/10 . Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10 and pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums.1 }) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.1658 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.1681 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.1694 \aliasA{rowSums}{colSums}{rowSums} [2333 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans, diagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums,d iagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' ] Underfull \hbox (badness 2922) in paragraph at lines 1750--1754 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1750--1754 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 1761--1764 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2334] [2335] Underfull \hbox (badness 3547) in paragraph at lines 1915--1918 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2336] [2337] [2338] [2339] [2340] [2341] Underfull \hbox (badness 7379) in paragraph at lines 2445--2447 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2342] [2343] [2344] Underfull \hbox (badness 10000) in paragraph at lines 2696--2699 []\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 , and typ-i-cally co-er-cion Underfull \hbox (badness 4846) in paragraph at lines 2721--2725 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2726--2730 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 dgCMatrix[][][] []\T1/ptm/m/n/10 or the su-per-classes [][][]\T1/pcr/m/n/10 dsparseMatrix[][][] []\T1/ptm/m/n/10 a nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ; [2345] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2780--2780 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2789--2791 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2793--2798 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 .symDiagonal []\T1/ptm/m/n/10 ([]\T1/pcr/ m/n/10 .trDiagonal[]\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2793--2798 [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 (or [][][]\T1/pcr/m /n/10 triangularMatrix[][][][]\T1/ptm/m/n/10 ) will have slot []\T1/pcr/m/n/10 uplo [2346] Underfull \hbox (badness 1097) in paragraph at lines 2816--2819 []\T1/pcr/m/n/10 Diagonal() []\T1/ptm/m/n/10 re-turns an ob-ject of class [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 or [][][]\T1/pcr/m/n/10 ldiMat rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2829--2834 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of [2347] Underfull \hbox (badness 3646) in paragraph at lines 2925--2928 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 2960--2964 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 2969--2975 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2348 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,di agonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.2975 ] Underfull \hbox (badness 10000) in paragraph at lines 2976--2980 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 2986--2990 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 3166--3168 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2351] [2352] Overfull \hbox (69.18036pt too wide) in paragraph at lines 3312--3312 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2353] Underfull \hbox (badness 2469) in paragraph at lines 3422--3425 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via Underfull \hbox (badness 10000) in paragraph at lines 3445--3450 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 3445--3450 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 3451--3460 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 3451--3460 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", [2354] [2355] Underfull \hbox (badness 10000) in paragraph at lines 3599--3603 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 3599--3603 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , [2356] Underfull \hbox (badness 1571) in paragraph at lines 3649--3652 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 3813--3818 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3813--3818 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 3825--3828 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2359] Underfull \hbox (badness 10000) in paragraph at lines 3896--3898 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 3938--3941 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3983--3983 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2362] Underfull \hbox (badness 3635) in paragraph at lines 4179--4183 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 4188--4191 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; [2363] Underfull \hbox (badness 10000) in paragraph at lines 4193--4197 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2364] [2365 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,dt rMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.4347 \item[\code{diag}:] Object of class \code{"character"}. Must be] Underfull \hbox (badness 2065) in paragraph at lines 4378--4382 []\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie ntely use a ``for-ward-solve'' or [2366] [2367] [2368] [2369] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe ll-Boeing/counterx/counterx.html[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4642--4642 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4649--4649 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4659--4659 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2370] [2371] [2372] [2373] Underfull \hbox (badness 10000) in paragraph at lines 4937--4942 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2374] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 5020--5020 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5024--5024 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2375] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5031--5031 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2376] [2377] Underfull \hbox (badness 4120) in paragraph at lines 5170--5173 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5214--5214 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5230--5230 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2379] Underfull \hbox (badness 1817) in paragraph at lines 5326--5335 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing []\T1/pcr/m/n/10 drop=FALSE[]\T1/ptm/m/n/10 ) stays wit hin the Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 7081) in paragraph at lines 5370--5373 []\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10 : This en-ables typ-i-cal Underfull \hbox (badness 4556) in paragraph at lines 5376--5383 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T he list must have two [2380] Underfull \hbox (badness 3302) in paragraph at lines 5401--5404 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : re-turn the kro-necker [2381] [2382] [2383] [2384] Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8 * tol, checkDN = TRUE, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN = TRUE, ...)[] [2385] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2386] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5962--5962 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2387] [2388] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6043--6043 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6050--6050 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2389] [2390] Underfull \hbox (badness 1062) in paragraph at lines 6204--6207 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 6233--6236 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2391] Underfull \hbox (badness 2635) in paragraph at lines 6402--6407 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6402--6407 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class [2392] Underfull \hbox (badness 10000) in paragraph at lines 6410--6413 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6566--6576 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6566--6576 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2393] Underfull \hbox (badness 3179) in paragraph at lines 6648--6651 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2394] Underfull \hbox (badness 10000) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2395] Underfull \hbox (badness 10000) in paragraph at lines 6830--6833 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2396] Underfull \hbox (badness 1430) in paragraph at lines 6904--6910 \T1/ptm/m/n/10 should be sig-nalled when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar. When []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar, []\T1/pcr/ m/n/10 lu(x, [2397] Underfull \hbox (badness 1675) in paragraph at lines 6929--6932 []\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met h-ods for dif-fer-ent types of ma-tri-ces. Use Overfull \hbox (9.78043pt too wide) in paragraph at lines 7001--7001 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2398] [2399] Underfull \hbox (badness 10000) in paragraph at lines 7141--7144 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , [2400] Underfull \hbox (badness 1490) in paragraph at lines 7163--7165 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2401] [2402] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.7358 \aliasA{det}{Matrix-class}{det} [2403 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,Ma trix,denseMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7439 \item[dim] \code{signature(x = "Matrix")}: extract matrix dimensions] Underfull \hbox (badness 1337) in paragraph at lines 7446--7449 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 7459--7462 Underfull \hbox (badness 10000) in paragraph at lines 7469--7471 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2404] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.7629 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.7723 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7816--7822 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2405] Underfull \hbox (badness 10000) in paragraph at lines 7889--7892 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 7897--7901 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 7907--7908 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2406] [2407] [2408] Underfull \hbox (badness 1062) in paragraph at lines 8087--8090 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 8121--8124 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2409] Underfull \hbox (badness 3312) in paragraph at lines 8177--8179 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2410] [2411] Overfull \hbox (85.38034pt too wide) in paragraph at lines 8279--8279 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8319--8319 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2412] Underfull \hbox (badness 2635) in paragraph at lines 8386--8391 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8386--8391 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8394--8397 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2413] Underfull \hbox (badness 2521) in paragraph at lines 8464--8470 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2414] Underfull \hbox (badness 1867) in paragraph at lines 8586--8588 []\T1/ptm/m/n/10 fast sim- [2415] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} [2416] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8720--8720 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8721--8721 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8867--8877 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2417] Underfull \hbox (badness 3179) in paragraph at lines 8938--8941 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2418] Underfull \hbox (badness 10000) in paragraph at lines 9036--9039 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2419] Underfull \hbox (badness 10000) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2420] [2421] Underfull \hbox (badness 10000) in paragraph at lines 9213--9214 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9214--9215 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9215--9216 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9216--9217 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9217--9218 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9218--9219 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9219--9220 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9220--9221 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9221--9222 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9222--9223 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9223--9224 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9224--9225 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9225--9226 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9226--9227 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9227--9228 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9228--9229 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9229--9230 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = [2422] Underfull \hbox (badness 10000) in paragraph at lines 9230--9231 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9231--9232 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9232--9233 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9233--9234 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9234--9235 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9235--9236 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9236--9237 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9237--9238 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9238--9239 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9239--9240 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9240--9241 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9241--9242 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9242--9243 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = [2423] Underfull \hbox (badness 10000) in paragraph at lines 9332--9334 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 5008) in paragraph at lines 9334--9337 []\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 : This is en-ables typ-i-cal [2424] Underfull \hbox (badness 4954) in paragraph at lines 9340--9347 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional Underfull \hbox (badness 1558) in paragraph at lines 9350--9354 []\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10 : Since per-mu-ta- Underfull \hbox (badness 3229) in paragraph at lines 9354--9358 \T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c es. See [2425] Overfull \hbox (36.78088pt too wide) in paragraph at lines 9433--9433 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9436--9436 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9438--9438 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9442--9442 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9443--9443 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] [2426] Underfull \hbox (badness 3989) in paragraph at lines 9468--9478 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9468--9478 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2427] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.9569 \aliasA{qr}{qr-methods}{qr} [2428] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9641--9641 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9652--9652 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] [2429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9671--9671 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9679--9679 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2430] Underfull \hbox (badness 2005) in paragraph at lines 9736--9742 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 9753--9756 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2431] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9852--9852 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9868--9868 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9874--9874 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9875--9875 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2432] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9893 ... the Reciprocal Condition Number}{rcond} [2433] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10011--10011 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2434] [2435] [2436] Underfull \hbox (badness 2150) in paragraph at lines 10202--10210 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2437] [2438] Underfull \hbox (badness 1558) in paragraph at lines 10342--10345 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n /10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional [2439] Overfull \hbox (52.98038pt too wide) in paragraph at lines 10404--10404 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10408--10408 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.10470 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (48.78088pt too wide) in paragraph at lines 10572--10572 []\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always preferred to [2441] Overfull \hbox (90.78088pt too wide) in paragraph at lines 10584--10584 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1616) in paragraph at lines 10619--10631 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 10636--10639 []\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p cr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10645--10652 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( [2442] Underfull \hbox (badness 10000) in paragraph at lines 10658--10668 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( Underfull \hbox (badness 3657) in paragraph at lines 10658--10668 \T1/pcr/m/n/10 sparse=FALSE, tol = .Machine$double.eps ) []\T1/ptm/m/n/10 : Che cks if []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10685--10689 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10692--10694 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10715--10716 []\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b, Underfull \hbox (badness 10000) in paragraph at lines 10721--10723 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10725--10726 []\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10733--10736 [][][]\T1/pcr/m/n/10 solve[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lu[][][ ][]\T1/ptm/m/n/10 , and class doc-u-men-ta-tions [][][]\T1/pcr/m/n/10 CHMfactor [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 , and [2443] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10751--10751 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10755--10755 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] Underfull \hbox (badness 10000) in paragraph at lines 10776--10779 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 10793--10793 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10795--10795 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] [2444] Underfull \hbox (badness 1648) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10812--10815 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10812--10815 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10823--10827 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10823--10827 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 1668) in paragraph at lines 10838--10843 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10918--10918 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10919--10919 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10920--10920 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2446] [2447] [2448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11107--11107 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Underfull \hbox (badness 1668) in paragraph at lines 11149--11154 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2449] Underfull \hbox (badness 10000) in paragraph at lines 11234--11237 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and [2450] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11246--11246 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11250--11250 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11251--11251 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11256--11256 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11259--11259 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11282--11282 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Underfull \vbox (badness 10000) has occurred while \output is active [2451] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11309--11309 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 11311--11311 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11313--11313 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2452] Underfull \hbox (badness 6842) in paragraph at lines 11411--11414 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 11446--11450 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2453] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2454] Underfull \hbox (badness 10000) in paragraph at lines 11616--11618 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\ T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11644--11644 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2455] Underfull \hbox (badness 5036) in paragraph at lines 11672--11674 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2456] Underfull \hbox (badness 2970) in paragraph at lines 11783--11789 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11783--11789 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11834--11837 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2457] Underfull \hbox (badness 10000) in paragraph at lines 11874--11879 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11889--11891 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2458] Underfull \vbox (badness 10000) has occurred while \output is active [2459] Underfull \hbox (badness 2310) in paragraph at lines 12014--12020 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2460] [2461] Underfull \hbox (badness 6188) in paragraph at lines 12105--12107 []\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm /m/n/10 : and many Underfull \hbox (badness 2591) in paragraph at lines 12131--12136 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2462] Underfull \hbox (badness 2057) in paragraph at lines 12207--12209 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2463] Underfull \hbox (badness 6641) in paragraph at lines 12294--12297 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2464] Underfull \hbox (badness 5133) in paragraph at lines 12338--12342 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 12338--12342 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2465] Underfull \hbox (badness 7649) in paragraph at lines 12445--12447 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2466] [2467] Underfull \hbox (badness 10000) in paragraph at lines 12563--12565 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2468] Underfull \hbox (badness 1668) in paragraph at lines 12692--12695 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2469] Underfull \hbox (badness 7362) in paragraph at lines 12743--12745 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2470] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12781--12781 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12782--12782 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2471] [2472] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12936--12936 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/ x))$modulus))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12941--12941 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2473] Underfull \hbox (badness 6910) in paragraph at lines 13147--13149 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2474] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. [2475] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2476] [2477]) (./boot-pkg.tex [2478] Chapter 18. [2479] [2480] [2481] [2482] [2483] [2484] [2485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2486] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2487] [2488] [2489] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2491] [2492] [2493] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2494] [2495] [2496] [2497] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2498] [2499] [2500] [2501] [2502] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2503] [2504] [2505] Underfull \vbox (badness 10000) has occurred while \output is active [2506] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2507] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2508] [2509] [2510] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2511] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2512] [2513] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2514] [2515] [2516] [2517] [2518] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2519] [2520] [2521] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2522] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2523] [2524] [2525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2526] [2527] [2528] [2529] [2530] [2531] [2532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2533] [2534] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2535] [2536] [2537] [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2550] [2551] [2552] [2553] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2563] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2564] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2565] [2566] [2567] [2568] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2569] [2570] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2571] [2572] [2573] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2574] [2575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2576] [2577] [2578] [2579] [2580] [2581] [2582] [2583]) (./class-pkg.tex [2584] Chapter 19. [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600]) (./cluster-pkg.tex Chapter 20. [2601] [2602] [2603] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2604] [2605] [2606] [2607] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2608] [2609] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2610] Underfull \hbox (badness 3078) in paragraph at lines 691--694 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2611] [2612] Underfull \hbox (badness 2941) in paragraph at lines 791--794 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 881--883 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2614] Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2615] Underfull \hbox (badness 4872) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1208--1212 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2619] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2620] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1477--1480 Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1528--1528 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2623] Underfull \hbox (badness 5741) in paragraph at lines 1568--1571 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2624] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2625] Underfull \hbox (badness 1552) in paragraph at lines 1686--1688 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1699--1703 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1699--1703 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2626] Underfull \hbox (badness 1540) in paragraph at lines 1775--1783 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2628] [2629] [2630] [2631] [2632] Underfull \hbox (badness 10000) in paragraph at lines 2207--2210 Underfull \hbox (badness 3179) in paragraph at lines 2221--2227 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2633] [2634] Underfull \hbox (badness 10000) in paragraph at lines 2379--2382 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2635] Underfull \hbox (badness 1292) in paragraph at lines 2447--2450 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2636] Underfull \hbox (badness 6675) in paragraph at lines 2456--2458 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2479--2482 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2637] [2638] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2639] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2640] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2641] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2642] [2643] [2644] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2645] [2646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2647] [2648] [2649] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2650] Underfull \hbox (badness 10000) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2651] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2652] [2653] [2654] Underfull \hbox (badness 10000) in paragraph at lines 3671--3674 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3671--3674 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2655] Underfull \hbox (badness 10000) in paragraph at lines 3734--3739 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2656] Underfull \hbox (badness 1748) in paragraph at lines 3796--3801 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3808--3811 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2657] [2658] [2659] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2661] Underfull \hbox (badness 2035) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2662] [2663] [2664] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2665] [2666] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4435--4435 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4437--4437 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4440--4440 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4442--4442 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2667] [2668] [2669] [2670] [2671] [2672] [2673] Underfull \hbox (badness 10000) in paragraph at lines 4823--4829 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4839--4841 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2674] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2675]) (./codetools-pkg.tex [2676] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2677] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2678] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2679] [2680] [2681]) (./foreign-pkg.tex [2682] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2683] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2684] [2685] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2686] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2687] [2688] [2689] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2691] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 568--574 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2693] Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2694] [2695] Underfull \hbox (badness 10000) in paragraph at lines 812--813 Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2696] Underfull \hbox (badness 10000) in paragraph at lines 869--873 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 869--873 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2697] Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2698] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2699] [2700] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2703] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2704]) (./lattice-pkg.tex Chapter 23. [2705] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2706] [2707] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2708] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2709] [2710] [2711] [2712] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2713] [2714] [2715] [2716] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2717] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2718] [2719] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2720] [2721] [2722] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2723] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to [2726] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2727] [2728] [2729] [2730] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2731] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2732] [2733] [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2740] [2741] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2742] Underfull \hbox (badness 6758) in paragraph at lines 2919--2923 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2919--2923 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2925--2927 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 2977--2983 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from [2743] Underfull \hbox (badness 2486) in paragraph at lines 3001--3005 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2744] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3104--3104 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3106--3106 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] [2745] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3117--3117 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2746] Underfull \hbox (badness 2913) in paragraph at lines 3187--3194 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3187--3194 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2747] [2748] [2749] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3475 \aliasA{parallel}{B\_08\_splom}{parallel} [2750] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2751] [2752] [2753] [2754] [2755] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2756] [2757] Underfull \hbox (badness 2277) in paragraph at lines 3970--3974 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 3970--3974 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2758] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in [2759] Underfull \hbox (badness 3219) in paragraph at lines 4136--4138 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4153--4157 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2760] Underfull \hbox (badness 5161) in paragraph at lines 4218--4222 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4218--4222 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2761] [2762] Underfull \hbox (badness 1067) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4361--4364 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4364--4366 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2763] [2764] [2765] [2766] [2767] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2768] [2769] Underfull \vbox (badness 1092) has occurred while \output is active [2770] Underfull \hbox (badness 10000) in paragraph at lines 4955--4958 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2771] [2772] Underfull \hbox (badness 1442) in paragraph at lines 5087--5090 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2773] [2774] [2775] [2776] [2777] Underfull \hbox (badness 3646) in paragraph at lines 5426--5429 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5456--5456 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5457--5457 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2778] Underfull \hbox (badness 10000) in paragraph at lines 5545--5548 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5545--5548 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2779] Underfull \hbox (badness 1635) in paragraph at lines 5571--5576 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2780] [2781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5736--5736 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5737--5737 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5740--5740 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5743--5743 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5745--5745 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5751--5751 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5752--5752 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5753--5753 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] [2782] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5754--5754 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5755--5755 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5771--5773 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5782--5784 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2783] Underfull \hbox (badness 2538) in paragraph at lines 5907--5911 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2784] [2785] Underfull \hbox (badness 10000) in paragraph at lines 6071--6075 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2786] Underfull \vbox (badness 10000) has occurred while \output is active [2787] [2788] Underfull \hbox (badness 4242) in paragraph at lines 6218--6223 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2789] [2790] Underfull \hbox (badness 3601) in paragraph at lines 6334--6339 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6334--6339 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2791] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6421--6421 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2792] [2793] Underfull \hbox (badness 1888) in paragraph at lines 6553--6560 []\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1 0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and [2794] Underfull \hbox (badness 10000) in paragraph at lines 6610--6613 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6610--6613 []\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn a valid color. The [2795] [2796] [2797] [2798] [2799] Underfull \hbox (badness 1320) in paragraph at lines 7016--7023 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7016--7023 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2800] [2801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7086--7086 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] Underfull \hbox (badness 10000) in paragraph at lines 7116--7120 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7116--7120 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2802] [2803] Underfull \hbox (badness 10000) in paragraph at lines 7221--7224 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by [2804] [2805] Underfull \hbox (badness 2012) in paragraph at lines 7387--7390 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7433--7433 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2807] [2808] Underfull \hbox (badness 2644) in paragraph at lines 7574--7578 []\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o n to Underfull \hbox (badness 2772) in paragraph at lines 7587--7590 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2809] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7657--7657 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2810] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7728--7728 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7733--7733 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2811] [2812] [2813] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7918--7918 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] Underfull \hbox (badness 1436) in paragraph at lines 7973--7979 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2822] [2823] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8706--8706 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8707--8707 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2824] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 8738--8741 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2825] Underfull \hbox (badness 1515) in paragraph at lines 8814--8818 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2826] [2827] Underfull \hbox (badness 6316) in paragraph at lines 8920--8925 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2828] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9030--9030 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2829] [2830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9169--9169 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2831] Underfull \hbox (badness 1028) in paragraph at lines 9228--9232 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2832] [2833] [2834] [2835] [2836] [2837] [2838] Underfull \hbox (badness 7238) in paragraph at lines 9692--9696 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9692--9696 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2839] [2840] [2841] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma} [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 10085--10090 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10158--10158 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2845] [2846]) (./mgcv-pkg.tex Chapter 24. [2847] [2848] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2849] Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 184--188 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 209--214 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2850] [2851] [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2854] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2855] [2856] [2857] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2858] [2859] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2860] [2861] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2862] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2873] [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2875] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2876] [2877] [2878] [2879] [2880] [2881] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1937--1937 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2882] [2883] [2884] [2885] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2162--2162 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2886] [2887] [2888] [2889] [2890] [2891] [2892] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2579--2582 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2592--2596 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2618--2624 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2893] [2894] [2895] Underfull \hbox (badness 1043) in paragraph at lines 2787--2793 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2896] [2897] Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2898] Underfull \vbox (badness 10000) has occurred while \output is active [2899] Underfull \vbox (badness 10000) has occurred while \output is active [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] [2902] [2903] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3240--3240 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, maxit = 200, [2904] [2905] [2906] [2907] [2908] [2909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3581--3581 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3584--3584 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 5189) in paragraph at lines 4063--4067 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2918] [2919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4180--4180 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2920] [2921] [2922] Underfull \hbox (badness 1184) in paragraph at lines 4350--4354 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2923] [2924] [2925] [2926] [2927] [2928] [2929] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4796--4796 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2930] [2931] [2932] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2933] [2934] Underfull \hbox (badness 1142) in paragraph at lines 5073--5077 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2935] Underfull \hbox (badness 10000) in paragraph at lines 5145--5154 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2936] [2937] Underfull \hbox (badness 5970) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2938] Underfull \vbox (badness 10000) has occurred while \output is active [2939] [2940] [2941] [2942] Underfull \hbox (badness 1577) in paragraph at lines 5614--5617 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5621--5622 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 6708) in paragraph at lines 6010--6011 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [2950] [2951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 6059--6059 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6084--6084 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6113--6113 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2953] [2954] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6235--6235 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2955] [2956] [2957] [2958] [2959] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6572--6572 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2960] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6574--6574 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6595--6599 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2961] [2962] [2963] Underfull \vbox (badness 10000) has occurred while \output is active [2964] [2965] [2966] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6914--6914 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Underfull \vbox (badness 10000) has occurred while \output is active [2972] [2973] [2974] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7346--7346 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7373--7373 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2975] [2976] [2977] [2978] [2979] [2980] [2981] [2982] [2983] Underfull \hbox (badness 1242) in paragraph at lines 7916--7917 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8003--8003 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2986] [2987] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8085--8085 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Underfull \vbox (badness 10000) has occurred while \output is active [3006] [3007] Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3008] Underfull \hbox (badness 10000) in paragraph at lines 9366--9369 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9366--9369 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3009] [3010] [3011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9587--9587 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9590--9590 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3012] [3013] [3014] Underfull \hbox (badness 1629) in paragraph at lines 9748--9753 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3015] [3016] [3017] [3018] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9960--9960 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 9997--10001 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3019] [3020] [3021] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10130--10130 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3022] [3023] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10291--10291 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3024] Underfull \vbox (badness 10000) has occurred while \output is active [3025] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10411--10411 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [3026] Underfull \hbox (badness 1205) in paragraph at lines 10449--10451 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10449--10451 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10455--10460 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3027] Underfull \hbox (badness 1205) in paragraph at lines 10539--10541 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10539--10541 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3028] Underfull \hbox (badness 10000) in paragraph at lines 10608--10611 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10608--10611 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3029] [3030] [3031] Underfull \hbox (badness 1253) in paragraph at lines 10738--10740 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 1946) in paragraph at lines 10991--10998 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 10999--11002 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10999--11002 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11065--11065 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11075--11075 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3038] Underfull \hbox (badness 10000) in paragraph at lines 11106--11109 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3039] [3040] [3041] [3042] [3043] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11408--11408 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3044] [3045] [3046] [3047] [3048] [3049] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11782--11782 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11796--11796 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3050] [3051] Underfull \hbox (badness 3861) in paragraph at lines 11898--11901 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 11907--11907 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3052] Underfull \hbox (badness 10000) in paragraph at lines 11924--11928 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 11964--11968 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12108--12108 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12119--12124 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3056] Underfull \hbox (badness 1803) in paragraph at lines 12196--12200 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12208--12220 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3057] Underfull \hbox (badness 2401) in paragraph at lines 12225--12229 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12225--12229 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3058] [3059] [3060] Underfull \hbox (badness 6876) in paragraph at lines 12420--12426 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3061] Underfull \hbox (badness 10000) in paragraph at lines 12461--12462 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 12579--12580 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3064] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12633--12633 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12645--12645 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3065] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12657--12657 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12662--12662 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12668--12668 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12669--12669 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3066] Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3067] [3068] Underfull \hbox (badness 10000) in paragraph at lines 12868--12869 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3069] [3070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12949--12949 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12950--12950 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3071] [3072] Underfull \hbox (badness 10000) in paragraph at lines 13103--13104 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3073] [3074] [3075] [3076] [3077] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13353--13353 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3078] Underfull \hbox (badness 10000) in paragraph at lines 13414--13416 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3079] [3080] Underfull \hbox (badness 10000) in paragraph at lines 13573--13576 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13573--13576 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13573--13576 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3081] [3082] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13659--13659 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3083] Underfull \hbox (badness 10000) in paragraph at lines 13704--13710 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13704--13710 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3084] [3085] [3086] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13918--13918 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3087] Underfull \vbox (badness 10000) has occurred while \output is active [3088] Underfull \hbox (badness 10000) in paragraph at lines 14021--14029 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14047--14048 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3089] [3090] [3091] Underfull \hbox (badness 7613) in paragraph at lines 14192--14195 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3092] Underfull \hbox (badness 1546) in paragraph at lines 14213--14214 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14259--14259 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3093] [3094] [3095] Underfull \hbox (badness 3396) in paragraph at lines 14405--14408 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14450--14452 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 10000) in paragraph at lines 14741--14743 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][][]\T1/ptm/m/n/10 ,[ ][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 p.spline[][ ][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 2158) in paragraph at lines 15061--15061 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3107] [3108] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3109] [3110] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3111] [3112] Underfull \hbox (badness 4846) in paragraph at lines 15405--15408 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3133] Underfull \hbox (badness 1715) in paragraph at lines 16645--16646 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3134] [3135] [3136] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 16859--16860 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16859--16860 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3138] Underfull \vbox (badness 10000) has occurred while \output is active [3139] [3140] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3141] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3142] [3143] [3144]) (./nlme-pkg.tex Chapter 25. [3145] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3146] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3147] [3148] [3149] [3150] [3151] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3152] [3153] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3162] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3170] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3171] [3172] [3173] [3174] [3175] Underfull \hbox (badness 2042) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3176] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3177] Underfull \hbox (badness 1132) in paragraph at lines 2147--2149 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3178] [3179] Underfull \hbox (badness 4168) in paragraph at lines 2258--2264 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 2849--2853 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3189] [3190] [3191] [3192] [3193] [3194 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3195] [3196] [3197] [3198] [3199] [3200] Underfull \hbox (badness 6493) in paragraph at lines 3585--3593 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3225] [3226] [3227] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 5597--5600 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3232] [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 2799) in paragraph at lines 6103--6109 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3241] Underfull \hbox (badness 7133) in paragraph at lines 6164--6168 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3242] Underfull \hbox (badness 2057) in paragraph at lines 6253--6264 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3243] Underfull \hbox (badness 10000) in paragraph at lines 6317--6319 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3244] [3245] [3246] [3247] Underfull \hbox (badness 7133) in paragraph at lines 6566--6570 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3248] Underfull \hbox (badness 10000) in paragraph at lines 6665--6671 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3249] Underfull \hbox (badness 10000) in paragraph at lines 6730--6732 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3250] [3251] [3252] [3253] Underfull \hbox (badness 10000) in paragraph at lines 7002--7009 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7025--7025 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7047--7049 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3255] [3256] [3257] Underfull \hbox (badness 10000) in paragraph at lines 7262--7267 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3258] [3259] [3260] Underfull \hbox (badness 1997) in paragraph at lines 7414--7422 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7414--7422 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7437--7440 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3261] [3262] [3263] Underfull \hbox (badness 3354) in paragraph at lines 7653--7655 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8213--8213 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] [3272] Underfull \hbox (badness 1642) in paragraph at lines 8222--8244 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3273] [3274] [3275] [3276] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8535--8537 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3277] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8579--8579 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] Underfull \hbox (badness 10000) in paragraph at lines 9336--9343 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3290] [3291] [3292] [3293] [3294] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3295] Underfull \hbox (badness 10000) in paragraph at lines 9718--9721 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9762--9765 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9762--9765 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304] [3305] [3306] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3307] Underfull \hbox (badness 1596) in paragraph at lines 10471--10497 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3308] [3309] [3310] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3311] [3312] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10809--10814 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] [3313] Underfull \hbox (badness 6961) in paragraph at lines 10831--10835 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= Underfull \hbox (badness 10000) in paragraph at lines 10850--10852 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3314] [3315] [3316] [3317] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3318] [3319] [3320] [3321] [3322] [3323] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11532--11532 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3324] [3325] [3326] [3327] [3328] [3329] Underfull \hbox (badness 6268) in paragraph at lines 11919--11929 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3330] [3331] [3332] [3333] Underfull \hbox (badness 10000) in paragraph at lines 12180--12186 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3334] [3335] [3336] [3337] [3338] Underfull \hbox (badness 6876) in paragraph at lines 12502--12504 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3339] [3340] Underfull \hbox (badness 2452) in paragraph at lines 12658--12665 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3341] Underfull \hbox (badness 10000) in paragraph at lines 12723--12729 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3351] [3352] [3353] [3354] [3355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13704--13707 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3357] Underfull \hbox (badness 1838) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3358] Underfull \hbox (badness 10000) in paragraph at lines 13811--13814 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13811--13814 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3359] Underfull \hbox (badness 10000) in paragraph at lines 13919--13922 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3360] [3361] Underfull \hbox (badness 10000) in paragraph at lines 14013--14015 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3362] [3363] [3364] [3365] [3366] [3367] [3368] [3369] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] Underfull \hbox (badness 2126) in paragraph at lines 15830--15834 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3389] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3390] Underfull \hbox (badness 1009) in paragraph at lines 15888--15897 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3391] [3392] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3393] [3394] [3395] [3396] [3397] Underfull \hbox (badness 10000) in paragraph at lines 16370--16376 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3398] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3399] [3400] [3401] [3402] [3403] [3404] [3405] Underfull \hbox (badness 1728) in paragraph at lines 16889--16892 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3406] [3407] [3408] [3409] [3410] Underfull \hbox (badness 1803) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3411] Underfull \hbox (badness 10000) in paragraph at lines 17294--17295 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17295--17296 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3412] [3413] [3414] [3415] Underfull \hbox (badness 10000) in paragraph at lines 17545--17553 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3416] [3417] [3418] [3419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3420] [3421] [3422] [3423] [3424] [3425] Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3426] Underfull \hbox (badness 3579) in paragraph at lines 18293--18298 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3427] Underfull \hbox (badness 3579) in paragraph at lines 18357--18362 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3428] Underfull \hbox (badness 3579) in paragraph at lines 18420--18425 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3429] Underfull \hbox (badness 1577) in paragraph at lines 18481--18483 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18483--18488 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3430] Underfull \hbox (badness 3579) in paragraph at lines 18546--18551 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3431] Underfull \hbox (badness 3579) in paragraph at lines 18618--18623 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3432] [3433] Underfull \hbox (badness 1009) in paragraph at lines 18764--18773 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3434] [3435] Underfull \hbox (badness 1009) in paragraph at lines 18896--18905 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3445] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3446] [3447] [3448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3450] [3451] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3452]) (./rpart-pkg.tex Chapter 27. [3453] [3454] [3455] [3456] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3457] [3458] [3459] [3460] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3461] [3462] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3463] [3464] [3465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3466] [3467] [3468] [3469] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3470] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3471] [3472] [3473] [3474] [3475] [3476] [3477] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3478] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3479] [3480] [3481]) (./spatial-pkg.tex [3482] Chapter 28. [3483] [3484] [3485] [3486] [3487] [3488] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501]) (./survival-pkg.tex [3502] Chapter 29. [3503] [3504] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3505] [3506] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3507] [3508] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3510] Overfull \hbox (6.78088pt too wide) in paragraph at lines 524--524 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3511] [3512] [3513] Overfull \hbox (20.58041pt too wide) in paragraph at lines 769--769 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival [3514] Overfull \hbox (48.78088pt too wide) in paragraph at lines 792--792 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3515] [3516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3517] [3518] [3519] Underfull \hbox (badness 1097) in paragraph at lines 1106--1108 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3520] [3521] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1241--1241 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3522] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1308 ...erapy for Stage B/C colon cancer}{colon} [3523] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1407--1407 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1408--1408 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3524] [3525] [3526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1598--1598 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1647--1647 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3527] [3528] [3529] [3530] [3531] Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3532] Underfull \hbox (badness 3861) in paragraph at lines 2048--2052 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3533] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2103--2103 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3534] [3535] [3536] [3537] [3538] [3539] [3540] [3541] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3542] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2744--2744 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3543] [3544] [3545] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3546] [3547] [3548] [3549] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3317--3317 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3551] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3352--3352 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3366--3368 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3377--3377 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3552] [3553] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3554] [3555] Overfull \hbox (467.89665pt too wide) in alignment at lines 3652--3652 [] [] [3556] [3557] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3774--3774 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3558] [3559] [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3565] [3566] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4360--4360 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4365--4365 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3568] [3569] [3570] [3571] [3572] [3573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4786--4786 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3574] [3575] [3576] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5016--5016 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5142--5142 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5150--5150 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3579] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5236--5236 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3580] [3581] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3582] Underfull \hbox (badness 1852) in paragraph at lines 5386--5388 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3583] [3584] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3585] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5615--5615 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5627--5627 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5629--5629 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] [3586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5653--5653 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3587] [3588] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3589] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5941--5941 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5943--5943 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3590] [3591] [3592] [3593] [3594] [3595] [3596] [3597] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3598] [3599] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6642--6642 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] [3600] Underfull \hbox (badness 1043) in paragraph at lines 6654--6657 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6962--6962 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6963--6963 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3605] [3606] [3607] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7135--7135 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3608] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7216--7216 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7220--7220 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7224 ...ata from a soldering experiment}{solder} [3609] [3610] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7330--7330 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3611] [3612] [3613] [3614] [3615] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7694--7694 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7695--7695 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3616] [3617] [3618] [3619] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8013--8013 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3620] [3621] [3622] [3623] Underfull \hbox (badness 1253) in paragraph at lines 8302--8305 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3624] [3625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8432--8432 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3626] [3627] [3628] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8662--8662 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8680--8680 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3629] Underfull \hbox (badness 1038) in paragraph at lines 8722--8728 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8774--8774 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3632] [3633] [3634] Underfull \hbox (badness 10000) in paragraph at lines 9080--9085 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9100--9100 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9107--9107 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3635] [3636] [3637] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9321--9321 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3638] Underfull \hbox (badness 2653) in paragraph at lines 9454--9459 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3639] [3640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9594--9594 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3641] [3642] [3643] [3644] [3645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9979--9979 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3646] Underfull \hbox (badness 1354) in paragraph at lines 10020--10024 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3647] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10066--10066 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3648] [3649] Underfull \hbox (badness 2035) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10230--10237 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3650] [3651] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10320--10320 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3652] [3653] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10477--10477 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3654] [3655] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10609--10609 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10612--10612 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3656] [3657] [3658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10772--10772 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3659] [3660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10930--10930 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10931--10931 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10937--10937 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10939--10939 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3661] [3662] [3663] [3664] [3665] [3666] [3667] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11380--11380 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3668] [3669] [3670]) (./fullrefman.ind [3671] [3672] [3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683] [3684] [3685] [3686] [3687] [3688] [3689] [3690] [3691] [3692] [3693] [3694] [3695] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2605--2607 []| \T1/pcr/m/n/10 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%*%,ndenseMatrix,ndenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 5113--5115 []\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 5115--5117 []\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5117--5119 []\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5119--5121 []\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5127--5129 []\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 5135--5137 []\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5145--5147 []\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5147--5149 []\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5149--5151 []\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method [3717] Overfull \hbox (8.8567pt too wide) in paragraph at lines 5153--5155 []\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5155--5157 []\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5157--5159 []\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5163--5165 []\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5165--5167 []\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5167--5169 []\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5171--5173 []\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method Overfull 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Arith,numeric,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 5980--5982 []\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5990--5992 []\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 5992--5994 []\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5994--5996 []\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 5996--5998 []\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method [3723] Overfull \hbox (2.8567pt too wide) in paragraph at lines 6278--6280 []\T1/pcr/m/n/10 as.logical,diagonalMatrix-method [3724] Overfull \hbox (2.8567pt too wide) in paragraph at lines 6360--6362 []\T1/pcr/m/n/10 as.numeric,diagonalMatrix-method [3725] Overfull \hbox (32.8567pt too wide) in paragraph at lines 6526--6528 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [3726] Overfull \hbox (46.01662pt too wide) in paragraph at lines 6696--6698 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3727] [3728] [3729] Overfull \hbox (26.8567pt too wide) in paragraph at lines 7352--7354 []\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7354--7356 []\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7356--7358 []\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7358--7360 []\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7362--7364 []\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7364--7366 []\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7366--7368 []\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7368--7370 []\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7370--7372 []\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7372--7374 []\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7378--7380 []\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7382--7384 []\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7392--7394 []\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7396--7398 []\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7398--7400 []\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7400--7402 []\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7402--7404 []\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3730] [3731] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7660--7662 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3732] [3733] [3734] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8168--8170 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8170--8172 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8172--8174 []\T1/pcr/m/n/10 coerce,CHMfactor,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8176--8178 []\T1/pcr/m/n/10 coerce,CHMfactor,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8182--8184 []\T1/pcr/m/n/10 coerce,CHMfactor,RsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8184--8186 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8186--8188 []\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8188--8190 []\T1/pcr/m/n/10 coerce,CHMfactor,TsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8190--8192 []\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8192--8194 []\T1/pcr/m/n/10 coerce,CsparseMatrix,generalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8194--8196 []\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8196--8198 []\T1/pcr/m/n/10 coerce,CsparseMatrix,packedMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8198--8200 []\T1/pcr/m/n/10 coerce,CsparseMatrix,RsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8200--8202 []\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8202--8204 []\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8204--8206 []\T1/pcr/m/n/10 coerce,CsparseMatrix,unpackedMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8206--8208 []\T1/pcr/m/n/10 coerce,CsparseMatrix,vector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8208--8210 []\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8210--8212 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coerce,ddiMatrix,dtCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8228--8230 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtRMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8230--8232 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8232--8234 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8234--8236 []\T1/pcr/m/n/10 coerce,ddiMatrix,ldiMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8236--8238 []\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8238--8240 []\T1/pcr/m/n/10 coerce,denseMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8240--8242 []\T1/pcr/m/n/10 coerce,denseMatrix,dMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8242--8244 []\T1/pcr/m/n/10 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in paragraph at lines 10447--10449 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method [3755] Overfull \hbox (44.8567pt too wide) in paragraph at lines 10449--10451 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 10451--10453 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 10453--10455 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 10455--10457 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 10457--10459 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 10459--10461 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method Overfull \hbox (46.01662pt too wide) in paragraph at lines 10496--10498 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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wide) in paragraph at lines 10941--10943 []\T1/pcr/m/n/10 determinant,dsRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10943--10945 []\T1/pcr/m/n/10 determinant,dsTMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10945--10947 []\T1/pcr/m/n/10 determinant,dsyMatrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10947--10949 []\T1/pcr/m/n/10 determinant,Matrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10949--10951 []\T1/pcr/m/n/10 determinant,Matrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 determinant,MatrixFactorization,missing-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10951--10953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 10953--10955 []\T1/pcr/m/n/10 determinant,pMatrix,logical-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 10955--10957 []\T1/pcr/m/n/10 determinant,triangularMatrix,logical-method [3758] Overfull \hbox (10.01662pt too wide) in paragraph at lines 11229--11231 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3759] Overfull \hbox (8.8567pt too wide) in paragraph at lines 11297--11299 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11299--11301 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method [3760] Overfull \hbox (46.01662pt too wide) in paragraph at lines 11643--11645 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3761] [3762] Overfull \hbox (8.8567pt too wide) in paragraph at lines 11963--11965 []\T1/pcr/m/n/10 expand,MatrixFactorization-method [3763] [3764] Overfull \hbox (80.8567pt too wide) in paragraph at lines 12523--12525 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12525--12527 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 12527--12529 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 12529--12531 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 12531--12533 []\T1/pcr/m/n/10 forceSymmetric,indMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 12533--12535 []\T1/pcr/m/n/10 forceSymmetric,indMatrix,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12535--12537 []\T1/pcr/m/n/10 forceSymmetric,matrix,character-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12537--12539 []\T1/pcr/m/n/10 forceSymmetric,matrix,missing-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 12539--12541 []\T1/pcr/m/n/10 forceSymmetric,packedMatrix,character-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 12541--12543 []\T1/pcr/m/n/10 forceSymmetric,packedMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 12543--12545 []\T1/pcr/m/n/10 forceSymmetric,RsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12545--12547 []\T1/pcr/m/n/10 forceSymmetric,RsparseMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 12547--12549 []\T1/pcr/m/n/10 forceSymmetric,TsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12549--12551 []\T1/pcr/m/n/10 forceSymmetric,TsparseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 12551--12553 []\T1/pcr/m/n/10 forceSymmetric,unpackedMatrix,character-method [3765] Overfull \hbox (74.8567pt too wide) in paragraph at lines 12553--12555 []\T1/pcr/m/n/10 forceSymmetric,unpackedMatrix,missing-method [3766] [3767] [3768] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13498--13500 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3769] [3770] Overfull \hbox (20.8567pt too wide) in paragraph at lines 13866--13868 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [3771] [3772] [3773] [3774] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14669--14671 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14685--14687 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method [3775] [3776] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14873--14875 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14885--14887 []\T1/pcr/m/n/10 isDiagonal,unpackedMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14955--14957 []\T1/pcr/m/n/10 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kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15133--15135 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15135--15137 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15137--15139 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 15139--15141 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15141--15143 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15143--15145 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15145--15147 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15149--15151 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15151--15153 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 15153--15155 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 15155--15157 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method [3778] Overfull \hbox (74.8567pt too wide) in paragraph at lines 15157--15159 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3779] [3780] [3781] Overfull \hbox (50.8567pt too wide) in paragraph at lines 15979--15981 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15985--15987 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15987--15989 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15989--15991 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15991--15993 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15993--15995 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15999--16001 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16007--16009 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 16009--16011 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16011--16013 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16013--16015 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16015--16017 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16021--16023 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method [3782] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16031--16033 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16039--16041 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16041--16043 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16043--16045 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16045--16047 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 16047--16049 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3783] [3784] [3785] [3786] Overfull 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paragraph at lines 18135--18137 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3793] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18344--18346 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 18376--18378 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3794] [3795] [3796] [3797] [3798] [3799] Overfull \hbox (46.01662pt too wide) in paragraph at lines 19692--19694 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19695--19697 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19697--19699 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19699--19701 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19701--19703 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19703--19705 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19705--19707 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19707--19709 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19709--19711 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19711--19713 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19715--19717 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19717--19719 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19719--19721 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19721--19723 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19723--19725 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19725--19727 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19727--19729 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3800] [3801] Overfull \hbox (4.01662pt too wide) in paragraph at lines 20078--20080 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 20154--20156 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3802] [3803] [3804] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20629--20631 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20638--20640 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20640--20642 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20642--20644 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20644--20646 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20656--20658 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20666--20668 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method [3805] Overfull \hbox (32.8567pt too wide) in paragraph at lines 20681--20683 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20687--20689 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20811--20813 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3806] Overfull \hbox (26.8567pt too wide) in paragraph at lines 21032--21034 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21034--21036 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21036--21038 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21038--21040 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21042--21044 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21044--21046 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21046--21048 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 21048--21050 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method [3807] Overfull \hbox (56.8567pt too wide) in paragraph at lines 21050--21052 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21052--21054 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21054--21056 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21060--21062 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21064--21066 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21074--21076 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21078--21080 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 21080--21082 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 21082--21084 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21084--21086 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 21086--21088 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21116--21118 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21118--21120 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21120--21122 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21122--21124 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21124--21126 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21126--21128 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21128--21130 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21130--21132 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 21132--21134 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3808] [3809] [3810] [3811] [3812] Overfull \hbox (20.8567pt too wide) in paragraph at lines 22117--22119 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22121--22123 []\T1/pcr/m/n/10 Schur,generalMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22129--22131 []\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 22131--22133 []\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method [3813] [3814] Overfull \hbox (26.8567pt too wide) in paragraph at lines 22515--22517 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 22517--22519 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (32.8567pt too wide) in paragraph at lines 22521--22523 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22525--22527 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22535--22537 []\T1/pcr/m/n/10 show,refClassRepresentation-method [3815] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22784--22786 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3816] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22786--22788 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22789--22791 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22797--22798 []\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22806--22808 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22810--22811 []\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22811--22813 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (23.3567pt too wide) in paragraph at lines 22818--22822 []\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22823--22825 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22874--22876 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 22911--22913 []\T1/pcr/m/n/10 solve,CHMfactor,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22919--22921 []\T1/pcr/m/n/10 solve,CHMfactor,sparseMatrix-method [3817] Overfull \hbox (14.8567pt too wide) in paragraph at lines 22935--22937 []\T1/pcr/m/n/10 solve,dgCMatrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22943--22945 []\T1/pcr/m/n/10 solve,dgCMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22971--22973 []\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22979--22981 []\T1/pcr/m/n/10 solve,dsCMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22997--22999 []\T1/pcr/m/n/10 solve,dtCMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22999--23001 []\T1/pcr/m/n/10 solve,dtCMatrix,dgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23001--23003 []\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23003--23005 []\T1/pcr/m/n/10 solve,dtCMatrix,dsCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23005--23007 []\T1/pcr/m/n/10 solve,dtCMatrix,dspMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23007--23009 []\T1/pcr/m/n/10 solve,dtCMatrix,dsyMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23009--23011 []\T1/pcr/m/n/10 solve,dtCMatrix,dtCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23011--23013 []\T1/pcr/m/n/10 solve,dtCMatrix,dtpMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23013--23015 []\T1/pcr/m/n/10 solve,dtCMatrix,dtrMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 23021--23023 []\T1/pcr/m/n/10 solve,dtCMatrix,sparseMatrix-method [3818] Overfull \hbox (2.8567pt too wide) in paragraph at lines 23043--23045 []\T1/pcr/m/n/10 solve,Matrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23045--23047 []\T1/pcr/m/n/10 solve,matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 23047--23049 []\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 23049--23051 []\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 23051--23053 []\T1/pcr/m/n/10 solve,MatrixFactorization,sparseVector-method [3819] Overfull \hbox (52.01662pt too wide) in paragraph at lines 23219--23221 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3820] Overfull \hbox (44.8567pt too wide) in paragraph at lines 23670--23672 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends Overfull \hbox (44.8567pt too wide) in paragraph at lines 23672--23674 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results Overfull \hbox (44.8567pt too wide) in paragraph at lines 23674--23676 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings [3821] [3822] [3823] [3824] [3825] Overfull \hbox (20.8567pt too wide) in paragraph at lines 24509--24511 []\T1/pcr/m/n/10 tcrossprod,ANY,RsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 24511--24513 []\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24513--24515 []\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 24515--24517 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 24517--24519 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 24519--24521 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 24521--24523 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 24523--24525 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 24525--24527 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 24527--24529 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 24529--24531 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ddenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 24531--24533 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 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tcrossprod,dgeMatrix,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 24549--24551 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 24551--24553 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24553--24555 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24555--24557 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 24557--24559 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method Overfull \hbox (92.8567pt too wide) in paragraph at lines 24559--24561 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 24561--24563 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 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[3] [4] Underfull \hbox (badness 6741) in paragraph at lines 137--143 []\T1/ptm/m/n/10 the small-est pos-i-tive floating-point num-ber []\T1/pcr/m/n/ 10 x []\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 + x != 1[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 137--143 \T1/ptm/m/n/10 It equals []\T1/pcr/m/n/10 double.base ^ ulp.digits []\T1/ptm/m/ n/10 if ei-ther []\T1/pcr/m/n/10 double.base []\T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 137--143 \T1/ptm/m/n/10 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0; oth -er-wise, it is []\T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 4454) in paragraph at lines 143--151 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/pcr/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/pcr/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 1028) in paragraph at lines 143--151 \T1/ptm/m/n/10 equals []\T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 143--151 []\T1/ptm/m/n/10 is 2 or []\T1/pcr/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 143--151 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/p cr/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As [5] Underfull \hbox (badness 3009) in paragraph at lines 228--240 []\T1/pcr/m/n/10 *.exponent[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 *.min.exp[]\T1/p tm/m/n/10 , and []\T1/pcr/m/n/10 *.max.exp[]\T1/ptm/m/n/10 , com-puted en-tirel y anal-o-gously to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 371--374 [][][]\T1/pcr/m/n/10 R.version[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 Sys.info[][][] []\T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-l ar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 569--575 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, v alue = TRUE)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 638--638 []\T1/pcr/m/n/9 agrep("laysy", c("1 lazy", "1", "1 LAZY"), max.distance = 2, i gnore.case = TRUE)[] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 914--914 []\T1/pcr/m/n/9 all.equal(tan(d45), one, tolerance = 0, scale = 1+(-2:2)/1e9) # "absolute"[] [16] Overfull \hbox (4.38043pt too wide) in paragraph at lines 935--935 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [17] [18] [19] [20] [21] [22] [23] (/usr/share/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texmf-dist/tex/latex/base/ts1cmtt.fd) [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1581--1587 Underfull \hbox (badness 10000) in paragraph at lines 1594--1596 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [26] [27] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1773--1773 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [28] Underfull \hbox (badness 1303) in paragraph at lines 1802--1805 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [29] [30] [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2059--2059 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 2097--2099 []\T1/ptm/m/n/10 If [][][]\T1/pcr/m/n/10 is.object[][][](x) []\T1/ptm/m/n/10 is true and it has a [][][]\T1/pcr/m/n/10 class[][][] []\T1/ptm/m/n/10 for which an [33] [34] [35] [36] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2362--2362 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2404--2404 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] [39] Underfull \hbox (badness 1107) in paragraph at lines 2566--2568 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as []\T1/pcr/m/n /10 x[]\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2733--2733 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3406--3406 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3437--3437 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3438--3438 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3445--3445 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3449--3449 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [53] [54] [55] [56] [57] [58] Underfull \hbox (badness 10000) in paragraph at lines 3897--3899 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [59] [60] [61] [62] [63] [64] [65] [66] Underfull \hbox (badness 4927) in paragraph at lines 4395--4399 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4395--4399 \T1/ptm/m/n/10 of class []\T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" []\T1/ptm/m/n/10 o r [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4479--4479 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4555--4558 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [69] [70] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4718--4718 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [71] Underfull \hbox (badness 1199) in paragraph at lines 4749--4755 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4760--4763 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4936--4936 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] [77] Underfull \hbox (badness 2521) in paragraph at lines 5192--5194 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [78] [79] [80] [81] [82] [83] Underfull \hbox (badness 1270) in paragraph at lines 5615--5623 []\T1/ptm/m/n/10 When a generic func-tion []\T1/pcr/m/n/10 fun []\T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute []\T1/pcr/m/n/10 c("first", [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6184--6192 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [93] [94] [95] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6381--6381 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6383--6383 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6384--6384 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [96] [97] Underfull \hbox (badness 1635) in paragraph at lines 6586--6589 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class []\T1/pcr/m/n /10 interrupt []\T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6590--6593 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [98] Underfull \hbox (badness 1308) in paragraph at lines 6633--6641 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s []\T1/pcr/m/n/10 interactive[]\T1/ptm/m/n/10 . This should [99] [100] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6797--6797 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Underfull \hbox (badness 4505) in paragraph at lines 6849--6852 []\T1/ptm/m/n/10 character string, par-tially matched to []\T1/pcr/m/n/10 c("de fault", "internal", [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6986--6991 []\T1/pcr/m/n/10 file[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pipe[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fifo[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 url[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 bzfile[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 xzfile[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 unz[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 socketConnection[]\T1/ptm/m/n/10 , [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 7234--7236 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from Underfull \hbox (badness 3302) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/pcr/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/pcr/m/n/10 "r" []\T1/ptm/m/n /10 only. This Underfull \hbox (badness 6592) in paragraph at lines 7276--7283 \T1/ptm/m/n/10 reads the X11 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http s : / / specifications . freedesktop . Underfull \hbox (badness 1735) in paragraph at lines 7276--7283 []\T1/pcr/m/n/10 "X11_primary" []\T1/ptm/m/n/10 and the sec-ondary se-lec-tion as []\T1/pcr/m/n/10 "X11_secondary"[]\T1/ptm/m/n/10 . On most sys- [107] [108] Underfull \vbox (badness 10000) has occurred while \output is active [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7480--7480 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7814--7816 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [115] [116] [117] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7973--7973 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7975--7975 []\T1/pcr/m/n/9 ## curlGetHeaders("ftp://cran.r-project.org") ## ftp::// suppo rt is vanishing[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [122] Underfull \hbox (badness 10000) in paragraph at lines 8322--8332 []\T1/pcr/m/n/10 data.frame []\T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8322--8332 [][][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)[]\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [123] [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8490--8490 [] \T1/pcr/m/n/9 c = seq(as.Date("2004-01-01"), by = "week", l ength.out = 3),[] [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8842--8854 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") []\T1/ptm/m /n/10 may give []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 , and [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9291--9295 []\T1/pcr/m/n/10 .Defunct []\T1/ptm/m/n/10 is called from de-funct func-tions. Func-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9382--9382 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9384--9384 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9412--9412 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9413--9413 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] [139] Underfull \hbox (badness 5403) in paragraph at lines 9544--9546 []\T1/pcr/m/n/10 ..deparseOpts []\T1/ptm/m/n/10 is the [][][]\T1/pcr/m/n/10 cha racter[][][] []\T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used b y Underfull \hbox (badness 6063) in paragraph at lines 9563--9565 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][][]\T1/pcr/m /n/10 formula[][][][]\T1/ptm/m/n/10 s, with [140] [141] [142] Underfull \hbox (badness 1603) in paragraph at lines 9794--9797 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [143] [144] [145] [146] [147] [148] [149] [150] [151] Underfull \hbox (badness 1917) in paragraph at lines 10410--10415 []\T1/pcr/m/n/10 provideDimnames(x) []\T1/ptm/m/n/10 pro-vides []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has [152] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10465--10465 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10466--10466 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [153] [154] Underfull \hbox (badness 1168) in paragraph at lines 10568--10573 []\T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of []\ T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . Cur-rently this is only used by [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10670--10670 []\T1/pcr/m/n/9 ## From R 4.1.0 to 4.1.2, ...names() sometimes did not match n ames(list(...));[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10672--10672 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10791--10796 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10791--10796 \T1/pcr/m/n/10 754-[]2019$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/ pcr/m/n/10 https : Overfull \hbox (42.78088pt too wide) in paragraph at lines 10822--10822 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10896--10896 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [159] [160] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11044--11044 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [161] [162] [163] Underfull \hbox (badness 6396) in paragraph at lines 11242--11250 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 11251--11253 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) []\T1/ptm/m/n/10 is equiv-a-len t to but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11468--11471 []\T1/ptm/m/n/10 Do not use []\T1/pcr/m/n/10 dyn.unload []\T1/ptm/m/n/10 on a D LL loaded by [][][]\T1/pcr/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] Underfull \hbox (badness 2744) in paragraph at lines 11904--11906 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11927--11927 []\T1/pcr/m/n/9 Encoding(x.) # "unknown" (UTF-8 loc.) | "latin1" (8859-1/CP-12 52 loc.) | ....[] [174] [175] [176] Underfull \hbox (badness 5288) in paragraph at lines 12179--12181 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 12189--12194 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][][]\T1/pcr/m/n/1 0 dev2bitmap[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bitmap[][][] []\T1/pt m/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12246--12249 []\T1/ptm/m/n/10 The path to HTML []\T1/pcr/m/n/10 tidy[]\T1/ptm/m/n/10 . Used by []\T1/pcr/m/n/10 R CMD check []\T1/ptm/m/n/10 if Underfull \hbox (badness 10000) in paragraph at lines 12264--12266 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12514--12516 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing []\T1/pc r/m/n/10 where []\T1/ptm/m/n/10 as Underfull \hbox (badness 5970) in paragraph at lines 12557--12559 []\T1/pcr/m/n/10 get0(): []\T1/ptm/m/n/10 The object---as from [][][]\T1/pcr/m/ n/10 get[][][](x, *)[]\T1/ptm/m/n/10 --- if []\T1/pcr/m/n/10 exists(x, *) []\T1 /ptm/m/n/10 is true, oth-er-wise [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13375--13375 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14100--14102 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14135--14138 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14268--14270 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/pcr /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/pcr/m/n/10 fsep = [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 14427--14429 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14548--14552 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14559--14562 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 14580--14580 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [210] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14605--14605 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [211] Underfull \hbox (badness 10000) in paragraph at lines 14702--14705 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 unlink[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 basename[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14712--14712 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [212] Underfull \hbox (badness 10000) in paragraph at lines 14778--14781 []\T1/pcr/m/n/10 packageNotFoundError []\T1/ptm/m/n/10 cre-ates an er-ror con-d i-tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14795--14795 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14824--14824 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 3965) in paragraph at lines 14856--14860 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [214] [215] [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15020--15020 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 15021--15021 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] [220] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15263--15263 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15266--15266 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [221] Underfull \hbox (badness 1168) in paragraph at lines 15352--15356 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 15352--15356 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [222] Underfull \hbox (badness 6944) in paragraph at lines 15449--15452 [][][]\T1/pcr/m/n/10 formatC[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 paste [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 as.character[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 sprintf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p rint[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 prettyNum[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 toString[][][][]\T1/ptm/m/n/10 , [223] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15474--15474 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [224] [225] Underfull \hbox (badness 10000) in paragraph at lines 15612--15614 []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (p os-si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15632--15632 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15638--15638 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] Underfull \hbox (badness 2790) in paragraph at lines 15645--15648 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/pcr/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [226] Underfull \hbox (badness 1024) in paragraph at lines 15676--15683 []\T1/pcr/m/n/10 "f" []\T1/ptm/m/n/10 gives num-bers in the usual []\T1/pcr/m/n /10 xxx.xxx []\T1/ptm/m/n/10 for-mat; []\T1/pcr/m/n/10 "e" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "E" []\T1/ptm/m/n/10 give [227] Underfull \hbox (badness 10000) in paragraph at lines 15751--15753 []\T1/ptm/m/n/10 This works via []\T1/pcr/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/pcr/m/n/10 .format.zeros(*, Underfull \hbox (badness 10000) in paragraph at lines 15773--15778 []\T1/ptm/m/n/10 For num-bers, []\T1/pcr/m/n/10 formatC() []\T1/ptm/m/n/10 call s []\T1/pcr/m/n/10 prettyNum() []\T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2426) in paragraph at lines 15779--15781 []\T1/ptm/m/n/10 If you set []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 it over-ri des the set-ting of []\T1/pcr/m/n/10 mode[]\T1/ptm/m/n/10 , so []\T1/pcr/m/n/10 formatC(123.45, mode = Underfull \hbox (badness 10000) in paragraph at lines 15790--15798 []\T1/pcr/m/n/10 prettyNum []\T1/ptm/m/n/10 is the util-ity func-tion for pret- ti-fy-ing []\T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 x []\T1/ptm/m/n /10 can be com-plex (or [228] [229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15898--15898 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] Underfull \vbox (badness 10000) has occurred while \output is active [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16754--16754 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] [243] Underfull \hbox (badness 2418) in paragraph at lines 16863--16867 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/pcr/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16870--16873 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 name []\T1/ptm/m/n/10 con-tains only one s ym-bol name and []\T1/pcr/m/n/10 unlist []\T1/ptm/m/n/10 is []\T1/pcr/m/n/10 TR UE[]\T1/ptm/m/n/10 , then the sin-gle Underfull \hbox (badness 2326) in paragraph at lines 16905--16912 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 is.loaded[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .C[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Fortran[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 .External[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 .Call[][][][] \T1/ptm/m/n/10 , [244] [245] Underfull \hbox (badness 10000) in paragraph at lines 17012--17016 []\T1/ptm/m/n/10 The spe-cial case []\T1/pcr/m/n/10 bindtextdomain(NULL) []\T1/ ptm/m/n/10 calls C level Underfull \hbox (badness 3302) in paragraph at lines 17012--17016 []\T1/pcr/m/n/10 textdomain(textdomain(NULL)) []\T1/ptm/m/n/10 for the pur-pose of flush-ing (i.e., emp-ty-ing) the [246] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17075--17075 []\T1/pcr/m/n/9 if(is.na(thisLang) || !nzchar(thisLang)) thisLang <- "en" # "f actory" default[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17078--17078 []\T1/pcr/m/n/9 gettext(enT, domain="R-stats")# "leeres Modell angegeben" (if translation works)[] Underfull \vbox (badness 10000) has occurred while \output is active [247] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17109--17109 []\T1/pcr/m/n/9 ## Here, we reset to the *original* setting before the full ex ample started:[] [248] [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17246--17246 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 17274--17281 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [250] [251] [252] [253] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17575--17575 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] [254] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17604--17604 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [255] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17660--17660 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [256] [257] [258] [259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18033--18033 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18098--18098 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [261] [262] [263] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18307--18307 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [264] [265] [266] [267] [268] Underfull \hbox (badness 1163) in paragraph at lines 18653--18655 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 https : / / unicode-[]org . github . io / icu / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18661--18661 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] [269] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18691--18691 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [270] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18785--18785 [] \T1/pcr/m/n/10 num.eq = FALSE, single.NA = FALSE, attrib.as.se t = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18786--18786 [] \T1/pcr/m/n/10 ignore.bytecode = FALSE, ignore.environment = F ALSE,[] [271] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18839--18839 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18845--18845 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18848--18848 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18854--18854 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [272] [273] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18981--18981 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18989--18989 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [274] [275] [276] Underfull \hbox (badness 10000) in paragraph at lines 19194--19196 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][][]\T 1/pcr/m/n/10 stop[][][] []\T1/ptm/m/n/10 and [277] [278] [279] [280] [281] Underfull \hbox (badness 10000) in paragraph at lines 19532--19538 Underfull \hbox (badness 10000) in paragraph at lines 19545--19547 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [282] [283] [284] Underfull \hbox (badness 4699) in paragraph at lines 19777--19780 []\T1/pcr/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , [285] [286] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19905--19905 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [287] [288] [289] Underfull \hbox (badness 4739) in paragraph at lines 20040--20042 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [290] Overfull \hbox (36.7804pt too wide) in paragraph at lines 20089--20089 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20090--20090 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [291] [292] [293] [294] [295] [296] [297] [298] [299] Underfull \hbox (badness 1975) in paragraph at lines 20709--20712 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [300] [301] [302] [303] [304] [305] Underfull \hbox (badness 1077) in paragraph at lines 21124--21129 []\T1/ptm/m/n/10 In late 2017 a []\T1/pcr/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/pcr/m/n/10 libcurl []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 21138--21145 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [306] Underfull \hbox (badness 1112) in paragraph at lines 21212--21221 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/pcr/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , [307] Underfull \hbox (badness 2970) in paragraph at lines 21272--21275 []\T1/pcr/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/pcr/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a Underfull \hbox (badness 2951) in paragraph at lines 21272--21275 \T1/ptm/m/n/10 hid-den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21385--21389 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 21385--21389 [][][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][][]\T1/ptm/m/n/10 : thi s will sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 21390--21397 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 is called with no []\T1/pcr/m/n/10 package []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 help []\T1/ptm/m /n/10 ar-gu-ment, it lists all avail-able pack- [310] [311] Underfull \hbox (badness 10000) in paragraph at lines 21521--21528 [][][]\T1/pcr/m/n/10 attach[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 detach [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 search[][][][]\T1/ptm/m/n/10 , [] [][]\T1/pcr/m/n/10 objects[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 autoloa d[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 requireNamespace[][][][]\T1/ptm/ m/n/10 , [312] Underfull \hbox (badness 10000) in paragraph at lines 21642--21646 []\T1/ptm/m/n/10 Do not use [][][]\T1/pcr/m/n/10 dyn.unload[][][] []\T1/ptm/m/n /10 on a DLL loaded by []\T1/pcr/m/n/10 library.dynam[]\T1/ptm/m/n/10 : use [313] Underfull \hbox (badness 5161) in paragraph at lines 21712--21717 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21712--21717 \T1/ptm/m/n/10 by []\T1/pcr/m/n/10 RShowDoc("LGPL-2.1")[]\T1/ptm/m/n/10 . Ver-s ion 3 of the li-cense can be dis-played by [314] [315] [316] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21880--21880 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21884--21884 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [317] Underfull \hbox (badness 3343) in paragraph at lines 21945--21949 [][][]\T1/pcr/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fil e.access[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 files[][][] []\T1/ptm/ m/n/10 for many more file han-dling func-tions and [318] [319] Overfull \hbox (4.38043pt too wide) in paragraph at lines 22083--22083 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 22094--22094 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [320] [321] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22205--22205 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 22208--22208 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 22255--22263 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [322] [323] Underfull \hbox (badness 2564) in paragraph at lines 22358--22361 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 22395--22395 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 22406--22406 []\T1/pcr/m/n/9 Sys.setenv("LANGUAGE" = "es") # set the language for error/war ning messages[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 22414--22414 [] \T1/pcr/m/n/9 sg <- matrix(unlist(strsplit(strsplit(Sys.getlocale(), sep)[[ 1]], "=")), nrow=2)[] [324] [325] Underfull \hbox (badness 1400) in paragraph at lines 22575--22579 [][][]\T1/pcr/m/n/10 raw[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logical[] [][] []\T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][][]\T1/pcr/m /n/10 double[][][] []\T1/ptm/m/n/10 (class [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23419--23419 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23420--23420 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 23423--23423 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [339] Overfull \hbox (20.58041pt too wide) in paragraph at lines 23520--23520 []\T1/pcr/m/n/9 match.arg(c("a", ""), c("", NA, "bb", "abc"), several.ok=TRUE ) # |--> "abc"[] [340] Underfull \hbox (badness 1655) in paragraph at lines 23554--23558 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [341] [342] [343] Underfull \hbox (badness 2277) in paragraph at lines 23803--23806 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] []\T1/pcr/m/n/10 crossprod[][][]() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 tcross prod() []\T1/ptm/m/n/10 are typ-i-cally prefer-able. [344] [345] [346] [347] [348] [349] [350] [351] [352] Underfull \hbox (badness 1484) in paragraph at lines 24392--24400 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 24392--24400 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [353] [354] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24466--24466 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [355] [356] [357] [358] [359] [360] [361] [362] Underfull \hbox (badness 1448) in paragraph at lines 25014--25022 []\T1/pcr/m/n/10 anyNA(recursive = FALSE) []\T1/ptm/m/n/10 works the same way a s []\T1/pcr/m/n/10 is.na[]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 anyNA(recursive = [363] Underfull \hbox (badness 3849) in paragraph at lines 25129--25134 []\T1/pcr/m/n/10 as.name []\T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter- nally to a char-ac-ter vec-tor (so meth-ods for [364] Underfull \hbox (badness 2165) in paragraph at lines 25206--25212 []\T1/ptm/m/n/10 For an [][][]\T1/pcr/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, Underfull \hbox (badness 1199) in paragraph at lines 25206--25212 \T1/ptm/m/n/10 i.e., []\T1/pcr/m/n/10 names(as.list(env, all.names = TRUE)) []\ T1/ptm/m/n/10 which are also given by [][][]\T1/pcr/m/n/10 ls[][][](env, Underfull \hbox (badness 3148) in paragraph at lines 25206--25212 \T1/pcr/m/n/10 all.names = TRUE, sorted = FALSE)[]\T1/ptm/m/n/10 . If the en-vi -ron-ment is used as a hash ta-ble, [365] [366] [367] Underfull \hbox (badness 2237) in paragraph at lines 25369--25371 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of []\T1/pcr/m/n/1 0 c("bytes", "chars", [368] [369] [370] Underfull \hbox (badness 6188) in paragraph at lines 25596--25599 []\T1/ptm/m/n/10 optional [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/pcr/m/n/10 print()[]\T1/ptm/m/n/10 , used by [371] [372] [373] Underfull \hbox (badness 1521) in paragraph at lines 25781--25795 \T1/ptm/m/n/10 tion []\T1/pcr/m/n/10 GetFinalPathNameByHandle []\T1/ptm/m/n/10 and in case of an er-ror (such as in-suf-fi-cient per- [374] [375] [376] [377] Underfull \hbox (badness 2197) in paragraph at lines 26095--26099 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 26095--26099 []\T1/pcr/m/n/10 .onAttach[]\T1/ptm/m/n/10 . These mes-sages (and any es-sen-ti al ones from []\T1/pcr/m/n/10 .onLoad[]\T1/ptm/m/n/10 ) should use [378] Underfull \hbox (badness 2846) in paragraph at lines 26109--26113 []\T1/ptm/m/n/10 Uses of []\T1/pcr/m/n/10 library []\T1/ptm/m/n/10 with ar-gu-m ent []\T1/pcr/m/n/10 help []\T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion ab out the pack- Underfull \hbox (badness 1990) in paragraph at lines 26109--26113 \T1/ptm/m/n/10 age should use []\T1/pcr/m/n/10 format []\T1/ptm/m/n/10 on the c om-puted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 26151--26151 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 26155--26155 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [379] Underfull \hbox (badness 10000) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 loadNamespace []\T1/ptm/m/n/10 does not at-tach the name space it loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 26204--26210 []\T1/pcr/m/n/10 attachNamespace []\T1/ptm/m/n/10 can be used to at-tach a fram e con-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 26217--26219 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/pcr/m/n/10 pkg %in% [380] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26284--26284 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [381] [382] [383] Underfull \hbox (badness 8189) in paragraph at lines 26479--26485 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 is.numeric []\T1/ptm/ m/n/10 re-turns []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode[][][] [384] [385] [386] Underfull \hbox (badness 1694) in paragraph at lines 26704--26707 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [387] [388] [389] [390] Underfull \hbox (badness 1603) in paragraph at lines 26976--26978 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [391] [392] Underfull \hbox (badness 1210) in paragraph at lines 27103--27111 []\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 starts up. Ini- [393] [394] Underfull \hbox (badness 3271) in paragraph at lines 27323--27326 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [395] [396] [397] [398] Underfull \hbox (badness 3138) in paragraph at lines 27629--27635 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/pcr/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/pcr/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 27629--27635 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 27642--27645 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/pcr/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence[][][]\T1/pcr/m/n/10 bug.report[][][] []\T1/pt m/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27668--27670 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 27695--27701 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27710--27715 []\T1/ptm/m/n/10 Used by [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [399] Underfull \hbox (badness 1009) in paragraph at lines 27728--27731 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/pcr/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/pcr/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 27744--27747 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "source" []\T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 build), []\T1/pcr/m/n/10 "mac.binary" []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 "both" []\T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS Underfull \hbox (badness 10000) in paragraph at lines 27752--27758 \T1/ptm/m/n/10 builds). ([]\T1/pcr/m/n/10 "mac.binary.el-capitan"[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 "mac.binary.mavericks"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 5091) in paragraph at lines 27752--27758 []\T1/pcr/m/n/10 "mac.binary.leopard" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "ma c.binary.universal" []\T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][][]\T1/pcr/m/n/10 up date.packages[][][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27767--27774 []\T1/pcr/m/n/10 c(CRAN="@CRAN@")[]\T1/ptm/m/n/10 , a value that causes some ut il-i-ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27767--27774 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke []\T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 27767--27774 \T1/pcr/m/n/10 <- getOption("repos"); r["CRAN"] <- "http://my.local.cran"; [400] [401] [402] [403] [404] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28115--28115 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 28128--28132 []\T1/ptm/m/n/10 where el-e-ment []\T1/pcr/m/n/10 A[c(arrayindex.x, arrayindex. y)] = FUN(X[arrayindex.x], [405] [406] Underfull \hbox (badness 1210) in paragraph at lines 28275--28278 []\T1/pcr/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/pcr/m/n/10 parse(tex t=s, [407] [408] [409] [410] Underfull \hbox (badness 7133) in paragraph at lines 28557--28563 [][][]\T1/pcr/m/n/10 toString[][][] []\T1/ptm/m/n/10 typ-i-cally calls []\T1/pc r/m/n/10 paste(*, collapse=", ")[]\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Overfull \hbox (42.18039pt too wide) in paragraph at lines 28579--28579 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28591--28591 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [411] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28604--28604 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 recycle0 = TRUE\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 allows more vectorized behaviour, i.e. zero-length recycling : [] Overfull \hbox (63.78036pt too wide) in paragraph at lines 28608--28608 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [412] [413] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28791--28791 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] [414] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28806--28806 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] Underfull \hbox (badness 1360) in paragraph at lines 28861--28865 []\T1/ptm/m/n/10 All other []\T1/pcr/m/n/10 type[]\T1/ptm/m/n/10 s give a warn- ing or an er-ror; us-ing, e.g., []\T1/pcr/m/n/10 type = [415] [416] [417] [418] [419] Underfull \hbox (badness 2277) in paragraph at lines 29173--29178 \T1/ptm/m/n/10 i.e., strictly in-clude the bounds of []\T1/pcr/m/n/10 x[]\T1/pt m/m/n/10 . New from \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0, al-low-ing [420] [421] Underfull \hbox (badness 1701) in paragraph at lines 29289--29293 []\T1/ptm/m/n/10 This func-tion is al-most never used: []\TS1/cmtt/m/n/10 `\T1/ pcr/m/n/10 name\TS1/cmtt/m/n/10 ` []\T1/ptm/m/n/10 or, more care-fully, [][][]\ T1/pcr/m/n/10 get[][][](name, envir = [422] Underfull \hbox (badness 1796) in paragraph at lines 29357--29360 []\T1/ptm/m/n/10 character string (or []\T1/pcr/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/pcr/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [423] [424] [425] Underfull \hbox (badness 10000) in paragraph at lines 29561--29564 []\T1/ptm/m/n/10 Option []\T1/pcr/m/n/10 width []\T1/ptm/m/n/10 con-trols the p rint-ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [426] [427] [428] [429] [430] [431] [432] [433] [434] [435] Overfull \hbox (25.98041pt too wide) in paragraph at lines 30256--30256 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [436] [437] [438] [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30549--30549 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30560--30560 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30566--30566 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30572--30572 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [441] Underfull \hbox (badness 7415) in paragraph at lines 30662--30666 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use []\T1/pcr/m/n/10 R.v ersion$os []\T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [442] Overfull \hbox (42.18039pt too wide) in paragraph at lines 30683--30683 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30729--30729 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [443] [444] Underfull \hbox (badness 3713) in paragraph at lines 30874--30885 []\T1/pcr/m/n/10 normal.kind []\T1/ptm/m/n/10 can be []\T1/pcr/m/n/10 "Kinderma n-Ramage"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Buggy Kinderman-Ramage" []\T1/ptm /m/n/10 (not [445] [446] Underfull \hbox (badness 1248) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 31026--31033 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [447] Underfull \hbox (badness 1533) in paragraph at lines 31144--31147 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [448] [449] [450] Overfull \hbox (42.78088pt too wide) in paragraph at lines 31289--31289 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 31307--31318 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/pcr/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [451] [452] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31451--31451 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 31453--31453 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31454--31454 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31455--31455 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31456--31456 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31463--31463 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [453] [454] [455] [456] [457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31771--31771 []\T1/pcr/m/n/9 ## Bit representation [ sign | exponent | mantissa ] of doubl e prec numbers :[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 31773--31773 []\T1/pcr/m/n/9 bitC <- function(x) noquote(vapply(as.double(x), function(x) { # split one double[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31783--31783 []\T1/pcr/m/n/9 d2bI <- function(x) vapply(as.double(x), function(x) intToBits (numToInts(x)), raw(64L))[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 31784--31784 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] Underfull \vbox (badness 10000) has occurred while \output is active [458] [459] Underfull \hbox (badness 4048) in paragraph at lines 31879--31884 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 31879--31884 \T1/ptm/m/n/10 one of []\T1/pcr/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/pcr/m/ n/10 "double"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 "int"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/ 10 , [460] [461] [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 2080) in paragraph at lines 32417--32427 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 infoRDS[]\T1/ptm/m/n/10 , an \T1/phv/m/n/ 10 R \T1/ptm/m/n/10 list with el-e-ments []\T1/pcr/m/n/10 version []\T1/ptm/m/n /10 (ver-sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 32451--32451 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [468] [469] [470] [471] [472] [473] [474] Underfull \hbox (badness 7558) in paragraph at lines 32971--32975 []\T1/pcr/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32981--32983 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the [475] Underfull \hbox (badness 10000) in paragraph at lines 32992--32994 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / Underfull \hbox (badness 1975) in paragraph at lines 32995--32999 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m /n/10 https : / / www . [476] [477] [478] [479] [480] Overfull \hbox (4.38043pt too wide) in paragraph at lines 33366--33366 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [481] Underfull \hbox (badness 10000) in paragraph at lines 33437--33441 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [482] [483] [484] Underfull \hbox (badness 2302) in paragraph at lines 33663--33668 []\T1/pcr/m/n/10 signif []\T1/ptm/m/n/10 rounds the val-ues in its first ar-gu- ment to the spec-i-fied num-ber of \T1/ptm/m/it/10 sig-nif-i-cant Underfull \hbox (badness 1824) in paragraph at lines 33663--33668 \T1/ptm/m/n/10 dig-its. Hence, for []\T1/pcr/m/n/10 numeric x[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 signif(x, dig) []\T1/ptm/m/n/10 is the same as []\T1/pcr/m/n/ 10 round(x, dig - [485] [486] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33796--33796 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33799--33799 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33806--33806 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [487] [488] [489] [490] [491] [492] [493] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34254--34254 [] \T1/pcr/m/n/10 useHash = (n > 1e+07 && !replace && is.null(prob) && size <= n/2))[] [494] [495] [496] [497] [498] [499] [500] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34691--34691 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [501] Underfull \hbox (badness 1158) in paragraph at lines 34795--34800 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [502] [503] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34981--34981 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [504] [505] [506] [507] Underfull \hbox (badness 4752) in paragraph at lines 35241--35244 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence []\T1/pcr/ m/n/10 1, 2, ..., length(along.with)[]\T1/ptm/m/n/10 . Underfull \hbox (badness 5563) in paragraph at lines 35245--35251 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence []\T1/pcr/m/n/10 1, 2 , ..., length(from) []\T1/ptm/m/n/10 (as if ar-gu-ment [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 []\T1/ptm/m/n/10 In Win-dows, com-mand line in-ter-pre-ta-tion is done by the a p-pli-ca-tion as well as Underfull \hbox (badness 3271) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 the shell. It may de-pend on the com-piler used: Mi-crosoft's ru les for the C run- Underfull \hbox (badness 10000) in paragraph at lines 35915--35926 \T1/ptm/m/n/10 time are given at [][]$\T1/pcr/m/n/10 https : / / docs . microso ft . com / en-[]us / cpp / c-[]language / Underfull \hbox (badness 1635) in paragraph at lines 35915--35926 \T1/pcr/m/n/10 parsing-[]c-[]command-[]line-[]arguments ? view = msvc-[]160$[][ ]\T1/ptm/m/n/10 . It may de-pend on the [518] [519] [520] [521] [522] [523] [524] [525] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36455--36455 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [526] [527] [528] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36707--36707 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36709--36709 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [529] Underfull \hbox (badness 4954) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 vec-tor, passed as []\T1/ pcr/m/n/10 control []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 deparse[][][]()[]\T 1/ptm/m/n/10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36752--36758 [][][]\T1/pcr/m/n/10 .deparseOpts[][][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \ T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [530] [531] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36863--36863 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [532] [533] [534] [535] [536] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37206--37206 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37221--37221 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [537] [538] [539] Underfull \hbox (badness 10000) in paragraph at lines 37446--37448 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [540] [541] [542] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37673--37673 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37674--37674 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [543] [544] [545] [546] [547] Overfull \hbox (63.78036pt too wide) in paragraph at lines 38005--38005 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [548] Underfull \hbox (badness 6110) in paragraph at lines 38101--38111 []\T1/ptm/m/n/10 A func-tion []\T1/pcr/m/n/10 .First []\T1/ptm/m/n/10 (and [][] []\T1/pcr/m/n/10 .Last[][][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-at e `\T1/pcr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 38101--38111 \T1/pcr/m/n/10 = character()) []\T1/ptm/m/n/10 will at-tach no ex-tra pack-ages on startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 38101--38111 \T1/ptm/m/n/10 set []\T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL []\T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us-ing [549] Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 38157--38163 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 38172--38179 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 38172--38179 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [550] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38234--38234 []\T1/pcr/m/n/9 # Variable expansion in double quotes, string literals with ba ckslashes in[] [551] [552] [553] Underfull \hbox (badness 1484) in paragraph at lines 38407--38411 []\T1/ptm/m/n/10 alternative to []\T1/pcr/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/pcr/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an Overfull \hbox (60.78088pt too wide) in paragraph at lines 38469--38469 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [554] [555] [556] [557] [558] [559] [560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 38955--38955 []\T1/pcr/m/n/9 (fF <- format(.POSIXct(notF))) # was all NA, now the last is still NA (not "NA")[] [561] [562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 39064--39064 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [563] [564] [565] Overfull \hbox (6.78088pt too wide) in paragraph at lines 39314--39314 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39358--39358 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [567] [568] [569] [570] [571] [572] [573] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39805--39805 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 39808--39808 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [574] Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][][]\T1/pcr/m/n/ 10 signif[][][]() []\T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 39859--39866 []\T1/pcr/m/n/10 summary.default[]\T1/ptm/m/n/10 ) or [][][]\T1/pcr/m/n/10 form at[][][]() []\T1/ptm/m/n/10 (for []\T1/pcr/m/n/10 summary.data.frame[]\T1/ptm/m /n/10 ). [575] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39912--39912 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [576] [577] [578] [579] Overfull \hbox (31.3804pt too wide) in paragraph at lines 40223--40223 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [580] [581] [582] Overfull \hbox (4.38043pt too wide) in paragraph at lines 40389--40389 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [583] Overfull \hbox (20.58041pt too wide) in paragraph at lines 40427--40427 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 2293) in paragraph at lines 40457--40463 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de- Underfull \hbox (badness 1237) in paragraph at lines 40457--40463 \T1/ptm/m/n/10 tails of wild-cards ex-pan-sion, see your sys-tem's doc-u-men-ta -tion on the []\T1/pcr/m/n/10 glob []\T1/ptm/m/n/10 sys-tem call. Underfull \hbox (badness 4792) in paragraph at lines 40476--40481 []\T1/ptm/m/n/10 If a file-name starts with []\T1/pcr/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 40476--40481 []\T1/pcr/m/n/10 Sys.glob("*.RData") []\T1/ptm/m/n/10 may or may not match `\T1 /pcr/m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [584] [585] [586] [587] Underfull \hbox (badness 10000) in paragraph at lines 40764--40768 []\T1/pcr/m/n/10 sys.status() []\T1/ptm/m/n/10 re-turns a list with com-po-nent s []\T1/pcr/m/n/10 sys.calls[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sys.parents []\ T1/ptm/m/n/10 and Underfull \hbox (badness 1584) in paragraph at lines 40779--40782 []\T1/pcr/m/n/10 sys.call []\T1/ptm/m/n/10 re-turns a call, []\T1/pcr/m/n/10 sy s.function []\T1/ptm/m/n/10 a func-tion def-i-ni-tion, and []\T1/pcr/m/n/10 sys .frame []\T1/ptm/m/n/10 and [588] [589] [590] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40917--40917 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [591] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40998--40998 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/cmtt /m/n/9 `\T1/pcr/m/n/9 A+C\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 could also be used [592] [593] Underfull \hbox (badness 1082) in paragraph at lines 41143--41146 []\T1/ptm/m/n/10 logical. If []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see Underfull \hbox (badness 10000) in paragraph at lines 41170--41172 [][][]\T1/pcr/m/n/10 source[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 lo adNamespace[][][] []\T1/ptm/m/n/10 which is called from [][][]\T1/pcr/m/n/10 li brary[][][](.) []\T1/ptm/m/n/10 and uses [594] [595] [596] Underfull \hbox (badness 1038) in paragraph at lines 41336--41339 []\T1/ptm/m/n/10 a log-i-cal (not []\T1/pcr/m/n/10 NA[]\T1/ptm/m/n/10 ) in-di-c at-ing whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [597] [598] [599] [600] [601] Underfull \hbox (badness 1442) in paragraph at lines 41701--41705 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: []\T1/pcr/m/n/10 stdout = TRUE []\T1/ptm/m/n/10 uses a pipe whereas []\T1/pcr/m/n/10 stdout = [602] [603] [604] [605] Underfull \hbox (badness 4096) in paragraph at lines 41955--41958 []\T1/ptm/m/n/10 Use [][][]\T1/pcr/m/n/10 ftable[][][] []\T1/ptm/m/n/10 for pri nt-ing (and more) of mul-ti-di-men-sional ta-bles. [][][]\T1/pcr/m/n/10 margin. table[][][][]\T1/ptm/m/n/10 , [606] Underfull \hbox (badness 7888) in paragraph at lines 42069--42073 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/pcr/m/n/10 bin []\T1/ptm/m/n/10 can have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/pcr/ m/n/10 length(bin) > [607] [608] [609] Overfull \hbox (63.78036pt too wide) in paragraph at lines 42223--42223 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (30.0281pt too wide) in paragraph at lines 42225--42225 [] \T1/pcr/m/n/9 array(list(\TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 2\TS1/cm tt/m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), names = nq),[] Overfull \hbox (55.67578pt too wide) in paragraph at lines 42227--42227 [] \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 4\TS1/cmtt/m/n/9 ` \T1/pcr/m /n/9 = NULL, \TS1/cmtt/m/n/9 `\T1/pcr/m/n/9 5\TS1/cmtt/m/n/9 ` \T1/pcr/m/n/9 = NULL), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 42240--42242 []\T1/pcr/m/n/10 removeTaskCallback []\T1/ptm/m/n/10 un-registers a func-tion t hat was reg-is-tered ear-lier via [610] Underfull \hbox (badness 10000) in paragraph at lines 42320--42323 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [611] [612] Underfull \hbox (badness 3872) in paragraph at lines 42438--42441 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [613] Underfull \hbox (badness 5475) in paragraph at lines 42504--42508 [][][]\T1/pcr/m/n/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 taskCallback Manager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [614] [615] [616] [617] [618] [619] Underfull \hbox (badness 1655) in paragraph at lines 42927--42934 \T1/ptm/m/n/10 may also be known as `[]\T1/pcr/m/n/10 GB[]\T1/ptm/m/n/10 ', `[] \T1/pcr/m/n/10 GB-Eire[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Belfast[]\T1 /ptm/m/n/10 ', `[]\T1/pcr/m/n/10 Europe/Guernsey[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 2253) in paragraph at lines 42935--42940 []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re-turns a char-ac-ter vec-tor, se e the ex-am-ples for typ-i-cal cases. It may Underfull \hbox (badness 1655) in paragraph at lines 42935--42940 \T1/ptm/m/n/10 have an at-tribute []\T1/pcr/m/n/10 "Version"[]\T1/ptm/m/n/10 , some-thing like `[]\T1/pcr/m/n/10 "2020a"[]\T1/ptm/m/n/10 '. (It does on sys-te ms us-ing Underfull \hbox (badness 4467) in paragraph at lines 42985--42994 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 OlsonNames []\T1/ptm/m/n/10 re- turns the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42985--42994 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [620] Underfull \hbox (badness 1082) in paragraph at lines 42995--43007 []\T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/1 0 ' in that di-rec-tory states the ver-sion. That op-tion is [621] Underfull \hbox (badness 1337) in paragraph at lines 43080--43088 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 43089--43092 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 43143--43146 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 43147--43149 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- [622] Overfull \hbox (31.3804pt too wide) in paragraph at lines 43156--43156 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [623] [624] [625] [626] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43499--43499 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43501--43501 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [627] Underfull \vbox (badness 10000) has occurred while \output is active [628] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43602--43602 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43604--43604 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [629] [630] [631] [632] Underfull \hbox (badness 6542) in paragraph at lines 43878--43880 []\T1/pcr/m/n/10 cospi(x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sinpi(x)[]\T1/ptm/ m/n/10 , and []\T1/pcr/m/n/10 tanpi(x)[]\T1/ptm/m/n/10 , com-pute []\T1/pcr/m/n /10 cos(pi*x)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 sin(pi*x)[]\T1/ptm/m/n/10 , an d [633] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43997--43997 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [634] Underfull \hbox (badness 1708) in paragraph at lines 44065--44073 []\T1/pcr/m/n/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 44065--44073 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/pcr/m/n/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [635] Underfull \hbox (badness 4859) in paragraph at lines 44105--44110 [][][]\T1/pcr/m/n/10 options[][][] []\T1/ptm/m/n/10 for set-ting er-ror han-dle rs and sup-press-ing the print-ing of er-ror mes-sages; [636] Underfull \hbox (badness 3895) in paragraph at lines 44167--44179 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture []\T1/pcr/m/n/10 TypeTable []\T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 44167--44179 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "integer"[]\T1/ptm/m/n/10 , [637] [638] [639] [640] [641] Overfull \hbox (9.78043pt too wide) in paragraph at lines 44490--44490 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [642] [643] [644] [645] [646] [647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44959--44959 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [648] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44968--44968 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platforms[] Underfull \hbox (badness 2057) in paragraph at lines 45034--45040 [][][]\T1/pcr/m/n/10 file[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.acc ess[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.append[][][][]\T1/ptm/m/n /10 , [][][]\T1/pcr/m/n/10 file.copy[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 file.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 file.exists[][][][] \T1/ptm/m/n/10 , [649] Underfull \hbox (badness 3861) in paragraph at lines 45043--45048 [][][]\T1/pcr/m/n/10 dir.create[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 di r.exists[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 normalizePath[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 path.expand[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 pipe[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Sys.glob[][][][]\ T1/ptm/m/n/10 , [650] Overfull \hbox (36.7804pt too wide) in paragraph at lines 45136--45136 []\T1/pcr/m/n/9 try( substr(x, 1,1) ) # gives \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 in valid multibyte string\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 error in a UTF-8 locale[] [651] Underfull \hbox (badness 1803) in paragraph at lines 45199--45202 []\T1/ptm/m/n/10 The atomic modes are []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "integer"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "numeric" []\ T1/ptm/m/n/10 (syn-onym []\T1/pcr/m/n/10 "double"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 45203--45209 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 mode = "any"[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 is.vector []\T1/ptm/m/n/10 may re-turn []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/ n/10 for the atomic modes, [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 and [652] [653] [654] Underfull \hbox (badness 3668) in paragraph at lines 45432--45434 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [655] Overfull \hbox (36.78088pt too wide) in paragraph at lines 45538--45538 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [656] [657] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45613--45613 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45621--45621 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [658] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45715--45715 []\T1/pcr/m/n/9 ## Show how easily you get month, day, year, day (of {month, w eek, yr}), ... :[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 45719--45719 []\T1/pcr/m/n/9 dt2df <- function(dt, dName = deparse(substitute(dt)), strings AsFactors = FALSE) {[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 45720--45720 [] \T1/pcr/m/n/9 DF <- as.data.frame(unclass(as.POSIXlt( dt )), stringsAsFa ctors=stringsAsFactors)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45727--45727 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Even simpler: Date -> Matrix - dropping time info {sec,min,hour, isdst}[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 45730--45730 []\T1/pcr/m/n/9 d2mat(seq(as.Date("2000-02-02"), by=1, length.out=30)) # has R 1.0.0\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s release date[] [659] Underfull \hbox (badness 10000) in paragraph at lines 45791--45796 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 arr.ind == TRUE []\T1/ptm/m/n/10 and []\T1 /pcr/m/n/10 x []\T1/ptm/m/n/10 is an [][][]\T1/pcr/m/n/10 array[][][] []\T1/ptm /m/n/10 (has a [][][]\T1/pcr/m/n/10 dim[][][] []\T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 2564) in paragraph at lines 45791--45796 []\T1/pcr/m/n/10 arrayInd(which(x), dim(x), dimnames(x))[]\T1/ptm/m/n/10 , name ly a ma-trix whose rows each [660] [661] Underfull \hbox (badness 2818) in paragraph at lines 45887--45893 []\T1/ptm/m/n/10 For a [][][]\T1/pcr/m/n/10 logical[][][] []\T1/ptm/m/n/10 vec- tor []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with both []\T1/pcr/m/n/10 FALSE []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 val-ues, []\T1/pcr/m/n/10 which.min(x) []\T1/ptm/m/n/10 and Overfull \hbox (15.18042pt too wide) in paragraph at lines 45922--45922 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [662] [663] [664] [665] [666] [667] [668] Underfull \hbox (badness 2846) in paragraph at lines 46381--46385 []\T1/pcr/m/n/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-ren tly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [669] Overfull \hbox (4.38043pt too wide) in paragraph at lines 46421--46421 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 46442--46446 []\T1/pcr/m/n/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-da rd' reg-exps, in-clud-ing el-e-ments named [670]) (./compiler-pkg.tex Chapter 2. [671] Underfull \hbox (badness 2884) in paragraph at lines 106--120 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 options []\T1/ptm/m/n/10 ar-gu-ment can b e used to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 106--120 \T1/ptm/m/n/10 rently four op-tions: []\T1/pcr/m/n/10 optimize[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressAll[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 suppressUndef ined[]\T1/ptm/m/n/10 , and [672] [673] [674]) (./datasets-pkg.tex Chapter 3. [675] [676] [677] [678] [679] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [680] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] [681] [682] [683] [684] Overfull \hbox (4.38043pt too wide) in paragraph at lines 617--617 [] \T1/pcr/m/n/9 start = c(lrc = log(.35)), algorithm = "plinear", t race = TRUE)[] [685] Underfull \hbox (badness 4779) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [686] [687] Underfull \hbox (badness 4779) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [688] [689] [690] Underfull \hbox (badness 1097) in paragraph at lines 1037--1041 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [691] Underfull \hbox (badness 4779) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [692] [693] [694] [695] [696] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1464--1464 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [697] [698] Underfull \hbox (badness 10000) in paragraph at lines 1549--1552 []\T1/ptm/m/n/10 Finally, []\T1/pcr/m/n/10 freeny []\T1/ptm/m/n/10 is a data fr ame with vari-ables []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lag.q uarterly.revenue[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1549--1552 []\T1/pcr/m/n/10 price.index[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 income.level[]\ T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 market.potential []\T1/ptm/m/n/10 ob-taine d from the above [699] [700] [701] Underfull \hbox (badness 4779) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [702] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1840--1840 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [703] [704] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1956--1956 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1957--1957 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [705] [706] [707] [708] Underfull \hbox (badness 4779) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [709] [710] [711] [712] [713] [714] [715] [716] Underfull \hbox (badness 4779) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [717] [718] [719] [720] [721] [722] [723] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3154--3154 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [724] [725] [726] [727] [728] [729] [730] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3611--3611 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [731] [732] [733] Underfull \hbox (badness 4779) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 c("nfnGroupedData", "nfGr oupedData", "groupedData", [734] [735] [736] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3968--3968 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 4006--4008 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750]) (./grDevices-pkg.tex Chapter 4. [751] [752] [753] [754] Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/pcr/m/n/10 axisTicks[][][]() []\T1/ ptm/m/n/10 just calls the C func-tion []\T1/pcr/m/n/10 CreateAtVector() []\T1/p tm/m/n/10 in [755] [756] [757] [758] Overfull \hbox (6.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] Underfull \hbox (badness 5175) in paragraph at lines 1192--1194 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [769] [770] [771] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1363--1363 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [772] [773] [774] Underfull \hbox (badness 3302) in paragraph at lines 1624--1628 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of Underfull \hbox (badness 10000) in paragraph at lines 1624--1628 []\T1/pcr/m/n/10 c("LinearGradient", "RadialGradient", "TilingPattern") [775] [776] [777] [778] [779] Underfull \hbox (badness 1565) in paragraph at lines 1914--1919 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 dev.print []\T1/ptm/m/n/10 i s to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1914--1919 \T1/ptm/m/n/10 sys-tem: see [][][]\T1/pcr/m/n/10 postscript[][][] []\T1/ptm/m/n /10 for how to set this up. Win-dows users may pre-fer to use [780] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1997--1997 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [781] Underfull \hbox (badness 1184) in paragraph at lines 2038--2048 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of []\T1/pcr /m/n/10 ghostscript[]\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 2038--2048 []\T1/pcr/m/n/10 "tiffg4"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffgray"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "tifflzw"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiffp ack"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tiff12nc"[]\T1/ptm/m/n/10 , []\T1/pcr/ m/n/10 "tiff24nc"[]\T1/ptm/m/n/10 , [782] Underfull \hbox (badness 10000) in paragraph at lines 2150--2152 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [783] [784] [785] Underfull \hbox (badness 6758) in paragraph at lines 2329--2332 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [786] [787] Underfull \hbox (badness 2326) in paragraph at lines 2447--2457 []\T1/ptm/m/n/10 are given, then it uses those in a call to []\T1/pcr/m/n/10 se tGraphicsEventHandlers []\T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2447--2457 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2447--2457 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2447--2457 []\T1/pcr/m/n/10 setGraphicsEventHandlers []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 setGraphicsEventEnv []\T1/ptm/m/n/10 on one or more graph-ics [788] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2550--2550 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] [789] [790] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2666--2666 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE) Overfull \hbox (30.78088pt too wide) in paragraph at lines 2667--2667 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [791] [792] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 2940--2941 [795] [796] [797] [798] [799] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3273--3273 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [800] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3358--3358 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [801] [802] [803] Underfull \hbox (badness 10000) in paragraph at lines 3516--3522 []\T1/pcr/m/n/10 nclass.FD []\T1/ptm/m/n/10 uses the Freedman-Diaconis choice b ased on the inter-quartile range [804] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3591--3591 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [805] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3675--3675 []\T1/pcr/m/n/9 (palette(gray(seq(0,.9,length.out = 25)))) # gray scales; prin t old palette[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3695--3695 []\T1/pcr/m/n/9 ## Demonstrate the colors 1:8 in different palettes using a cu stom matplot()[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3702--3702 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [806] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3758--3758 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [807] Underfull \hbox (badness 8170) in paragraph at lines 3787--3790 []\T1/ptm/m/n/10 the type of palettes to list: []\T1/pcr/m/n/10 "qualitative"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sequential"[]\T1/ptm/m/n/10 , [808] Underfull \hbox (badness 2189) in paragraph at lines 3848--3853 []\T1/ptm/m/n/10 For ex-am-ple, []\T1/pcr/m/n/10 "Dark 3" []\T1/ptm/m/n/10 work s well for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3886--3890 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [809] Underfull \vbox (badness 10000) has occurred while \output is active [810] Underfull \hbox (badness 5260) in paragraph at lines 4016--4019 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a C in-te-ger for-mat such as [811] [812] [813] [814] [815] Underfull \hbox (badness 5939) in paragraph at lines 4349--4354 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 onefile[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 family[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 fonts[]\T1/ptm/m/n/10 , [816] [817] [818] [819] [820] [821] [822] [823] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4869--4869 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [824] [825] Underfull \hbox (badness 1348) in paragraph at lines 5074--5077 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [826] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5098--5098 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 5139--5145 []\T1/ptm/m/n/10 For use with []\T1/pcr/m/n/10 onefile = FALSE []\T1/ptm/m/n/10 give a []\T1/pcr/m/n/10 printf []\T1/ptm/m/n/10 for-mat such as [827] Underfull \hbox (badness 1112) in paragraph at lines 5172--5176 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), []\T1/pcr/m/n/10 "CP1251.enc" [828] Underfull \hbox (badness 1755) in paragraph at lines 5314--5316 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [829] [830] [831] Underfull \hbox (badness 7344) in paragraph at lines 5494--5496 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 5505--5509 [][][]\T1/pcr/m/n/10 postscriptFonts[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 Devices[][][][]\T1/ptm/m/n/10 , and [][][]\T1/pcr/m/n/10 check.options[][][] []\T1/ptm/m/n/10 which is called from both [832] [833] Underfull \hbox (badness 1552) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Bookman"[]\T1 /ptm/m/n/10 , []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "He lvetica"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Pal atino" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "Times"[]\T1/ptm/m/n/10 ; []\T1/pc r/m/n/10 "URWGothic"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5632--5641 []\T1/pcr/m/n/10 "URWBookman"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusMon"[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "NimbusSan" []\T1/ptm/m/n/10 (syn-onym []\T1/p cr/m/n/10 "URWHelvetica"[]\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5642--5644 []\T1/ptm/m/n/10 There are also map-pings for []\T1/pcr/m/n/10 "ComputerModern" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ComputerModernItalic" []\T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5674--5680 []\T1/pcr/m/n/10 "Japan1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1HeiMin"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Japan1GothicBBB"[]\T1/ptm/m/n/10 , and []\T1/p cr/m/n/10 "Japan1Ryumin" []\T1/ptm/m/n/10 for [834] Underfull \hbox (badness 5388) in paragraph at lines 5700--5702 []\T1/pcr/m/n/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/p cr/m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [835] [836] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5803--5803 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [837] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5915--5915 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [838] [839] Underfull \hbox (badness 10000) in paragraph at lines 6001--6003 []\T1/ptm/m/n/10 Calling []\T1/pcr/m/n/10 quartz() []\T1/ptm/m/n/10 sets [][][] \T1/pcr/m/n/10 .Device[][][] []\T1/ptm/m/n/10 to []\T1/pcr/m/n/10 "quartz" []\T 1/ptm/m/n/10 for on-screen de-vices and to [840] [841] [842] [843] [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6368--6368 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 6382--6385 []\T1/pcr/m/n/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space (r ed/green/blue) into HSV space [845] [846] [847] [848] [849] [850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6717--6717 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6724--6724 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [851] [852] [853] [854] Underfull \hbox (badness 10000) in paragraph at lines 6990--6995 []\T1/ptm/m/n/10 arguments []\T1/pcr/m/n/10 width[]\T1/ptm/m/n/10 , []\T1/pcr/m /n/10 height[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pointsize[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 record[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 rescale[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 xpinch[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 ypinch[]\T1/ptm/m/n/ 10 , []\T1/pcr/m/n/10 bg[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 canvas[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 gamma[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 xpos[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 ypos[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 buffered[]\T1/ ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 restoreConsole[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 clickToConfi rm[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 title[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 fillOddEven []\T1/ptm/m/n/10 and [855] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7096--7096 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [856] Underfull \hbox (badness 3590) in paragraph at lines 7135--7138 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 2393) in paragraph at lines 7135--7138 \T1/pcr/m/n/10 en . wikipedia . org / wiki / Xlib$[][]\T1/ptm/m/n/10 ) and one us-ing cairo-graph-ics ([][]$\T1/pcr/m/n/10 https : / / www . Overfull \hbox (12.78088pt too wide) in paragraph at lines 7146--7146 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [857] Underfull \hbox (badness 1189) in paragraph at lines 7211--7213 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [858] Underfull \hbox (badness 10000) in paragraph at lines 7316--7318 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for CJ K lan-guages and [859] Underfull \hbox (badness 10000) in paragraph at lines 7362--7369 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of [] \T1/pcr/m/n/10 quote(pi) []\T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7362--7369 []\T1/pcr/m/n/10 expression(10^degree)[]\T1/ptm/m/n/10 ) have been seen on Linu x sys-tems which have the Wine [860] Underfull \hbox (badness 5607) in paragraph at lines 7446--7450 []\T1/pcr/m/n/10 type = "Xlib" []\T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-d o-Color', `GrayScale', []\T1/pcr/m/n/10 StaticGray []\T1/ptm/m/n/10 and [861] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7498--7498 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [862] [863] Underfull \hbox (badness 5637) in paragraph at lines 7630--7636 []\T1/pcr/m/n/10 "Courier"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Helvetica" []\T1 /ptm/m/n/10 (the de-fault), []\T1/pcr/m/n/10 "Helvetica-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 7663--7666 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [864] [865] [866] Underfull \hbox (badness 1231) in paragraph at lines 7832--7834 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., []\T1/pcr/m/n/10 number[i] []\T1/ptm/m/n/10 is the mul-ti-plic-ity of [867] [868]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use []\T1/pcr/m/n/10 library(help = [869] [870] [871] [872] [873] [874] [875] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 at = NULL[]\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [876] [877] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [878] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][][]\T1/pcr /m/n/10 par[][][]("xaxp") []\T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][][]\T1/pcr/m/n/10 par[][][]("yaxp") []\T1/ptm/m/n/10 de-pend-ing on the []\T 1/pcr/m/n/10 side []\T1/ptm/m/n/10 ar-gu-ment ([]\T1/pcr/m/n/10 par("xaxp") []\ T1/ptm/m/n/10 if [879] [880] Overfull \hbox (47.58038pt too wide) in paragraph at lines 770--770 []\T1/pcr/m/n/9 ## 1e-01 1e+01 1e+03 1e+05 1e+07 1e+09 1e+11 ; since R 4.2.0: 1e-2 1e0 1e2 .. 1e10[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 782--782 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 819--819 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [881] [882] [883] Underfull \hbox (badness 10000) in paragraph at lines 966--970 [][][]\T1/pcr/m/n/10 plot[][][](..., type = "h")[]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 dotchart[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 hist[][][] []\T1 /ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-abl e. Overfull \hbox (133.98029pt too wide) in paragraph at lines 983--983 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 985--985 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 987--987 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [884] [885] [886] [887] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1271--1271 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [888] [889] [890] Underfull \hbox (badness 2503) in paragraph at lines 1433--1442 \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 horizontal []\T1/ptm/m/n/10 is false, and []\T1/pcr/m/n/10 xlim []\T1/ptm/m/n/10 hor-i-zon-tally. []\T1/pcr/m/n/10 xaxt[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 yaxt[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3375) in paragraph at lines 1468--1470 []\T1/ptm/m/n/10 whisker line type (de-fault: []\T1/pcr/m/n/10 "dashed"[]\T1/pt m/m/n/10 ), [891] [892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1543--1543 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1549--1549 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1550--1550 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [893] [894] [895] [896] [897] Underfull \hbox (badness 10000) in paragraph at lines 1853--1859 [][][]\T1/pcr/m/n/10 contourLines[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 filled.contour[][][] []\T1/ptm/m/n/10 for color-filled con-tours, [][][]\T1/pcr /m/n/10 contourplot[][][] []\T1/ptm/m/n/10 (and Overfull \hbox (9.78043pt too wide) in paragraph at lines 1873--1873 []\T1/pcr/m/n/9 contour(x, x, z, ylim = c(-6, 6), nlevels = 20, lty = 2, metho d = "simple",[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 contour(z, levels=levs[-c(1,length(levs))], col = 1:5, lwd = 1 :3 *1.5, lty = 1:3)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1901--1901 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1910--1910 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [898] [899] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1995--1995 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [900] [901] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2124--2124 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.values = given .depth, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2129--2129 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [902] [903] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2303--2303 []\T1/pcr/m/n/10 dotchart(x, labels = NULL, groups = NULL, gdata = NULL, offse t = 1/8, Overfull \hbox (54.78088pt too wide) in paragraph at lines 2304--2304 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [904] Underfull \hbox (badness 1430) in paragraph at lines 2335--2337 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/pcr/m/n/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [905] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2416--2416 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2428--2435 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [906] Underfull \hbox (badness 7273) in paragraph at lines 2510--2514 [][][]\T1/pcr/m/n/10 contour[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 image [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 hcl.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gray.colors[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 palette[][][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 contourplot[][][] []\T1/p tm/m/n/10 and [907] [908] [909] [910] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2758--2758 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [911] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2795--2795 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [912] [913] Underfull \hbox (badness 1226) in paragraph at lines 2923--2927 \T1/pcr/m/n/10 1)[]\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies []\T1 /pcr/m/n/10 counts/n []\T1/ptm/m/n/10 and in gen-eral sat-isfy [914] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2980--2980 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [915] Underfull \hbox (badness 10000) in paragraph at lines 3042--3045 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][][]\T1 /pcr/m/n/10 hist.default[][][] []\T1/ptm/m/n/10 such as Overfull \hbox (15.18042pt too wide) in paragraph at lines 3093--3093 []\T1/pcr/m/n/9 ## The default fuzz in hist.default() "kills" this, with a "w rong" message:[] [916] [917] [918] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3257--3257 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3262--3262 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 useRaster []\T1/ptm/m/n/10 is not spec-i-f ied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") []\T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3404--3409 [][][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage []\T1/pt m/m/n/10 is []\T1/pcr/m/n/10 "yes" []\T1/ptm/m/n/10 or it is [921] [922] [923] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3590--3590 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3613--3613 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [924] [925] [926] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3798--3798 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3799--3799 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3803--3803 [] \T1/pcr/m/n/9 cex = 1+(-1:2)/8, trace = TRUE)# trace: show computed l engths & coords[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3813--3813 [] \T1/pcr/m/n/9 title("legend(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 top\TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 , lty = c(2, -1, 1), pch = c(NA, 3, 4), merge = TRUE)",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3844--3844 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3870--3870 []\T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Filled\TS1/pcr/m/n/9 ' \T1/pc r/m/n/9 boxes -- see also example(barplot) which may call legend(*, fill=)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3872--3872 []\T1/pcr/m/n/9 legend("topright", rownames(VADeaths), fill = gray.colors(nrow (VADeaths)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3883--3883 []\T1/pcr/m/n/9 legend("bottomright", paste("sin(", 1:7, "pi * x)"), col = 1:7 , lty = 1:7,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3898--3898 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Underfull \vbox (badness 10000) has occurred while \output is active [928] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3906--3906 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3908--3908 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3916--3916 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3926--3926 []\T1/pcr/m/n/9 legend("bottomleft", c("This legend", "has", "optimally sized" , "columns."),[] [929] Underfull \hbox (badness 10000) in paragraph at lines 3988--3992 [][][]\T1/pcr/m/n/10 lines.formula[][][] []\T1/ptm/m/n/10 for the for-mula meth od; [][][]\T1/pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , par-tic-u-larly for []\ T1/pcr/m/n/10 type %in% [930] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4100--4100 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [931] [932] [933] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4254--4254 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [934] Underfull \hbox (badness 3930) in paragraph at lines 4333--4335 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [935] [936] [937] [938] [939] Underfull \hbox (badness 1286) in paragraph at lines 4644--4647 []\T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify []\T1/pcr/m/n /10 oma []\T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4652--4657 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [940] [941] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4748--4748 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [942] Underfull \hbox (badness 1264) in paragraph at lines 4944--4957 \T1/ptm/m/n/10 func-tions such as [][][]\T1/pcr/m/n/10 plot.default[][][][]\T1/ ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.window[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 points[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lines[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 abline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 axis[][][][]\T1/ptm/m/n/10 , [943] [944] [945] [946] Underfull \hbox (badness 10000) in paragraph at lines 5210--5213 [947 ] Underfull \hbox (badness 10000) in paragraph at lines 5271--5273 [948 ] [949] [950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5517--5517 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5518--5518 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [951] [952] [953] [954] [955] [956] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5884--5884 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [957] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.5943 \aliasA{plot}{plot.default}{plot} [958] [959] [960] [961] [962] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6275--6275 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6281--6281 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [963] [964] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6405--6405 [] \T1/pcr/m/n/10 main = paste("Histogram of", paste(x$xname, co llapse = "\n")),[] [965] [966] [967] [968] Underfull \hbox (badness 10000) in paragraph at lines 6711--6713 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [969] [970] Underfull \hbox (badness 1028) in paragraph at lines 6805--6807 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6848--6849 [][] [971 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6942--6942 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [972] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6973--6973 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [973] [974] Underfull \hbox (badness 10000) in paragraph at lines 7095--7097 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 7122--7122 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7128--7128 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [975] Underfull \hbox (badness 2600) in paragraph at lines 7185--7187 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther []\T 1/pcr/m/n/10 "winding" []\T1/ptm/m/n/10 or [976] [977] [978] [979] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7417--7417 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [980] [981] [982] [983] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7804--7804 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7808--7808 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [986] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7820--7820 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [987] [988] [989] [990] [991] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8169--8169 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8172--8172 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8176--8176 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [992] [993] [994] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8347--8347 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8348--8348 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [995] [996] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8452--8452 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] [997] Underfull \hbox (badness 1112) in paragraph at lines 8511--8515 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 number[i] == 1[]\T1/ptm/m/n/10 , a (sligh tly en-larged) usual plot-ting sym-bol ([]\T1/pcr/m/n/10 pch[]\T1/ptm/m/n/10 ) is drawn. For [998] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8586--8586 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [999] [1000] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8723--8723 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [1001] [1002] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8908--8908 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [1003] Underfull \hbox (badness 1215) in paragraph at lines 8936--8938 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/pcr/m /n/10 par(c("font.sub", Underfull \hbox (badness 1584) in paragraph at lines 8970--8976 []\T1/ptm/m/n/10 The po-si-tions of []\T1/pcr/m/n/10 xlab[]\T1/ptm/m/n/10 , []\ T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sub []\T1/ptm/m/n/10 a re []\T1/pcr/m/n/10 line []\T1/ptm/m/n/10 (de-fault for []\T1/pcr/m/n/10 xlab [ ]\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 ylab []\T1/ptm/m/n/10 be-ing [1004] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9018 \HeaderA{units}{Graphical Units}{units} [1005] Underfull \hbox (badness 1205) in paragraph at lines 9083--9085 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9202--9202 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [1008]) (./grid-pkg.tex Chapter 6. [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] Underfull \hbox (badness 4859) in paragraph at lines 634--637 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1019] [1020] [1021] [1022] [1023] [1024] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1028--1028 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1025] [1026] [1027] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1239--1239 [] \T1/pcr/m/n/9 vpList(vpStack(viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1240--1240 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1241--1241 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 viewport(x=0.1, y=0.1, width=0.5 , height=0.5,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1244--1244 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1028] [1029] [1030] [1031] Underfull \hbox (badness 3219) in paragraph at lines 1503--1506 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [1032] [1033] [1034] [1035] [1036] [1037] [1038] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1891--1891 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1039] [1040] [1041] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2105--2105 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2106--2106 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2107--2107 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1042] Underfull \hbox (badness 2961) in paragraph at lines 2142--2147 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns []\T1/pcr/m/n/10 preDrawDetails[]\T1/ptm/m/n/10 , [1043] Underfull \hbox (badness 4479) in paragraph at lines 2230--2233 []\T1/ptm/m/n/10 Both func-tions call []\T1/pcr/m/n/10 editDetails []\T1/ptm/m/ n/10 to al-low a grob to per-form cus-tom ac-tions and [1044] [1045] [1046] Underfull \hbox (badness 2894) in paragraph at lines 2437--2444 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1047] [1048] [1049] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2593--2593 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] [1050] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2664--2664 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1051] [1052] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2826--2826 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1053] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2858--2858 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1054] [1055] Underfull \hbox (badness 10000) in paragraph at lines 3041--3043 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1056] [1057] [1058] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3228--3228 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1059] [1060] [1061] [1062] [1063] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3543--3543 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1064] [1065] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3639--3639 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, width=0.25, height=0.25, just= c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3676--3682 []\T1/ptm/m/n/10 There are two hooks called []\T1/pcr/m/n/10 "before.grid.newpa ge" []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 "grid.newpage" []\T1/ptm/m/n/10 (see [1066] [1067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1068] [1069] [1070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3976--3976 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3991--3991 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1071] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4012--4012 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] Underfull \hbox (badness 1067) in paragraph at lines 4761--4764 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1084] [1085] [1086] [1087] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4977--4977 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1088] [1089] Underfull \hbox (badness 7256) in paragraph at lines 5112--5114 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1090] [1091] [1092] [1093] [1094] [1095] Underfull \hbox (badness 2726) in paragraph at lines 5561--5565 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 gridCoords []\T1/ptm/m/n/10 a nu-meric ve c-tor. For []\T1/pcr/m/n/10 gridGrobCoords []\T1/ptm/m/n/10 a list Underfull \hbox (badness 1231) in paragraph at lines 5561--5565 \T1/ptm/m/n/10 of []\T1/pcr/m/n/10 "GridCoords" []\T1/ptm/m/n/10 ob-jects. For []\T1/pcr/m/n/10 gridGTreeCoords []\T1/ptm/m/n/10 a list of ei-ther [1096] [1097] Underfull \hbox (badness 2080) in paragraph at lines 5632--5637 []\T1/ptm/m/n/10 Either a []\T1/pcr/m/n/10 "GridGrobCoords" []\T1/ptm/m/n/10 ob -ject (a list of lists with com-po-nents []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 y[]\T1/ptm/m/n/10 ) or a [1098] [1099] [1100] Underfull \hbox (badness 10000) in paragraph at lines 5812--5814 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 grid.legend()[]\T1/ptm/m/n/10 : all the a r-gu-ments above are passed to [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6900--6900 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1118] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7020--7020 []\T1/pcr/m/n/10 viewportTransform(group, shear=groupShear(), flip=groupFlip() , device=TRUE) [1119] [1120] Underfull \hbox (badness 1867) in paragraph at lines 7122--7124 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in []\T1/pcr/m/n/10 downViewport []\T1/ptm/m/n/10 or [1121] Underfull \hbox (badness 10000) in paragraph at lines 7159--7165 [][][]\T1/pcr/m/n/10 viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 push Viewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 popViewport[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 seekViewport[][][][]\T1/ptm/m/n/10 , [1122] [1123] [1124] [1125] [1126] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7495--7495 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1127]) (./methods-pkg.tex [1128] Chapter 7. [1129] [1130] Underfull \hbox (badness 1688) in paragraph at lines 166--171 []\T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how co-erce meth-ods work. Use [1131] [1132] [1133] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] []\T1/ptm/m/n/10 for other in- for-ma-tion about group generic func-tions; [][]Meth- [1134] [1135] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1136] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1137] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] [1153] [1154] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/pcr/m/n/10 insertSource []\T1/ptm/m/n/ 10 can be an ob-ject of class [1155] [1156] [1157] Underfull \hbox (badness 1478) in paragraph at lines 2213--2218 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/pcr/m/n/10 where = [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 2327--2331 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][][]\T1/pcr/m/n/10 environment [][][][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call [1160] [1161] [1162] Underfull \hbox (badness 3792) in paragraph at lines 2573--2576 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/pcr/m/n/10 setGeneric[][][] []\ T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 c re-ate ob-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2604--2608 []\T1/ptm/m/n/10 Object of class []\T1/pcr/m/n/10 "optionalMethod" []\T1/ptm/m/ n/10 (a union of classes []\T1/pcr/m/n/10 "function" []\T1/ptm/m/n/10 and [1163] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2660--2660 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1164] [1165] [1166] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2879--2879 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1167] [1168] [1169] [1170] [1171] [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 3402--3407 []\T1/ptm/m/n/10 Function []\T1/pcr/m/n/10 implicitGeneric() []\T1/ptm/m/n/10 r e-turns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3402--3407 []\T1/pcr/m/n/10 setGenericImplicit() []\T1/ptm/m/n/10 turns a generic im-plici t, []\T1/pcr/m/n/10 prohibitGeneric() []\T1/ptm/m/n/10 pre-vents [1174] [1175] Underfull \hbox (badness 10000) in paragraph at lines 3530--3534 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][][]\T1/pcr/m/n/10 getClass[][][] []\T1/ptm/m/n/10 and the de-scrip-tion of class [1176] Overfull \hbox (14.78088pt too wide) in paragraph at lines 3641--3650 [] [1177] [1178] Underfull \hbox (badness 10000) in paragraph at lines 3761--3762 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longit ude = Underfull \hbox (badness 10000) in paragraph at lines 3808--3809 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { [1179] Underfull \hbox (badness 10000) in paragraph at lines 3845--3846 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , Underfull \hbox (badness 6157) in paragraph at lines 3907--3911 []\T1/ptm/m/n/10 A call to [][][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) [] \T1/ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1180] [1181] [1182] [1183] [1184] [1185] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4312--4312 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4313--4313 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1186] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4370--4370 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1187] [1188] [1189] Underfull \hbox (badness 2126) in paragraph at lines 4578--4586 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][][]\T1/pcr/m/n/10 setMethod[][][]()[]\T1/ptm/m/n/10 , [1190] [1191] [1192] Underfull \hbox (badness 10000) in paragraph at lines 4815--4824 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1193] [1194] [1195] [1196] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1197] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5231--5231 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5245--5245 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1198] [1199] Underfull \hbox (badness 10000) in paragraph at lines 5363--5364 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1200] [1201] Underfull \hbox (badness 3803) in paragraph at lines 5520--5522 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1202] [1203] [1204] Underfull \hbox (badness 1087) in paragraph at lines 5752--5757 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1205] [1206] [1207] [1208] [1209] [1210] Underfull \hbox (badness 10000) in paragraph at lines 6218--6234 []\T1/ptm/m/n/10 The de-fault method for []\T1/pcr/m/n/10 $initialize() []\T1/p tm/m/n/10 is equiv-a-lent to in-vok-ing the method [1211] [1212] Underfull \hbox (badness 1248) in paragraph at lines 6351--6355 []\T1/ptm/m/n/10 Typically, a spe-cial-ized []\T1/pcr/m/n/10 $initialize() []\T 1/ptm/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 then in-vokes []\T1/pcr/m/n/10 $initFields() []\T1/ptm/m/n/10 to per-form stan-dard ini-tial-iza-tion, as shown in the [1213] Underfull \hbox (badness 4647) in paragraph at lines 6506--6508 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1214] [1215] Underfull \hbox (badness 2875) in paragraph at lines 6655--6664 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6655--6664 [][][]\T1/pcr/m/n/10 setValidity[][][][]\T1/ptm/m/n/10 ). Such meth-ods are of- ten a good idea; they will be called by call-ing [1216] Underfull \vbox (badness 10000) has occurred while \output is active [1217] [1218] [1219] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6981 \aliasA{S4}{S3Part}{S4} [1220] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1221] [1222] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7208--7208 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7212--7212 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1223] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7237 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7239 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7240 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7242 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7243 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7304--7308 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1224] Underfull \hbox (badness 6708) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "abs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sign"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "sqrt"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ceiling"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "floor"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trunc" []\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cummax"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "acosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "asin"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "asinh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "atan"[]\T1/p tm/m/n/10 , []\T1/pcr/m/n/10 "atanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "exp"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "expm1"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "c os"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7317--7329 []\T1/pcr/m/n/10 "cosh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cospi"[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 "sin"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "sinh"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "sinpi"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tan"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanh"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "tanp i"[]\T1/ptm/m/n/10 , [1225] [1226] Underfull \hbox (badness 1694) in paragraph at lines 7480--7482 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7504--7507 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is []\T1/pcr/m/n/10 selectS uperClasses() []\T1/ptm/m/n/10 which calls [1227] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7525--7525 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8630--8630 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1241] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8705--8705 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1242] [1243] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8967--8967 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1246] [1247] [1248] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9175--9175 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1249] [1250] [1251] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9437--9437 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1252] [1253] [1254] [1255] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9745--9745 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1256] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9855--9855 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9866--9866 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1257] [1258] [1259] [1260] [1261] [1262] [1263] [1264] [1265] [1266] Underfull \hbox (badness 10000) in paragraph at lines 10564--10566 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., []\T1/pcr/m/n/10 "functi on" []\T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10572--10576 []\T1/pcr/m/n/10 "functionWithTrace" []\T1/ptm/m/n/10 ex-tends []\T1/pcr/m/n/10 "function"[]\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1267] [1268] [1269]) (./parallel-pkg.tex [1270] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/p cr/m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [][] RNG[][][]: see [1271] Underfull \hbox (badness 4242) in paragraph at lines 97--99 []\T1/ptm/m/n/10 a vec-tor for []\T1/pcr/m/n/10 clusterApply []\T1/ptm/m/n/10 a nd []\T1/pcr/m/n/10 clusterApplyLB[]\T1/ptm/m/n/10 , a ma-trix for [1272] [1273] Underfull \hbox (badness 1024) in paragraph at lines 214--217 []\T1/ptm/m/n/10 Two ex-cep-tions: []\T1/pcr/m/n/10 parLapply []\T1/ptm/m/n/10 has ar-gu-ment []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 not []\T1/pcr/m/n/10 x []\T1 /ptm/m/n/10 for con-sis-tency with [][][]\T1/pcr/m/n/10 lapply[][][][]\T1/ptm/m /n/10 , and [1274] Underfull \hbox (badness 1320) in paragraph at lines 301--304 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 445--447 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for []\T1/pcr/m/ n/10 Rscript []\T1/ptm/m/n/10 such as [1277] [1278] [1279] [1280] [1281] Underfull \hbox (badness 1917) in paragraph at lines 779--788 []\T1/pcr/m/n/10 mcfork []\T1/ptm/m/n/10 re-turns an ob-ject of the class []\T1 /pcr/m/n/10 "childProcess" []\T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 779--788 []\T1/pcr/m/n/10 "masterProcess" []\T1/ptm/m/n/10 to the child: both the classe s in-herit from class []\T1/pcr/m/n/10 "process"[]\T1/ptm/m/n/10 . If [1282] [1283] Overfull \hbox (60.78088pt too wide) in paragraph at lines 872--872 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1284] [1285] [1286] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1063--1063 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1067--1067 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1287] Underfull \hbox (badness 5388) in paragraph at lines 1182--1187 []\T1/pcr/m/n/10 mcparallel []\T1/ptm/m/n/10 re-turns an ob-ject of the class [ ]\T1/pcr/m/n/10 "parallelJob" []\T1/ptm/m/n/10 which in-her-its from [1288] Underfull \hbox (badness 10000) in paragraph at lines 1206--1214 []\T1/ptm/m/n/10 The be-haviour with []\T1/pcr/m/n/10 mc.set.seed = TRUE []\T1/ ptm/m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1289] [1290] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1359--1359 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1373--1373 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1291] Underfull \hbox (badness 1577) in paragraph at lines 1402--1405 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/pcr/m/n/10 .Random.seed []\T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1449--1451 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 nextRNGStream []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 nextRNGSubStream[]\T1/ptm/m/n/10 , a value which can be as-signed to [1292] [1293]) (./splines-pkg.tex [1294] Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 496--496 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1303] Underfull \hbox (badness 1043) in paragraph at lines 597--599 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and []\T1/pcr/m/n/10 splineOrder(objec t) - 1 []\T1/ptm/m/n/10 spec-i-fy-ing the [1304] [1305] Overfull \hbox (25.98041pt too wide) in paragraph at lines 712--712 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1306] [1307] [1308]) (./stats-pkg.tex Chapter 10. [1309] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() []\T1/ptm/m/n/10 re-turns a char-ac-ter string, one of []\T1/pcr/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ordered"[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 "factor"[]\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1310] [1311] [1312] [1313] [1314] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1315] Overfull \hbox (6.78088pt too wide) in paragraph at lines 468--468 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1316] [1317] [1318] [1319] [1320] [1321] Underfull \hbox (badness 1024) in paragraph at lines 887--889 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/pcr/m/n/10 l m []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 aov[]\T1/ptm/m/n/10 , or a for-mula for [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1625--1625 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1628--1628 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1333] [1334] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1775--1775 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1335] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1787--1787 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346] [1347] [1348] [1349] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2805--2805 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1350] [1351] [1352] [1353] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3053--3053 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1354] [1355] [1356] Underfull \hbox (badness 10000) in paragraph at lines 3264--3266 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Bartlett test of homo geneity of [1357] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3313--3313 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3314--3314 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1358] [1359] [1360] [1361] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3642. [1362] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1363] [1364] [1365] [1366] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3987--3987 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1367] [1368] [1369] [1370] [1371] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4276--4276 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4277--4277 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1372] [1373] [1374] [1375] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4518--4518 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1376] [1377] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4693--4693 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1378] [1379] Underfull \hbox (badness 3989) in paragraph at lines 4787--4794 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1380] [1381] [1382] [1383] [1384] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5172--5172 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5174--5174 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1385] [1386] [1387] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5396--5396 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5414--5414 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1388] [1389] [1390] [1391] Underfull \hbox (badness 1436) in paragraph at lines 5624--5629 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5624--5629 \T1/ptm/m/n/10 one of the strings []\T1/pcr/m/n/10 "everything"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "all.obs"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "complete.obs" []\T1/ptm/m/n/10 , [1392] [1393] [1394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5827--5827 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1395] [1396] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5994--5994 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1397] [1398] [1399] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6179--6179 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1400] [1401] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6287--6287 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1402] [1403] [1404] [1405] Underfull \hbox (badness 5954) in paragraph at lines 6550--6552 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1406] Underfull \hbox (badness 2503) in paragraph at lines 6632--6635 []\T1/ptm/m/n/10 Objects of class []\T1/pcr/m/n/10 "hclust" []\T1/ptm/m/n/10 ca n be con-verted to class []\T1/pcr/m/n/10 "dendrogram" []\T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6636--6638 []\T1/pcr/m/n/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro-g ram []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6639--6644 \T1/ptm/m/n/10 has []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y [ ]\T1/ptm/m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be- fore \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, [1407] Underfull \hbox (badness 7238) in paragraph at lines 6675--6678 [][][]\T1/pcr/m/n/10 dendrapply[][][] []\T1/ptm/m/n/10 for ap-ply-ing a func-ti on to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][][]\T1/pcr/m/n/10 order.dend rogram[][][] []\T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6687--6687 []\T1/pcr/m/n/9 str(dend1, max.level = 2, last.str = "\TS1/pcr/m/n/9 '\T1/pcr /m/n/9 ") # only the first two sub-levels[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6710--6710 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6725--6725 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] [1408] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6740--6740 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1409] [1410] [1411] Underfull \vbox (badness 10000) has occurred while \output is active [1412] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6994--6994 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1413] [1414] Underfull \vbox (badness 10000) has occurred while \output is active [1415] [1416] [1417] [1418] Underfull \hbox (badness 10000) in paragraph at lines 7394--7398 []\T1/pcr/m/n/10 "maximum"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "manhattan"[]\T1/ ptm/m/n/10 , []\T1/pcr/m/n/10 "canberra"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "bi nary" []\T1/ptm/m/n/10 or [1419] Underfull \hbox (badness 6493) in paragraph at lines 7493--7496 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/pcr/m/n/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1420] [1421] Underfull \hbox (badness 10000) in paragraph at lines 7630--7633 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1422] [1423] [1424] [1425] [1426] [1427] Underfull \hbox (badness 10000) in paragraph at lines 8042--8047 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences [] \T1/pcr/m/n/10 x[t][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 x[t-1][]\T1/ptm/m/n/10 , ..., [1428] [1429] [1430] [1431] [1432] [1433] Underfull \hbox (badness 1210) in paragraph at lines 8397--8399 []\T1/ptm/m/n/10 Components of []\T1/pcr/m/n/10 control []\T1/ptm/m/n/10 can al so be sup-plied as named ar-gu-ments to [1434] [1435] [1436] [1437] [1438] [1439] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1440] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8905--8905 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8908--8908 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9488--9488 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9489--9489 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1449] [1450] [1451] Underfull \hbox (badness 7291) in paragraph at lines 9668--9670 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1452] [1453] [1454] [1455] [1456] [1457] [1458] Underfull \hbox (badness 6944) in paragraph at lines 10160--10166 [][][]\T1/pcr/m/n/10 ftable.formula[][][] []\T1/ptm/m/n/10 for the for-mula in- ter-face (which al-lows a []\T1/pcr/m/n/10 data = . []\T1/ptm/m/n/10 ar-gu-ment ); [1459] [1460] [1461] Underfull \hbox (badness 3758) in paragraph at lines 10374--10377 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1462] [1463] [1464] [1465] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10618--10618 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10644--10649 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1466] Underfull \hbox (badness 4132) in paragraph at lines 10683--10687 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10737--10743 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form []\T1/pcr/m/n/10 first:second []\T1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1467] Underfull \hbox (badness 10000) in paragraph at lines 10788--10791 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][][]\T1/pcr/m/n/10 coeffic ients[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 effects[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 fitted.values []\T1/ptm/m/n/10 and [1468] [1469] [1470] Underfull \hbox (badness 2142) in paragraph at lines 11005--11008 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1471] Underfull \hbox (badness 1708) in paragraph at lines 11086--11090 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1472] Underfull \hbox (badness 10000) in paragraph at lines 11128--11134 [][][]\T1/pcr/m/n/10 glm[][][] []\T1/ptm/m/n/10 for com-put-ing []\T1/pcr/m/n/1 0 glm.obj[]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 anova.glm[][][][]\T1/ptm/m/n/1 0 ; the cor-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11166--11171 []\T1/pcr/m/n/10 "average" []\T1/ptm/m/n/10 (= UP-GMA), []\T1/pcr/m/n/10 "mcqui tty" []\T1/ptm/m/n/10 (= WPGMA), []\T1/pcr/m/n/10 "median" []\T1/ptm/m/n/10 (= [1473] [1474] Underfull \hbox (badness 2635) in paragraph at lines 11299--11302 \T1/ptm/m/n/10 There are [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/n/10 , [][ ][]\T1/pcr/m/n/10 plot[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 identify []\ T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 identify.hclust[][][][]\T1/ptm/m/n/10 ) meth-ods and the [1475] [1476] [1477] Underfull \hbox (badness 1694) in paragraph at lines 11482--11485 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1478] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11580--11580 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1479] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11613--11613 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11626--11630 []\T1/ptm/m/n/10 Character string to se-lect an []\T1/pcr/m/n/10 "additive" []\ T1/ptm/m/n/10 (the de-fault) or [1480] [1481] [1482] [1483] [1484] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11948--11948 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1485] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11963 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 12023--12023 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1486] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12035--12035 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12088--12093 []\T1/ptm/m/n/10 The op-tional []\T1/pcr/m/n/10 infl[]\T1/ptm/m/n/10 , []\T1/pc r/m/n/10 res []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 sd []\T1/ptm/m/n/10 ar-gu-me nts are there to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12105--12107 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1487] [1488] [1489] [1490] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12360--12360 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12361--12361 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1491] [1492] [1493] [1494] [1495] [1496] Underfull \hbox (badness 10000) in paragraph at lines 12707--12709 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/pcr/m/n/10 solve.de fault[][][] []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12730--12732 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1497] [1498] [1499] [1500] [1501] Underfull \hbox (badness 3417) in paragraph at lines 13037--13039 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class []\T1/pcr/ m/n/10 "kmeans"[]\T1/ptm/m/n/10 , typ-i-cally the re-sult []\T1/pcr/m/n/10 ob [ ]\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 ob <- Underfull \hbox (badness 2894) in paragraph at lines 13043--13047 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 13043--13047 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 "Hartigan-Wong"[]\T1/ptm/m/n/10 ): if pos-i-ti ve (or true), trac-ing in-for-ma-tion on the [1502] [1503] [1504] [1505] [1506] [1507] Underfull \hbox (badness 1496) in paragraph at lines 13457--13463 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1508] [1509] [1510] [1511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13706--13706 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1512] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13807--13807 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1513] Underfull \hbox (badness 4518) in paragraph at lines 13855--13860 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1514] [1515] [1516] Underfull \hbox (badness 10000) in paragraph at lines 14062--14066 []\T1/ptm/m/n/10 More []\T1/pcr/m/n/10 lm() []\T1/ptm/m/n/10 ex-am-ples are ava il-able e.g., in [][][]\T1/pcr/m/n/10 anscombe[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 attitude[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 freeny[][][] []\T1/ptm/m/n/10 , [1517] [1518] [1519] [1520] [1521] Underfull \hbox (badness 1163) in paragraph at lines 14402--14410 \T1/ptm/m/n/10 els, [][][]\T1/pcr/m/n/10 influence[][][] []\T1/ptm/m/n/10 (etc on that page) for re-gres-sion di-ag-nos-tics, [][][]\T1/pcr/m/n/10 weighted.re siduals[][][][]\T1/ptm/m/n/10 , [1522] [1523] Underfull \hbox (badness 4518) in paragraph at lines 14522--14527 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1524] [1525] [1526] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14710--14710 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1527] [1528] [1529] [1530] [1531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15054--15054 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15055--15055 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15148--15148 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1533] [1534] [1535] [1536] [1537] [1538] [1539] Underfull \hbox (badness 2726) in paragraph at lines 15557--15560 []\T1/ptm/m/n/10 character; one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m/n/10 , [ ]\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cauchit"[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 "cloglog"[]\T1/ptm/m/n/10 , [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15651--15651 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] [1549] [1550] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16278--16278 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1551] [1552] Underfull \hbox (badness 1490) in paragraph at lines 16425--16430 \T1/ptm/m/n/10 those spec-i-fied in []\T1/pcr/m/n/10 ... []\T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1553] Underfull \hbox (badness 1648) in paragraph at lines 16491--16493 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, [1554] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16576--16576 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts.arg = list(a = "contr.sum" , b = contr.poly))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16577--16577 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] [1563] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17134--17134 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1564] [1565] [1566] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17366--17366 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] [1575] [1576] Underfull \vbox (badness 10000) has occurred while \output is active [1577] Overfull \hbox (42.18039pt too wide) in paragraph at lines 18088--18088 []\T1/pcr/m/n/9 ## adjusting the convergence test by adding \TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 scaleOffset\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 to its denominator RSS:[] Underfull \vbox (badness 10000) has occurred while \output is active [1578] Overfull \hbox (74.58035pt too wide) in paragraph at lines 18106--18106 []\T1/pcr/m/n/9 ## Here, requiring close convergence, must use more accurate n umerical differentiation,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 18107--18107 []\T1/pcr/m/n/9 ## as this typically gives Error: "step factor .. reduced belo w \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 .."[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 18111--18111 []\T1/pcr/m/n/9 ## central differencing works here typically (PR#18165: not co nverging on *some*):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18112--18112 []\T1/pcr/m/n/9 ctr2 <- nls.control(nDcentral=TRUE, tol = 8e-8, # <- even smal ler than above[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 18115--18115 [] \T1/pcr/m/n/9 (grepl("^aarch64.*linux", R.version$platform) && grepl ("^NixOS", osVersion)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18147--18147 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1579] [1580] [1581] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18323--18323 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1582] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18370--18370 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18417--18417 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1583] [1584] [1585] [1586] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18623--18623 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1587] [1588] [1589] [1590] [1591] Underfull \hbox (badness 1248) in paragraph at lines 18938--18941 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18951--18955 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 18959--18963 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 control$trace []\T1/ptm/m/n/10 is pos-i-tive . De-faults to ev-ery 10 it-er-a-tions for []\T1/pcr/m/n/10 "BFGS" []\T1/ptm/m/ n/10 and [1592] Underfull \hbox (badness 2042) in paragraph at lines 19017--19019 []\T1/ptm/m/n/10 indicates an er-ror from the []\T1/pcr/m/n/10 "L-BFGS-B" []\T1 /ptm/m/n/10 method; see com-po-nent [1593] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19123--19123 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19166--19166 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19184--19184 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 19187--19187 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19207--19207 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1595] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19210--19210 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19245--19256 []\T1/ptm/m/n/10 The func-tion []\T1/pcr/m/n/10 f []\T1/ptm/m/n/10 is never eva l-u-ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m /n/10 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/ 10 tol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19245--19256 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately []\T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) []\T1/ptm/m/n/10 and $\OML /cmm/m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1596] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19308--19308 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1597] [1598] [1599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19535--19535 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1600] [1601] Underfull \hbox (badness 1337) in paragraph at lines 19646--19649 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1602] [1603] [1604] [1605] [1606] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19965--19965 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1607] [1608] Overfull \hbox (24.78088pt too wide) in paragraph at lines 20053--20053 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage* " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 20055--20055 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20057--20057 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1609] Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 "bottomleft", legend = "Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s di stance", lty = cook.lty, Underfull \hbox (badness 10000) in paragraph at lines 20117--20123 \T1/pcr/m/n/10 col = cook.col, text.col = cook.col, bty = "n", x.intersp Underfull \hbox (badness 10000) in paragraph at lines 20125--20131 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment []\T 1/pcr/m/n/10 iter []\T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 20136--20139 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 1 or 2, to be used in []\T1/pcr/m /n/10 ylim <- [1610] [1611] [1612] [1613] [1614] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20437--20437 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20447--20450 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1615] Underfull \hbox (badness 1107) in paragraph at lines 20505--20507 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate [] \T1/pcr/m/n/10 x[]\T1/ptm/m/n/10 . De-faults to [1616] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20560--20560 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20567--20567 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1617] [1618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20661--20661 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1619] [1620] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20790--20790 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1621] Underfull \hbox (badness 7740) in paragraph at lines 20853--20855 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/pcr/m/n/10 "Exact Poisson test" [ ]\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20901--20901 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1622] Underfull \hbox (badness 10000) in paragraph at lines 20957--20959 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 poly(*, simple=TRUE)[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 polym(*, coefs=)[]\T1/ptm/m/n/10 , and [1623] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20994--20994 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20999--20999 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21854--21854 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1637] Underfull \hbox (badness 6859) in paragraph at lines 21921--21928 [][][]\T1/pcr/m/n/10 predict.glm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 p redict.lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.loess[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.nls[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 predict.poly[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21932--21938 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/pcr/m/n/10 predict.ar[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.Arima[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1638] [1639] [1640] [1641] [1642] [1643] [1644] [1645] [1646] [1647] [1648] [1649] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22678--22678 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1650] [1651] [1652] [1653] [1654] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22962--22962 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22963--22963 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1655] [1656] [1657] [1658] [1659] Underfull \hbox (badness 1337) in paragraph at lines 23289--23295 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 []\T1/ptm/m/n/10 Wicklin, R. (2017) Sam-ple quan-tiles: A com-par-i-son of 9 de f-i-ni-tions; Underfull \hbox (badness 10000) in paragraph at lines 23848--23850 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23855--23856 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1668] [1669] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23966--23966 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1670] Underfull \hbox (badness 1028) in paragraph at lines 24024--24027 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for []\T 1/pcr/m/n/10 write() []\T1/ptm/m/n/10 and [1671] [1672] Underfull \hbox (badness 10000) in paragraph at lines 24139--24142 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7099) in paragraph at lines 24194--24196 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 reorder[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1673] Underfull \hbox (badness 7099) in paragraph at lines 24258--24260 []\T1/ptm/m/n/10 This, as [][][]\T1/pcr/m/n/10 relevel[][][]()[]\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][][]\T1/pcr/m/n/10 factor[][][](x, l evels = [1674] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24293--24293 []\T1/pcr/m/n/9 bymedianR <- with(InsectSprays, reorder(spray, count, median, decreasing=TRUE))[] [1675] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24369--24369 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24486--24486 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24487--24487 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24488--24488 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24489--24489 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1678] [1679] Underfull \hbox (badness 10000) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 stack[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 aperm[] [][][]\T1/ptm/m/n/10 ; [][][]\T1/pcr/m/n/10 relist[][][] []\T1/ptm/m/n/10 for r e-shap-ing the re-sult of [][][]\T1/pcr/m/n/10 unlist[][][][]\T1/ptm/m/n/10 . [ ][][]\T1/pcr/m/n/10 xtabs[][][] []\T1/ptm/m/n/10 and Underfull \hbox (badness 2495) in paragraph at lines 24649--24654 [][][]\T1/pcr/m/n/10 as.data.frame.table[][][] []\T1/ptm/m/n/10 for cre-at-ing con-tin-gency ta-bles and con-vert-ing them back to [1680] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24660--24660 []\T1/pcr/m/n/9 ## long to wide (direction = "wide") requires idvar and timeva r at a minimum[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 24661--24661 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24680--24680 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1681] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24784--24784 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1682] Underfull \hbox (badness 1033) in paragraph at lines 24827--24833 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where Underfull \hbox (badness 10000) in paragraph at lines 24848--24851 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/pcr/m/n/10 y = r unmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/pcr/m/n/10 y[j] = [1683] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24930--24930 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1684] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24959--24959 []\T1/pcr/m/n/9 ## An example with initial NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s - used to fail badly (notably for "Turlach"):[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 24971--24971 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 6268) in paragraph at lines 25429--25434 [][][]\T1/pcr/m/n/10 SSasympOrig[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 S Sbiexp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfol[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSfpl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSgo mpertz[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 SSlogis[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 SSmicmen[][][][]\T1/ptm/m/n/10 , [1692] [1693] [1694] [1695] Underfull \hbox (badness 1867) in paragraph at lines 25638--25640 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallba ck = use.fallback) []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25653--25657 \T1/pcr/m/n/10 <- sum(!is.na([][]coef[][][](object))) []\T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was Overfull \hbox (20.58041pt too wide) in paragraph at lines 25689--25689 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 25696--25696 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1696] [1697] [1698] Underfull \hbox (badness 2495) in paragraph at lines 25879--25888 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1699] [1700] Underfull \hbox (badness 2197) in paragraph at lines 26021--26024 []\T1/pcr/m/n/10 psmirnov []\T1/ptm/m/n/10 gives the dis-tri-bu-tion func-tion, []\T1/pcr/m/n/10 qsmirnov []\T1/ptm/m/n/10 gives the quan-tile func-tion, and [1701] Overfull \hbox (24.78088pt too wide) in paragraph at lines 26041--26041 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 26048--26050 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1702] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26135--26135 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 26160--26160 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 26163--26163 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1703] [1704] [1705] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26392--26392 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26396--26402 []\T1/ptm/m/n/10 The de-fault []\T1/pcr/m/n/10 all.knots = FALSE []\T1/ptm/m/n/ 10 and []\T1/pcr/m/n/10 nknots = .nknots.smspl[]\T1/ptm/m/n/10 , en-tails us-in g only [1706] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26442--26442 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26463--26463 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1707] [1708] [1709] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26655--26655 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1710] [1711] [1712] [1713] [1714] [1715] [1716] Overfull \hbox (36.78088pt too wide) in paragraph at lines 27035--27035 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1717] [1718] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27216--27216 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 27222--27222 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)) for when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27231--27231 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 27232--27232 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1719] Underfull \hbox (badness 2922) in paragraph at lines 27301--27306 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1720] Overfull \hbox (9.78043pt too wide) in paragraph at lines 27338--27338 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27341--27341 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27350--27350 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27351--27351 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 27355--27355 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1721] Underfull \hbox (badness 3240) in paragraph at lines 27409--27412 [][][]\T1/pcr/m/n/10 nls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 selfStart [][][][]\T1/ptm/m/n/10 ; []\T1/pcr/m/n/10 example(SSasympOff) []\T1/ptm/m/n/10 gives graph show-ing the []\T1/pcr/m/n/10 SSasympOff [1722] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27430--27430 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27433--27433 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1723] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27516--27516 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27520--27520 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27530--27530 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 27535--27535 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1724] Underfull \hbox (badness 2922) in paragraph at lines 27571--27577 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27593--27593 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1725] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27609--27609 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 27623--27623 []\T1/pcr/m/n/9 ## Fails by default (scaleOffset=0) on most platforms {also af ter increasing maxiter !}[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27625--27625 [] \T1/pcr/m/n/9 nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, trace=TRUE)[] Overfull \hbox (128.58029pt too wide) in paragraph at lines 27628--27628 []\T1/pcr/m/n/9 fmX1 <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data = d atN, control = list(scaleOffset=1))[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 27630--27630 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1726] [1727] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27742--27742 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1728] Underfull \hbox (badness 2922) in paragraph at lines 27804--27809 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (69.18036pt too wide) in paragraph at lines 27842--27842 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1729] Underfull \hbox (badness 2922) in paragraph at lines 27891--27896 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1730] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27922--27922 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] Underfull \hbox (badness 2922) in paragraph at lines 27956--27961 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27981--27981 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27985--27985 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28005--28005 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 28015--28015 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] [1732] Underfull \hbox (badness 2922) in paragraph at lines 28050--28055 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 inpu t[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 28072--28072 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1733] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28090--28090 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 28142--28147 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28170--28170 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 28173--28173 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 28176--28176 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 28179--28179 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1735] [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] Underfull \hbox (badness 3396) in paragraph at lines 29062--29064 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.glm"[]\T1/ptm/m/ n/10 , usu-ally, a re-sult of a call to [1749] [1750] Underfull \hbox (badness 2237) in paragraph at lines 29239--29241 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1751] [1752] [1753] Underfull \hbox (badness 2591) in paragraph at lines 29403--29405 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.nls"[]\T1/ptm/m/ n/10 , usu-ally the re-sult of a call to [1754] Underfull \hbox (badness 2237) in paragraph at lines 29449--29452 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /pcr/m/n/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1755] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29522--29522 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1756] Underfull \hbox (badness 3407) in paragraph at lines 29631--29635 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see []\T1/pcr/m/n/10 corr []\T1/ptm/m/n/10 be-low) [1757] [1758] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29701--29701 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1759] Underfull \hbox (badness 1337) in paragraph at lines 29764--29768 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1760] [1761] [1762] Overfull \hbox (9.78043pt too wide) in paragraph at lines 30028--30028 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1763] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30056--30056 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 30082--30085 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1764] [1765] Overfull \hbox (20.58041pt too wide) in paragraph at lines 30161--30161 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1766] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30239--30239 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1767] Underfull \hbox (badness 2205) in paragraph at lines 30328--30333 []\T1/ptm/m/n/10 If a []\T1/pcr/m/n/10 specials []\T1/ptm/m/n/10 ar-gu-ment was given to [][][]\T1/pcr/m/n/10 terms.formula[][][] []\T1/ptm/m/n/10 there is a [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30927--30927 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30928--30928 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1777] [1778] [1779] [1780] [1781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 31228--31228 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31229--31229 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1782] [1783] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31355--31355 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31364--31364 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1784] [1785] [1786] Underfull \hbox (badness 1337) in paragraph at lines 31581--31585 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] Underfull \hbox (badness 1337) in paragraph at lines 32110--32114 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1795] [1796] [1797] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32317--32317 []\T1/pcr/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 32319--32319 []\T1/pcr/m/n/9 wilcox.test((4:2)/10, (3:1)/10, paired=TRUE, digits.rank = 9) # same ties as (4:2, 3:1)[] [1798] [1799] [1800] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32478--32478 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32563--32563 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1802] [1803] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32696--32696 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1804]) (./stats4-pkg.tex Chapter 11. [1805] [1806] [1807] Overfull \hbox (15.18042pt too wide) in paragraph at lines 224--224 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] Underfull \vbox (badness 10000) has occurred while \output is active [1808] Overfull \hbox (9.78043pt too wide) in paragraph at lines 278--278 []\T1/pcr/m/n/9 ## Boundary case: This works, but fails if limits are set clos er to 0 and 1[] [1809] [1810] [1811] [1812] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1813] [1814] [1815]) (./tcltk-pkg.tex [1816] Chapter 12. [1817] [1818] [1819] [1820] Overfull \hbox (36.7804pt too wide) in paragraph at lines 355--355 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1821] [1822] [1823] Underfull \vbox (badness 10000) has occurred while \output is active [1824] Underfull \hbox (badness 1292) in paragraph at lines 666--673 []\T1/pcr/m/n/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-i ng any Tk or Tcl com-mand by sim-ply run-ning [1825] [1826] [1827] [1828] [1829] [1830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1079--1079 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1831] [1832] [1833] [1834] [1835] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] []\T1/ptm/m/n/10 (a text ver-sion ex-cep t on Win-dows and the ma-cOS GUI), [][][]\T1/pcr/m/n/10 menu[][][] []\T1/ptm/m/ n/10 (whose [1836]) (./tools-pkg.tex Chapter 13. [1837] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1838] Underfull \hbox (badness 1253) in paragraph at lines 167--170 []\T1/pcr/m/n/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing will be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1839] Overfull \hbox (4.38043pt too wide) in paragraph at lines 218--218 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1840] Underfull \hbox (badness 5147) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 288--301 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][][]\T1/pcr/m/n /10 bibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 288--301 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named []\T1/pcr/m/n /10 formatArticle[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 formatBook[]\T1/ptm/m/n/10 , [1841] Overfull \hbox (42.78088pt too wide) in paragraph at lines 373--373 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 392--394 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gin e to use. Over-rides any [1842] [1843] Underfull \hbox (badness 1142) in paragraph at lines 463--467 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [1844] [1845] [1846] [1847] [1848] [1849] [1850] Overfull \hbox (0.78088pt too wide) in paragraph at lines 911--911 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 966--966 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1851] [1852] [1853] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1134--1134 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1135--1135 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] [1854] Underfull \hbox (badness 1014) in paragraph at lines 1174--1176 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1180--1182 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1217--1220 \T1/ptm/m/n/10 ing []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results []\ T1/ptm/m/n/10 and [1855] Underfull \hbox (badness 10000) in paragraph at lines 1225--1228 []\T1/pcr/m/n/10 check_packages_in_dir []\T1/ptm/m/n/10 re-turns an ob-ject in- her-it-ing from class [1856] [1857] Underfull \hbox (badness 10000) in paragraph at lines 1374--1377 []\T1/pcr/m/n/10 codocClasses []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 codocData [ ]\T1/ptm/m/n/10 re-turn ob-jects of class []\T1/pcr/m/n/10 "codocClasses" []\T1 /ptm/m/n/10 and [1858] [1859] Underfull \hbox (badness 4647) in paragraph at lines 1543--1548 []\T1/pcr/m/n/10 CRAN_package_db() []\T1/ptm/m/n/10 re-turns a data frame with char-ac-ter columns con-tain-ing most Underfull \hbox (badness 7869) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' meta-data for the cu r-rent pack-ages in the CRAN pack-age repos-i- Underfull \hbox (badness 1681) in paragraph at lines 1543--1548 \T1/ptm/m/n/10 tory, in-clud-ing in par-tic-u-lar the De-scrip-tion and Main-ta iner in-for-ma-tion not pro-vided by [1860] Underfull \hbox (badness 2762) in paragraph at lines 1595--1598 []\T1/ptm/m/n/10 Internal func-tions []\T1/pcr/m/n/10 CRAN_aliases_db[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 CR AN_current_db []\T1/ptm/m/n/10 and [1861] [1862] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1707--1707 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1714--1722 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1714--1722 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 1714--1722 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1863] [1864] [1865] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1926 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1927 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1866] [1867] [1868] [1869] Underfull \hbox (badness 1142) in paragraph at lines 2196--2202 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 loadPkgRdMacros []\T1/ptm/m/n/10 func-tio n first looks for an []\T1/pcr/m/n/10 "RdMacros" []\T1/ptm/m/n/10 en-try in the pack-age [1870] Overfull \hbox (101.58032pt too wide) in paragraph at lines 2230--2230 [] \T1/pcr/m/n/9 r"(\newcommand{\Rlogo}{\if{html}{\figure{Rlogo.svg}{option s: width=100 alt="R logo"}})",[] Underfull \hbox (badness 2359) in paragraph at lines 2258--2265 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2258--2265 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1871] Underfull \hbox (badness 1342) in paragraph at lines 2310--2316 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1872] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2384--2384 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2399--2407 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 2399--2407 []\T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", Underfull \hbox (badness 1558) in paragraph at lines 2399--2407 \T1/pcr/m/n/10 "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string []\T1/pcr/m/n/1 0 "all" []\T1/ptm/m/n/10 is short-hand for that vec-tor, [1873] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2435--2435 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2468--2468 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1874] [1875] [1876] [1877] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2752--2752 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1878] Underfull \hbox (badness 2486) in paragraph at lines 2797--2805 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1879] [1880] [1881] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3009--3009 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3013--3013 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1882] [1883] [1884] Underfull \hbox (badness 1072) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec- tor of links, as re-turned by [1885] [1886] [1887] [1888] [1889] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3534--3534 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1890] Underfull \hbox (badness 5417) in paragraph at lines 3572--3582 []\T1/ptm/m/n/10 By de-fault, the tags \T1/pcr/m/n/10 \S3method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \S4method\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \command\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \docType\T1/ptm/m/n/10 , \T1/pcr/m/n/10 \email\T1/ptm/m/n/10 , [1891] [1892] [1893] Underfull \hbox (badness 4108) in paragraph at lines 3782--3789 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1894] [1895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3882--3882 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3885--3885 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3902--3904 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3919--3925 []\T1/pcr/m/n/10 testInstalledBasic []\T1/ptm/m/n/10 runs the ba-sic tests, if in-stalled. This should be run with [1896] [1897] Underfull \hbox (badness 7832) in paragraph at lines 4041--4044 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/pcr/m/n/10 texi2dvi []\T1/ptm/m/n/10 5 .0 and later; []\T1/pcr/m/n/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op-ti on [1898] [1899] [1900] [1901] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4276--4276 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1902] [1903] Overfull \hbox (96.78088pt too wide) in paragraph at lines 4438--4438 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, mergeOpts = "", copyright, bugs) Underfull \hbox (badness 3118) in paragraph at lines 4449--4453 []\T1/ptm/m/n/10 a string, by de-fault empty, of op-tions to []\T1/pcr/m/n/10 m sgmerge []\T1/ptm/m/n/10 in ad-di-tion to Underfull \hbox (badness 10000) in paragraph at lines 4453--4456 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `[]\T1/pcr/m/n/10 Copyrig ht[]\T1/ptm/m/n/10 ' and [1904] Underfull \hbox (badness 6859) in paragraph at lines 4469--4474 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory []\T1/pcr/m/n/10 po []\T1/ ptm/m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\ T1/ptm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4477--4483 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1905] [1906] [1907] Underfull \hbox (badness 10000) in paragraph at lines 4703--4705 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 vignetteEngine[][][][]\T1/ptm/m/n/10 , such as []\T1/pcr/m/n/10 "utils::Sweave" []\T1/ptm/m/n/10 or [1908] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4746--4749 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4750--4760 []\T1/pcr/m/n/10 "Package"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Version"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Priority"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Depe nds"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Imports"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4788--4794 []\T1/pcr/m/n/10 write_PACKAGES []\T1/ptm/m/n/10 scans the named di-rec-tory fo r R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4788--4794 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1909] Underfull \hbox (badness 1571) in paragraph at lines 4816--4820 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4842--4847 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][][ ]\T1/pcr/m/n/10 update_PACKAGES[][][] []\T1/ptm/m/n/10 for ef-fi-ciently up-dat -ing ex-ist-ing [1910] [1911] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4984--4984 []\T1/pcr/m/n/9 xgettext(tmpPkg, asCall=TRUE )[[1]] # default; shows \TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 sqrt(as.complex(x)) \TS1/pcr/m/n/9 '[] [1912]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/pcr/m/n/10 insertions[]\T1/ptm/m/n/10 ', [1913] [1914] [1915] [1916] Overfull \hbox (4.38043pt too wide) in paragraph at lines 258--258 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1917] Underfull \hbox (badness 10000) in paragraph at lines 378--383 \T1/ptm/m/n/10 are []\T1/pcr/m/n/10 c("vertical", "horizontal", "cascade", "min imize", [1918] Underfull \hbox (badness 10000) in paragraph at lines 384--386 []\T1/ptm/m/n/10 a [][][]\T1/pcr/m/n/10 list[][][] []\T1/ptm/m/n/10 of win-dow han-dles, by de-fault pro-duced by [1919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 452--452 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 469--469 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1920] [1921] [1922] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 689--689 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 690--690 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 691--691 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 692--692 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 726--732 []\T1/ptm/m/n/10 Functions []\T1/pcr/m/n/10 aspell_package_Rd_files[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 726--732 []\T1/pcr/m/n/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 a spell_package_C_files []\T1/ptm/m/n/10 per-form spell check- [1923] [1924] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1049--1049 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1928] Underfull \hbox (badness 1748) in paragraph at lines 1115--1123 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use []\T1/pcr/m/n/ 10 bibtex = T|F []\T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1092) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 as [][][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max", 1 ) []\T1/ptm/m/n/10 which is []\T1/pcr/m/n/10 1 []\T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1115--1123 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1127--1129 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1929] Underfull \hbox (badness 10000) in paragraph at lines 1235--1238 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1930] [1931] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1318--1318 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1932] [1933] [1934] [1935] [1936] Underfull \hbox (badness 1859) in paragraph at lines 1721--1730 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- Underfull \hbox (badness 2042) in paragraph at lines 1721--1730 \T1/ptm/m/n/10 mand []\T1/pcr/m/n/10 data.frame(x, y, z, monday, tuesday) []\T1 /ptm/m/n/10 never re-turns. Do not re-port that [1937] [1938] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1826--1826 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1939] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1861--1861 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1940] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2007--2007 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1941] Underfull \hbox (badness 2277) in paragraph at lines 2076--2081 []\T1/pcr/m/n/10 charClass []\T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/p tm/m/n/10 4.1.0. A less di-rect way to ex-am-ine char-ac-ter classes [1942] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2109--2109 []\T1/pcr/m/n/9 cl <- c("alnum", "alpha", "blank", "digit", "graph", "punct", "upper", "xdigit")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/9 X <- as.data.frame(X); row.names(X) <- sQuote(intToUtf8(x, mul tiple = TRUE))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2119--2119 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1943] [1944] [1945] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2267--2267 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1946] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2319--2319 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1947] [1948] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2489--2489 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] [1949] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2512--2512 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1950] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2632--2632 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1951] Underfull \hbox (badness 1082) in paragraph at lines 2706--2710 [][][]\T1/pcr/m/n/10 citation[][][] []\T1/ptm/m/n/10 for more in-for-ma-tion ab out cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file s; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2711 ... the Clipboard in MS Windows}{clipboard} [1952] Underfull \hbox (badness 1163) in paragraph at lines 2742--2744 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1953] Underfull \hbox (badness 10000) in paragraph at lines 2835--2837 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1954] [1955] [1956] [1957] Underfull \hbox (badness 10000) in paragraph at lines 3053--3055 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1958] [1959] [1960] [1961] Underfull \hbox (badness 1762) in paragraph at lines 3346--3349 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set []\T1/pcr/m/n/10 package = [1962] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3438--3438 []\T1/pcr/m/n/9 try(data(package = "rpart"), silent = TRUE) # list the data se ts in the rpart package[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3439--3439 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1963] Underfull \hbox (badness 2452) in paragraph at lines 3515--3518 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class []\ T1/pcr/m/n/10 R_dataentry[]\T1/ptm/m/n/10 . Re-sources [1964] [1965] [1966] [1967] [1968] [1969] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3931--3931 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1970] Underfull \hbox (badness 4779) in paragraph at lines 4010--4015 []\T1/ptm/m/n/10 Support for method []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [1971] Underfull \hbox (badness 1072) in paragraph at lines 4073--4077 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/pcr/m/n/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [1972] Underfull \hbox (badness 7238) in paragraph at lines 4129--4134 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 "libcurl" []\T1/ptm/m/n/10 and []\T1/ pcr/m/n/10 "curl" []\T1/ptm/m/n/10 meth-ods, prox-ies can be set \T1/ptm/m/it/1 0 via \T1/ptm/m/n/10 the en-vi-ron- Underfull \hbox (badness 1337) in paragraph at lines 4129--4134 \T1/ptm/m/n/10 ment vari-ables []\T1/pcr/m/n/10 http_proxy []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 ftp_proxy[]\T1/ptm/m/n/10 . See [][]$\T1/pcr/m/n/10 https : / / curl . se / libcurl / c / Underfull \hbox (badness 1184) in paragraph at lines 4144--4160 \T1/ptm/m/n/10 string con-tain-ing `[]\T1/pcr/m/n/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron- [1973] Underfull \hbox (badness 4660) in paragraph at lines 4261--4264 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [1974] Underfull \hbox (badness 10000) in paragraph at lines 4285--4287 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/pcr/m/n/10 do wnload.file[][][] []\T1/ptm/m/n/10 and [1975] [1976] Underfull \hbox (badness 1565) in paragraph at lines 4470--4474 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1977] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4553--4553 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1978] Underfull \hbox (badness 1910) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 is saved, then ini-tial-ized to a spec-i-fied state, the ex-am-p le is run and Underfull \hbox (badness 1655) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 the (saved) state is re-stored. []\T1/pcr/m/n/10 setRNG = TRUE [ ]\T1/ptm/m/n/10 sets the same state as Underfull \hbox (badness 2846) in paragraph at lines 4587--4594 []\T1/pcr/m/n/10 R CMD [][]check[][][] []\T1/ptm/m/n/10 does for run-ning a pac k-age's ex-am-ples. This is cur- Underfull \hbox (badness 3460) in paragraph at lines 4587--4594 \T1/ptm/m/n/10 rently equiv-a-lent to []\T1/pcr/m/n/10 setRNG = {RNGkind("defau lt", "default", Underfull \hbox (badness 1931) in paragraph at lines 4594--4601 []\T1/ptm/m/n/10 logical (or []\T1/pcr/m/n/10 "default"[]\T1/ptm/m/n/10 ) in-di -cat-ing if [][][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1979] [1980] [1981] [1982] Underfull \hbox (badness 5939) in paragraph at lines 4840--4842 []\T1/ptm/m/n/10 An en-try in []\T1/pcr/m/n/10 getOption("repos") []\T1/ptm/m/n /10 named `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' which is not the de-fault [1983] [1984] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4983--4983 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1985] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5054 ...mat Unordered and Ordered Lists}{format} [1986] [1987] [1988] [1989] [1990] [1991] [1992] [1993] Underfull \hbox (badness 1622) in paragraph at lines 5577--5581 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1994] [1995] [1996] [1997] [1998] Underfull \hbox (badness 1448) in paragraph at lines 5956--5961 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [1999] [2000] [2001] Overfull \hbox (96.78088pt too wide) in paragraph at lines 6106--6106 []\T1/pcr/m/n/10 ## NB: The methods for \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 data.f rame\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 and \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 array\ TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 are identical to the \TS1/pcr/m/n/10 '\T1/pcr/ m/n/10 matrix\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 one[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 6118--6118 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [2002] [2003] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6251--6251 [] \T1/pcr/m/n/9 ## BUT if I use "useAttrib(.)", this is *not* ok, when n i s of length 2:[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6252--6252 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [2004] [2005] [2006] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [2007] Underfull \hbox (badness 10000) in paragraph at lines 6546--6548 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [2008] Underfull \hbox (badness 1502) in paragraph at lines 6595--6600 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6595--6600 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6768--6777 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [2011] Underfull \hbox (badness 2150) in paragraph at lines 6832--6835 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2012] Underfull \hbox (badness 5175) in paragraph at lines 6848--6851 []\T1/pcr/m/n/10 hsearch_db() []\T1/ptm/m/n/10 builds and caches the help searc h database for sub-se-quent use by [2013] Underfull \hbox (badness 3118) in paragraph at lines 6971--6973 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2014] [2015] [2016] Underfull \hbox (badness 5091) in paragraph at lines 7146--7148 []\T1/ptm/m/n/10 download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 means to use []\T1/pcr/m/n/10 c("Depends ", "Imports", "LinkingTo", Underfull \hbox (badness 10000) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "Suggests") []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pkgs []\T1/ptm /m/n/10 and []\T1/pcr/m/n/10 c("Depends", "Imports", Underfull \hbox (badness 1270) in paragraph at lines 7176--7183 \T1/pcr/m/n/10 "LinkingTo") []\T1/ptm/m/n/10 for added de-pen-den-cies: this in -stalls all the pack-ages Underfull \hbox (badness 1270) in paragraph at lines 7191--7201 \T1/ptm/m/n/10 for the `[]\T1/pcr/m/n/10 --configure-args[]\T1/ptm/m/n/10 ' fla g in the call to []\T1/pcr/m/n/10 R CMD INSTALL[]\T1/ptm/m/n/10 . If [2017] Underfull \hbox (badness 4441) in paragraph at lines 7234--7237 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed to Underfull \hbox (badness 2837) in paragraph at lines 7234--7237 []\T1/pcr/m/n/10 R CMD INSTALL []\T1/ptm/m/n/10 for a source pack-age in-stall. E.g., []\T1/pcr/m/n/10 c("--html", Underfull \hbox (badness 1424) in paragraph at lines 7242--7245 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2018] Underfull \hbox (badness 2376) in paragraph at lines 7313--7320 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/pcr/m/n /10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7313--7320 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 7321--7324 []\T1/ptm/m/n/10 Using pack-ages with []\T1/pcr/m/n/10 type = "source" []\T1/pt m/m/n/10 al-ways works pro-vided the pack-age con-tains no [2019] Underfull \hbox (badness 1314) in paragraph at lines 7401--7408 []\T1/pcr/m/n/10 install.packages []\T1/ptm/m/n/10 needs to be able to com-pute all the de-pen-den-cies of []\T1/pcr/m/n/10 pkgs []\T1/ptm/m/n/10 from [2020] Underfull \hbox (badness 10000) in paragraph at lines 7481--7486 [][][]\T1/pcr/m/n/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pac kages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 7504--7504 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [2021] Underfull \hbox (badness 5133) in paragraph at lines 7540--7544 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7554--7557 []\T1/pcr/m/n/10 installed.packages []\T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2022] [2023] Underfull \hbox (badness 4132) in paragraph at lines 7725--7727 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of []\T1/pcr/m/n/10 libtool []\T1/ptm/m/n/10 in-stalled at [2024] [2025] [2026] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7892--7892 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2027] [2028] [2029] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8035--8035 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) Underfull \hbox (badness 10000) in paragraph at lines 8075--8077 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [2030] [2031] Underfull \hbox (badness 10000) in paragraph at lines 8180--8182 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 8185--8187 []\T1/ptm/m/n/10 typically the re-sult of []\T1/pcr/m/n/10 methods(..)[]\T1/ptm /m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2032] [2033] [2034] [2035] Underfull \hbox (badness 1859) in paragraph at lines 8413--8416 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by Underfull \hbox (badness 1052) in paragraph at lines 8432--8442 \T1/ptm/m/n/10 ac-cord-ing to ver-sion us-ing \T1/pcr/m/n/10 section \T1/ptm/m/ n/10 el-e-ments with names start-ing with a suit-able pre-fix [2036] Underfull \hbox (badness 1655) in paragraph at lines 8507--8510 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class []\T1/pcr/m/n/10 "news_d b"[]\T1/ptm/m/n/10 , with [][][]\T1/pcr/m/n/10 attributes[][][] "package" []\T1 /ptm/m/n/10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8518--8518 []\T1/pcr/m/n/9 db4 <- news(Version == "4.0.0" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8526--8526 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8534--8534 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2037] [2038] Underfull \hbox (badness 1917) in paragraph at lines 8621--8623 []\T1/pcr/m/n/10 "B"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "KiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "MiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "GiB"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "TiB"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "PiB"[]\T1/ptm/m/ n/10 , [2039] [2040] [2041] [2042] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8893--8893 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8894--8894 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8895--8895 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2043] Underfull \hbox (badness 10000) in paragraph at lines 8923--8925 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 asDateBuilt()[]\T1/ptm/m/n/10 , a [][][]\ T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 8937--8939 []\T1/pcr/m/n/10 packageVersion() []\T1/ptm/m/n/10 is a con-ve-nience short-cut , al-low-ing things like []\T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8945--8950 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2044] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8991--8991 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8992--8992 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [2045] [2046] Underfull \hbox (badness 10000) in paragraph at lines 9121--9126 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("ok", "upgrade", Underfull \hbox (badness 10000) in paragraph at lines 9128--9131 []\T1/ptm/m/n/10 plus []\T1/pcr/m/n/10 "Status"[]\T1/ptm/m/n/10 , a fac-tor wit h lev-els []\T1/pcr/m/n/10 c("installed", "not [2047] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9244--9244 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9245--9245 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2048] [2049] [2050] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9418--9418 [] \T1/pcr/m/n/9 "S original, "),[] [2051] Underfull \hbox (badness 1789) in paragraph at lines 9551--9553 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] Underfull \hbox (badness 5203) in paragraph at lines 10124--10127 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the []\T1/pcr/m/n/10 $ []\T1/ptm/m/ n/10 ex-trac-tor are de-ter-mined by the generic func-tion [2061] [2062] [2063] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10374--10374 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2064] [2065] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10535--10535 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2066] [2067] [2068] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10716--10716 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2069] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10802--10802 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10805--10805 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10810--10810 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2070] Underfull \hbox (badness 2027) in paragraph at lines 10882--10885 []\T1/ptm/m/n/10 Using []\T1/pcr/m/n/10 row.names = NULL []\T1/ptm/m/n/10 force s row num-ber-ing. Miss-ing or []\T1/pcr/m/n/10 NULL [2071] [2072] [2073] [2074] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11161--11161 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 11162--11162 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 \T1/ptm/m/n/10 for []\T1/pcr/m/n/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/ pcr/m/n/10 HKEY_CLASSES_ROOT[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 11169--11174 []\T1/pcr/m/n/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_USER S[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2075] [2076] [2077] [2078] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11402--11402 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2079] [2080] [2081] [2082] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . Overfull \hbox (20.58041pt too wide) in paragraph at lines 11681--11681 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11686--11686 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11819--11819 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11820--11820 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2085] [2086] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11955--11955 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2087] [2088] Underfull \hbox (badness 1917) in paragraph at lines 12087--12090 []\T1/ptm/m/n/10 If `[]\T1/pcr/m/n/10 --default-packages[]\T1/ptm/m/n/10 ' is n ot used, then []\T1/pcr/m/n/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron-me nt vari- Underfull \hbox (badness 4328) in paragraph at lines 12087--12090 \T1/ptm/m/n/10 able []\T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES[]\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over Overfull \hbox (106.98032pt too wide) in paragraph at lines 12110--12110 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2089] Overfull \hbox (54.78088pt too wide) in paragraph at lines 12202--12202 [] \T1/pcr/m/n/10 restrict = c("functions", "descriptions", "news", "Rfunctions",[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 12203--12203 [] \T1/pcr/m/n/10 "Rmanuals", "READMEs", "views", "vig nettes"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12205--12205 [] \T1/pcr/m/n/10 sortby = c("score", "date:late", "date:early", "s ubject",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 12206--12206 [] \T1/pcr/m/n/10 "subject:descending", "size", "size:de scending"),[] [2090] Underfull \hbox (badness 6725) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 score[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 date: late []\T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 2662) in paragraph at lines 12229--12237 \T1/ptm/m/n/10 der, []\T1/pcr/m/n/10 subject:descending []\T1/ptm/m/n/10 for re -verse al-pha-bet-i-cal or-der, []\T1/pcr/m/n/10 size []\T1/ptm/m/n/10 or Overfull \hbox (9.78043pt too wide) in paragraph at lines 12274--12274 []\T1/pcr/m/n/9 fullquery <- RSiteSearch("lattice", restrict = c("vignettes"," Rfunctions"))[] [2091] Underfull \hbox (badness 1377) in paragraph at lines 12330--12333 []\T1/ptm/m/n/10 Character string spec-i-fy-ing whether emacs style ([]\T1/pcr/ m/n/10 "etags"[]\T1/ptm/m/n/10 ) or vi style [2092] Underfull \hbox (badness 3646) in paragraph at lines 12365--12367 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / Overfull \hbox (30.78088pt too wide) in paragraph at lines 12403--12403 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2093] [2094] [2095] Underfull \hbox (badness 10000) in paragraph at lines 12585--12589 []\T1/ptm/m/n/10 The de-fault for []\T1/pcr/m/n/10 stylepath []\T1/ptm/m/n/10 i s now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12618--12624 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a Underfull \hbox (badness 2027) in paragraph at lines 12633--12641 []\T1/ptm/m/n/10 The use of fancy quotes (see [][][]\T1/pcr/m/n/10 sQuote[][][] []\T1/ptm/m/n/10 ) can cause prob-lems when set-ting \T1/phv/m/n/10 R \T1/ptm/m /n/10 out-put in [2096] [2097] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12794--12794 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2098] Underfull \hbox (badness 1009) in paragraph at lines 12812--12824 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 2600) in paragraph at lines 12852--12854 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI ([]\T1/pcr/m/n/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2099] Underfull \hbox (badness 1043) in paragraph at lines 12895--12900 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2100] [2101] [2102] [2103] Underfull \hbox (badness 1888) in paragraph at lines 13188--13191 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 13205--13208 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2104] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2105] Underfull \hbox (badness 2158) in paragraph at lines 13306--13309 []\T1/ptm/m/n/10 Repository `[]\T1/pcr/m/n/10 CRAN[]\T1/ptm/m/n/10 ' is treated spe-cially: the value is taken from the cur-rent set-ting of Overfull \hbox (0.78088pt too wide) in paragraph at lines 13354--13354 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2106] [2107] [2108] Underfull \hbox (badness 2302) in paragraph at lines 13511--13513 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2109] Underfull \hbox (badness 3333) in paragraph at lines 13619--13621 []\T1/pcr/m/n/10 getSrcFilename []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 getSrcDir ectory []\T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2110] [2111] [2112] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13786--13786 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13810--13815 []\T1/ptm/m/n/10 logical; if []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), [][][]\T1/pcr/m/n/10 deparse[][][](control = ) []\T1/ptm/m/n/10 will not ha ve Underfull \hbox (badness 5970) in paragraph at lines 13819--13822 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 13819--13822 [][][]\T1/pcr/m/n/10 options[][][]("width")[]\T1/ptm/m/n/10 ; note that this ha s only a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 13830--13839 []\T1/ptm/m/n/10 (see [][][]\T1/pcr/m/n/10 options[][][][]\T1/ptm/m/n/10 ) whic h de-faults to []\T1/pcr/m/n/10 "no" []\T1/ptm/m/n/10 for back com-pat-i-bil-it y rea-sons; [2113] Underfull \hbox (badness 1442) in paragraph at lines 13846--13850 []\T1/ptm/m/n/10 numeric or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 as by de-fau lt, de-ter-min-ing the []\T1/pcr/m/n/10 nlines []\T1/ptm/m/n/10 ar-gu-ment to Overfull \hbox (36.7804pt too wide) in paragraph at lines 13892--13892 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2114] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13919--13919 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13926--13926 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13928--13928 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2115] [2116] [2117] Underfull \hbox (badness 10000) in paragraph at lines 14094--14096 []\T1/ptm/m/n/10 Options other than []\T1/pcr/m/n/10 memory = "none" []\T1/ptm/ m/n/10 ap-ply only to files pro-duced by [2118] Underfull \hbox (badness 10000) in paragraph at lines 14204--14207 []\T1/ptm/m/n/10 further ar-gu-ments passed to the driver's setup func-tion. Se e Underfull \hbox (badness 1389) in paragraph at lines 14204--14207 [][][]\T1/pcr/m/n/10 RweaveLatexSetup[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/ m/n/10 RtangleSetup[][][][]\T1/ptm/m/n/10 , re-spec-tively, for the ar-gu- [2119] Underfull \hbox (badness 6300) in paragraph at lines 14252--14259 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fau lt) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 turn, and se-lected if their []\T1/pcr/m/n/10 extension []\T1/pt m/m/n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14252--14259 \T1/ptm/m/n/10 name. Ob-jects []\T1/pcr/m/n/10 SweaveSyntaxNoweb []\T1/ptm/m/n/ 10 (with []\T1/pcr/m/n/10 extension = "[.][rsRS]nw$"[]\T1/ptm/m/n/10 ) and [2120] [2121] Underfull \hbox (badness 2020) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `[]\T1/pcr/m/n/10 -h[]\T1/ptm/m/ n/10 ' (fol-low sym-bolic links, also `[]\T1/pcr/m/n/10 -L[]\T1/ptm/m/n/10 ' on some plat-forms), Underfull \hbox (badness 1194) in paragraph at lines 14417--14425 \T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 --acls[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 -- exclude-backups[]\T1/ptm/m/n/10 ', `[]\T1/pcr/m/n/10 --exclude-vcs[]\T1/ptm/m/n /10 ' (and sim-i-lar) and on Win-dows [2122] Underfull \hbox (badness 1622) in paragraph at lines 14426--14433 []\T1/ptm/m/n/10 A con-ve-nient and ro-bust way to set op-tions for GNU []\T1/p cr/m/n/10 tar []\T1/ptm/m/n/10 is via en-vi-ron-ment vari-able [2123] Underfull \hbox (badness 5022) in paragraph at lines 14567--14571 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 is set t o the com-mand []\T1/pcr/m/n/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / pubs . Underfull \hbox (badness 10000) in paragraph at lines 14574--14577 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2124] [2125] [2126] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14740--14740 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2127] [2128] [2129] [2130] [2131] [2132] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15181--15181 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 15187--15187 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 15208--15210 []\T1/ptm/m/n/10 Download method, see [][][]\T1/pcr/m/n/10 download.file[][][][ ]\T1/ptm/m/n/10 . Un-used if a non-[]\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 15223--15227 \T1/ptm/m/n/10 able at the repos-i-to-ries, or []\T1/pcr/m/n/10 NULL []\T1/ptm/ m/n/10 which makes an in-ter-nal call to [2133] Underfull \hbox (badness 1694) in paragraph at lines 15237--15241 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][][]\T1/pcr/m/n/10 ins talled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/ptm/m/n/10 Arguments such as []\T1/pcr/m/n/10 destdir []\T1/ptm/m/n/10 an d []\T1/pcr/m/n/10 dependencies []\T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 \T1/ptm/m/n/10 passed to [][][]\T1/pcr/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 and []\T1/pcr/m/n/10 ignore_repo_cache[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15243--15248 []\T1/pcr/m/n/10 max_repo_cache_age []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 noCac he []\T1/ptm/m/n/10 to [][][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15249--15251 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15279--15284 []\T1/pcr/m/n/10 available = NULL []\T1/ptm/m/n/10 make a call to []\T1/pcr/m/n /10 available.packages(contriburl = Underfull \hbox (badness 1226) in paragraph at lines 15279--15284 \T1/pcr/m/n/10 contriburl, method = method) []\T1/ptm/m/n/10 and hence by de-fa ult fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 15300--15305 []\T1/ptm/m/n/10 Take care when us-ing []\T1/pcr/m/n/10 dependencies []\T1/ptm/ m/n/10 (passed to [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 ) with [2134] Underfull \hbox (badness 10000) in paragraph at lines 15308--15311 [][][]\T1/pcr/m/n/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 download.pa ckages[][][][]\T1/ptm/m/n/10 , Overfull \hbox (15.18042pt too wide) in paragraph at lines 15362--15362 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2135] [2136] [2137] Underfull \hbox (badness 2293) in paragraph at lines 15569--15572 [][][]\T1/pcr/m/n/10 browseVignettes[][][] []\T1/ptm/m/n/10 for an HTML-based v i-gnette browser; [][][]\T1/pcr/m/n/10 RShowDoc[][][](, [2138] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15585--15585 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2139] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15652--15652 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15674--15674 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2140] [2141] Underfull \hbox (badness 1297) in paragraph at lines 15805--15807 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2142] Underfull \hbox (badness 4036) in paragraph at lines 15852--15854 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 winMenuDel []\T1/ptm/m/n/10 func-tion wil l delete a menu and all of its items and sub-menus. [2143] [2144] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15972--15972 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2145] Underfull \hbox (badness 1715) in paragraph at lines 16024--16027 []\T1/ptm/m/n/10 arguments to []\T1/pcr/m/n/10 write.table[]\T1/ptm/m/n/10 : [] \T1/pcr/m/n/10 append[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 col.names[]\T1/ptm/m/n /10 , []\T1/pcr/m/n/10 sep[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dec []\T1/ptm/m/n /10 and Underfull \hbox (badness 10000) in paragraph at lines 16069--16071 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. []\T1/pcr/m/n/10 file = [2146] [2147] [2148]) [2149] [2150] (./KernSmooth-pkg.tex Chapter 15. [2151] Overfull \hbox (24.78088pt too wide) in paragraph at lines 123--123 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2152] [2153] [2154] [2155] [2156] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2157] [2158] [2159] [2160]) (./MASS-pkg.tex Chapter 16. [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] Overfull \hbox (20.58041pt too wide) in paragraph at lines 772--772 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2418--2418 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2422--2422 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2195] [2196] [2197] [2198] Underfull \hbox (badness 6559) in paragraph at lines 2701--2704 []\T1/ptm/m/n/10 further ar-gu-ments for []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 and graph-i-cal pa-ram-e-ters. Note that [2199] [2200] [2201] Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "gamma"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "geometric"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "log-normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lo gnormal"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2871--2876 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "negative binomi al"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "normal"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n /10 "Poisson"[]\T1/ptm/m/n/10 , [2202] [2203] Underfull \hbox (badness 4686) in paragraph at lines 3039--3041 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2204] [2205] [2206] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3234--3234 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2207] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3364--3364 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2208] [2209] [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] Underfull \hbox (badness 1845) in paragraph at lines 4164--4166 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley ([]\T1/pcr/m/n/10 "manchuria"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "svansota"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "velv et"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "trebi" []\T1/ptm/m/n/10 and [2220] [2221] [2222] [2223] [2224] [2225] [2226] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4658--4658 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2227] [2228] [2229] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4880--4880 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2230] [2231] [2232] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5930--5930 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2244] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5991--5991 []\T1/pcr/m/n/10 negative.binomial(theta = stop("\TS1/pcr/m/n/10 '\T1/pcr/m/n/ 10 theta\TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 must be specified"), link = "log") [2245] [2246] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6151 ...sical N, P, K Factorial Experiment}{npk} [2247] [2248] [2249] [2250] [2251] [2252] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6571--6571 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2253] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6659--6659 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2254] [2255] [2256] [2257] [2258] [2259] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7098--7098 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7115--7115 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2260] Underfull \hbox (badness 3138) in paragraph at lines 7193--7199 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2261] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7263--7263 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2262] [2263] Underfull \hbox (badness 1389) in paragraph at lines 7372--7375 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/pcr/m/n/10 min(p, [2264] [2265] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7502--7502 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2266] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7567--7567 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2267] [2268] [2269] [2270] [2271] [2272] Underfull \hbox (badness 4686) in paragraph at lines 8005--8007 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2273] [2274] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8124--8124 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8148--8152 []\T1/ptm/m/n/10 A func-tion to spec-ify the ac-tion to be taken if []\T1/pcr/m /n/10 NA[]\T1/ptm/m/n/10 s are found. The [2275] [2276] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289] [2290] [2291] [2292] [2293] [2294] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9529--9529 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2295] Underfull \hbox (badness 2035) in paragraph at lines 9641--9643 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els []\ T1/pcr/m/n/10 "R on L"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "L on R"[]\T1/ptm/m/n /10 , Underfull \hbox (badness 1158) in paragraph at lines 9656--9659 []\T1/ptm/m/n/10 how much the stu-dent smokes. (Fac-tor, lev-els []\T1/pcr/m/n/ 10 "Heavy"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Regul" []\T1/ptm/m/n/10 (reg-u-l arly), [2296] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9738--9738 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9740--9740 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9743--9743 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2297] [2298] [2299] [2300] [2301] [2302] [2303] [2304] [2305] [2306] [2307] [2308] [2309]) (./Matrix-pkg.tex [2310] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2311] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2312] Underfull \hbox (badness 2229) in paragraph at lines 153--156 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 153--156 \T1/ptm/m/n/10 an []\T1/pcr/m/n/10 "[][]abIndex[][][]" []\T1/ptm/m/n/10 vec-tor , these ar-gu-ments will be con-cate-nated to a new [2313] Underfull \hbox (badness 10000) in paragraph at lines 256--259 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 262--264 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for []\T1/pcr/m/n/10 "[ ][]sparseVector[][][]"[]\T1/ptm/m/n/10 's, see [2314] [2315] Overfull \hbox (15.18042pt too wide) in paragraph at lines 445--445 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2316] Underfull \hbox (badness 5119) in paragraph at lines 488--492 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 1668) in paragraph at lines 492--497 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse Overfull \hbox (4.38043pt too wide) in paragraph at lines 522--522 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 524--524 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] [2317] Overfull \hbox (15.18042pt too wide) in paragraph at lines 533--533 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2318] Overfull \hbox (52.98038pt too wide) in paragraph at lines 647--647 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 648--648 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 649--649 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @return a sparse (N*k x N*k) matrix of class \code{"\linkS4class{dgCMatrix}"}.[] [2319] Overfull \hbox (31.3804pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 663--663 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2320] Underfull \hbox (badness 1874) in paragraph at lines 737--740 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 https : / / netlib . org / [2321] [2322] Underfull \hbox (badness 1107) in paragraph at lines 860--865 \T1/ptm/m/n/10 sity'' of []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/ 10 y[]\T1/ptm/m/n/10 , see e.g., the \T1/phv/m/n/10 R \T1/ptm/m/n/10 code in [] \T1/pcr/m/n/10 selectMethod(cbind2, Underfull \hbox (badness 10000) in paragraph at lines 903--908 []\T1/ptm/m/n/10 Our class def-i-ni-tion help pages men-tion-ing []\T1/pcr/m/n/ 10 cbind2() []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 rbind2() []\T1/ptm/m/n/10 met h-ods: [2323] Overfull \hbox (72.78088pt too wide) in paragraph at lines 967--967 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2324] Underfull \hbox (badness 3612) in paragraph at lines 1054--1057 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "pMatrix") []\T1/ptm/m/n/10 re-turns the per-mu-ta-tion [2325] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol.1}) has been already used, duplicate ignored \relax l.1154 ...- 'Matrix' S4 Generic and Methods}{chol} [2326] [2327] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1301--1301 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2328] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1396--1396 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2329] Underfull \hbox (badness 2277) in paragraph at lines 1424--1427 []\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer -ent types of ma-tri-ces. Use [2330] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1498--1498 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1512--1512 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1520--1520 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1529--1529 []\T1/pcr/m/n/9 str(re <- lapply(rr, expand), max.level=2) ## each has a \TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 P\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and a \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 L\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 matrix[] [2331] Underfull \hbox (badness 10000) in paragraph at lines 1565--1572 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 4673) in paragraph at lines 1565--1572 []\T1/pcr/m/n/10 new("BunchKaufman", ...)[]\T1/ptm/m/n/10 , etc, or rather by c alls of the form [][][]\T1/pcr/m/n/10 chol[][][](pm) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1783) in paragraph at lines 1600--1604 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend [2332] Underfull \hbox (badness 1221) in paragraph at lines 1616--1622 \T1/ptm/m/n/10 ply an $\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 nu-meric [][][]\T1/pcr/m/n/10 matrix[][][][]\T1/ptm/m/n/10 . Hence, for com-pat-i-bil-ity, the []\T1/pcr/m/n/10 "Cholesky" []\T1/ptm/m/n/10 and pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums.1 }) has been already used, duplicate ignored \relax l.1657 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.1658 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.1681 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.1694 \aliasA{rowSums}{colSums}{rowSums} [2333 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans, diagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums,d iagonalMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.1733 ## S4 method for signature 'CsparseMatrix' ] Underfull \hbox (badness 2922) in paragraph at lines 1750--1754 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1750--1754 \T1/ptm/m/n/10 class [][][]\T1/pcr/m/n/10 sparseVector[][][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is in-her-it-ing fr om a Underfull \hbox (badness 1237) in paragraph at lines 1761--1764 [][][]\T1/pcr/m/n/10 dimnames[][][](x) []\T1/ptm/m/n/10 are only kept (as [][][ ]\T1/pcr/m/n/10 names[][][](v)[]\T1/ptm/m/n/10 ) when the re-sult-ing []\T1/pcr /m/n/10 v []\T1/ptm/m/n/10 is [][][]\T1/pcr/m/n/10 numeric[][][][]\T1/ptm/m/n/1 0 , since [2334] [2335] Underfull \hbox (badness 3547) in paragraph at lines 1915--1918 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2336] [2337] [2338] [2339] [2340] [2341] Underfull \hbox (badness 7379) in paragraph at lines 2445--2447 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")[]\T1/ptm/m/n/10 : com-putes the LU de-com-po-si-tion of a square [2342] [2343] [2344] Underfull \hbox (badness 10000) in paragraph at lines 2696--2699 []\T1/pcr/m/n/10 signature(from = "dgTMatrix", to = "matrix")[]\T1/ptm/m/n/10 , and typ-i-cally co-er-cion Underfull \hbox (badness 4846) in paragraph at lines 2721--2725 []\T1/ptm/m/n/10 Note that both []\T1/pcr/m/n/10 new(.) []\T1/ptm/m/n/10 and [] [][]\T1/pcr/m/n/10 spMatrix[][][] []\T1/ptm/m/n/10 con-struc-tors for []\T1/pcr /m/n/10 "dgTMatrix" []\T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2726--2730 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2733--2736 []\T1/ptm/m/n/10 Class [][][]\T1/pcr/m/n/10 dgCMatrix[][][] []\T1/ptm/m/n/10 or the su-per-classes [][][]\T1/pcr/m/n/10 dsparseMatrix[][][] []\T1/ptm/m/n/10 a nd [][][]\T1/pcr/m/n/10 TsparseMatrix[][][][]\T1/ptm/m/n/10 ; [2345] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2780--2780 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2789--2791 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2793--2798 []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 .symDiagonal []\T1/ptm/m/n/10 ([]\T1/pcr/ m/n/10 .trDiagonal[]\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2793--2798 [][][]\T1/pcr/m/n/10 symmetricMatrix[][][] []\T1/ptm/m/n/10 (or [][][]\T1/pcr/m /n/10 triangularMatrix[][][][]\T1/ptm/m/n/10 ) will have slot []\T1/pcr/m/n/10 uplo [2346] Underfull \hbox (badness 1097) in paragraph at lines 2816--2819 []\T1/pcr/m/n/10 Diagonal() []\T1/ptm/m/n/10 re-turns an ob-ject of class [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 or [][][]\T1/pcr/m/n/10 ldiMat rix[][][] []\T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2829--2834 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][] []\T1/ptm/m/n/10 (the re-sult-ing clas s de-pend-ing on []\T1/pcr/m/n/10 shape []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 k ind[]\T1/ptm/m/n/10 ) rep-re-sen-ta-tion of [2347] Underfull \hbox (badness 3646) in paragraph at lines 2925--2928 []\T1/ptm/m/n/10 the [][][]\T1/pcr/m/n/10 dimnames[][][][]\T1/ptm/m/n/10 , a [] [][]\T1/pcr/m/n/10 list[][][][]\T1/ptm/m/n/10 , see the [][][]\T1/pcr/m/n/10 Ma trix[][][] []\T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 6542) in paragraph at lines 2960--2964 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these gr oup meth-ods re-turn a Underfull \hbox (badness 4518) in paragraph at lines 2969--2975 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")[]\T1/ptm/m/n/10 : the re-sult is from class [2348 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,di agonalMatrix,nMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.2975 ] Underfull \hbox (badness 10000) in paragraph at lines 2976--2980 []\T1/pcr/m/n/10 (object = "diagonalMatrix")[]\T1/ptm/m/n/10 : Re-turns an ob-j ect of S3 class Underfull \hbox (badness 2318) in paragraph at lines 2986--2990 [][][]\T1/pcr/m/n/10 Diagonal[][][]() []\T1/ptm/m/n/10 as con-struc-tor of thes e ma-tri-ces, and [][][]\T1/pcr/m/n/10 isDiagonal[][][][]\T1/ptm/m/n/10 . [][][ ]\T1/pcr/m/n/10 ddiMatrix[][][] []\T1/ptm/m/n/10 and [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 3166--3168 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")[]\T1/ptm/m/n/10 : this group con-tains [2351] [2352] Overfull \hbox (69.18036pt too wide) in paragraph at lines 3312--3312 []\T1/pcr/m/n/9 stopifnot(all.equal(S9p0, S9p))# same as as default, but diffe rent from the random one[] [2353] Underfull \hbox (badness 2469) in paragraph at lines 3422--3425 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")[]\T1/ptm/m/n/10 : Re-turns the [][] []\T1/pcr/m/n/10 determinant[][][] []\T1/ptm/m/n/10 of []\T1/pcr/m/n/10 x[]\T1/ ptm/m/n/10 , via Underfull \hbox (badness 10000) in paragraph at lines 3445--3450 []\T1/ptm/m/n/10 Currently the va-lid-ity meth-ods for these classes such as Underfull \hbox (badness 2020) in paragraph at lines 3445--3450 [][][]\T1/pcr/m/n/10 getValidity[][][](getClass("dpoMatrix")) []\T1/ptm/m/n/10 for ef-fi-ciency rea-sons only check the di- Underfull \hbox (badness 1748) in paragraph at lines 3451--3460 \T1/pcr/m/n/10 error=identity), "error") []\T1/ptm/m/n/10 . In-deed, when \T1/p tm/m/it/10 co-erc-ing \T1/ptm/m/n/10 to these classes, a ver-sion Underfull \hbox (badness 1590) in paragraph at lines 3451--3460 \T1/ptm/m/n/10 of [][][]\T1/pcr/m/n/10 Cholesky[][][]() []\T1/ptm/m/n/10 or [][ ][]\T1/pcr/m/n/10 chol[][][]() []\T1/ptm/m/n/10 is typ-i-cally used, e.g., see []\T1/pcr/m/n/10 selectMethod("coerce", [2354] [2355] Underfull \hbox (badness 10000) in paragraph at lines 3599--3603 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsCMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 2103) in paragraph at lines 3599--3603 []\T1/pcr/m/n/10 new("dsTMatrix", ...)[]\T1/ptm/m/n/10 , or au-to-mat-i-cally v ia e.g., []\T1/pcr/m/n/10 as(*, "symmetricMatrix")[]\T1/ptm/m/n/10 , [2356] Underfull \hbox (badness 1571) in paragraph at lines 3649--3652 []\T1/pcr/m/n/10 signature(x = "dsCMatrix", pivot = "logical")[]\T1/ptm/m/n/10 : Re-turns (and stores) the [2357] [2358] Underfull \hbox (badness 10000) in paragraph at lines 3813--3818 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [] \T1/pcr/m/n/10 "dsparseMatrix"[]\T1/ptm/m/n/10 , class []\T1/pcr/m/n/10 "sparse Matrix"[]\T1/ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3813--3818 \T1/ptm/m/n/10 class []\T1/pcr/m/n/10 "dsparseMatrix" []\T1/ptm/m/n/10 or []\T1 /pcr/m/n/10 "RsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/pcr/m/n/10 "compMatri x" []\T1/ptm/m/n/10 by class Underfull \hbox (badness 1400) in paragraph at lines 3825--3828 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")[]\T1/ptm/m/n/10 : if []\T1/pcr/m/n/10 uplo == [2359] Underfull \hbox (badness 10000) in paragraph at lines 3896--3898 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form []\T1/pcr/m/n/10 new("dsyMatrix", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1365) in paragraph at lines 3938--3941 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/10 , or []\T1/pcr/m/n/10 x = "dsyMatrix" [2360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3983--3983 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2361] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4116--4116 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2362] Underfull \hbox (badness 3635) in paragraph at lines 4179--4183 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ddenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Cla ss Underfull \hbox (badness 10000) in paragraph at lines 4188--4191 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; [2363] Underfull \hbox (badness 10000) in paragraph at lines 4193--4197 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/n /10 : the [2364] [2365 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,dt rMatrix,dgeMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.4347 \item[\code{diag}:] Object of class \code{"character"}. Must be] Underfull \hbox (badness 2065) in paragraph at lines 4378--4382 []\T1/pcr/m/n/10 signature(a = "dtrMatrix", b = "....")[]\T1/ptm/m/n/10 efficie ntely use a ``for-ward-solve'' or [2366] [2367] [2368] [2369] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwe ll-Boeing/counterx/counterx.html[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4642--4642 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4646--4646 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4649--4649 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4659--4659 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2370] [2371] [2372] [2373] Underfull \hbox (badness 10000) in paragraph at lines 4937--4942 []\T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 compMatrix[][][][]\T1/ptm/m/n/10 , and the non-general vir-tual classes: [][][]\T1/pcr/m/n/10 symmetricMatrix[][ ][][]\T1/ptm/m/n/10 , [2374] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5018--5018 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 5020--5020 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5024--5024 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2375] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5031--5031 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2376] [2377] Underfull \hbox (badness 4120) in paragraph at lines 5170--5173 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/pcr/m/n/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use Overfull \hbox (47.58038pt too wide) in paragraph at lines 5188--5188 []\T1/pcr/m/n/9 stopifnot(!is.null(leg <- imgC$legend), is.list(leg$right)) # failed for 2 days ..[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5208--5208 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5214--5214 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5215--5215 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5219--5219 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [2378] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5227--5227 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5230--5230 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2379] Underfull \hbox (badness 1817) in paragraph at lines 5326--5335 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing []\T1/pcr/m/n/10 drop=FALSE[]\T1/ptm/m/n/10 ) stays wit hin the Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 7081) in paragraph at lines 5370--5373 []\T1/pcr/m/n/10 signature(from = "integer", to = "indMatrix")[]\T1/ptm/m/n/10 : This en-ables typ-i-cal Underfull \hbox (badness 4556) in paragraph at lines 5376--5383 []\T1/pcr/m/n/10 signature(from = "list", to = "indMatrix")[]\T1/ptm/m/n/10 : T he list must have two [2380] Underfull \hbox (badness 3302) in paragraph at lines 5401--5404 []\T1/pcr/m/n/10 signature(X = "indMatrix", Y = "indMatrix")[]\T1/ptm/m/n/10 : re-turn the kro-necker [2381] [2382] [2383] [2384] Overfull \hbox (138.78088pt too wide) in paragraph at lines 5776--5776 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, tol1 = 8 * tol, checkDN = TRUE, ...)[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5782--5782 []\T1/pcr/m/n/10 isSymmetric(object, tol = 100 * .Machine$double.eps, checkDN = TRUE, ...)[] [2385] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5841--5841 []\T1/pcr/m/n/9 isSymmetric(as(M, "generalMatrix")) # still symmetric, even if not "formally"[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5845--5845 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs = TRUE) # includes S3 g eneric from base[] [2386] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5937--5937 []\T1/pcr/m/n/9 isTriangular(as(M, "generalMatrix")) # still triangular, even if not "formally"[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5962--5962 []\T1/pcr/m/n/10 KhatriRao(X, Y = X, FUN = "*", sparseY = TRUE, make.dimnames = FALSE) [2387] [2388] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6042--6042 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6043--6043 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6050--6050 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2389] [2390] Underfull \hbox (badness 1062) in paragraph at lines 6204--6207 []\T1/pcr/m/n/10 ldenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 6233--6236 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2391] Underfull \hbox (badness 2635) in paragraph at lines 6402--6407 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6402--6407 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class [2392] Underfull \hbox (badness 10000) in paragraph at lines 6410--6413 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6566--6576 []\T1/pcr/m/n/10 lsTMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltTMatrix[]\T 1/ptm/m/n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6566--6576 [][][]\T1/pcr/m/n/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pc r/m/n/10 lgCMatrix[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lsCMatrix[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 ltCMatrix[]\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\ T1/ptm/m/n/10 --in [2393] Underfull \hbox (badness 3179) in paragraph at lines 6648--6651 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2394] Underfull \hbox (badness 10000) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2395] Underfull \hbox (badness 10000) in paragraph at lines 6830--6833 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2396] Underfull \hbox (badness 1430) in paragraph at lines 6904--6910 \T1/ptm/m/n/10 should be sig-nalled when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar. When []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 is sin-gu-lar, []\T1/pcr/ m/n/10 lu(x, [2397] Underfull \hbox (badness 1675) in paragraph at lines 6929--6932 []\T1/pcr/m/n/10 lu() []\T1/ptm/m/n/10 is a generic func-tion with spe-cial met h-ods for dif-fer-ent types of ma-tri-ces. Use Overfull \hbox (9.78043pt too wide) in paragraph at lines 7001--7001 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2398] [2399] Underfull \hbox (badness 10000) in paragraph at lines 7141--7144 []\T1/ptm/m/n/10 vector of all non-zero en-tries of []\T1/pcr/m/n/10 x[]\T1/ptm /m/n/10 ; ex-ists \T1/ptm/b/n/10 only \T1/ptm/m/n/10 when []\T1/pcr/m/n/10 as(x , [2400] Underfull \hbox (badness 1490) in paragraph at lines 7163--7165 []\T1/pcr/m/n/10 mat2triplet() []\T1/ptm/m/n/10 is con-cep-tu-ally the \T1/ptm/ m/it/10 in-verse \T1/ptm/m/n/10 func-tion of [][][]\T1/pcr/m/n/10 spMatrix[][][ ] []\T1/ptm/m/n/10 and (one case of) [2401] [2402] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.7358 \aliasA{det}{Matrix-class}{det} [2403 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.coerce,Ma trix,denseMatrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7439 \item[dim] \code{signature(x = "Matrix")}: extract matrix dimensions] Underfull \hbox (badness 1337) in paragraph at lines 7446--7449 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "list")[]\T1/ptm/m/n/10 : set the []\T1/pcr/m/n/10 dimnames []\T1/ptm/m/n/10 to a Underfull \hbox (badness 10000) in paragraph at lines 7459--7462 Underfull \hbox (badness 10000) in paragraph at lines 7469--7471 []\T1/pcr/m/n/10 signature(from = "ANY", to = "Matrix")[]\T1/ptm/m/n/10 : This re-lies on a cor-rect [2404] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.7532 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.7629 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.7723 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7816--7822 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][][]\T1/ pcr/m/n/10 t[][][](.)[]\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2405] Underfull \hbox (badness 10000) in paragraph at lines 7889--7892 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", y = "dgeMatrix")[]\T1/ptm/m/n/10 : Ma-trix mul-ti-pli-ca-tion; Underfull \hbox (badness 10000) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 3557) in paragraph at lines 7892--7897 []\T1/pcr/m/n/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-tr ix mul-ti-pli-ca-tion. Mul-ti- Underfull \hbox (badness 6608) in paragraph at lines 7897--7901 \T1/ptm/m/n/10 sig-na-tures, use []\T1/pcr/m/n/10 showMethods("crossprod", clas s = "dgeMatrix")[]\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 1552) in paragraph at lines 7907--7908 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na- [2406] [2407] [2408] Underfull \hbox (badness 1062) in paragraph at lines 8087--8090 []\T1/pcr/m/n/10 ndenseMatrix []\T1/ptm/m/n/10 is the vir-tual class of all den se \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both Underfull \hbox (badness 6063) in paragraph at lines 8121--8124 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-call y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2409] Underfull \hbox (badness 3312) in paragraph at lines 8177--8179 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/pcr/m/n/10 X <- (X + t(X))/2 [] \T1/ptm/m/n/10 should be done, af-ter []\T1/pcr/m/n/10 X <- [2410] [2411] Overfull \hbox (85.38034pt too wide) in paragraph at lines 8279--8279 [] \T1/pcr/m/n/9 all.equal(n.A.m, unname(as.matrix(n.A$mat)), tolerance = 1e -15)# seen rel.d.= 1.46e-16[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8319--8319 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2412] Underfull \hbox (badness 2635) in paragraph at lines 8386--8391 []\T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-rec tly. Class []\T1/pcr/m/n/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/ 10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8386--8391 \T1/ptm/m/n/10 Class []\T1/pcr/m/n/10 "denseMatrix"[]\T1/ptm/m/n/10 , by class []\T1/pcr/m/n/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class []\T1/pcr/m/n/10 "Matri x"[]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8394--8397 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ); use, e.g., [2413] Underfull \hbox (badness 2521) in paragraph at lines 8464--8470 []\T1/pcr/m/n/10 signature(from = "matrix", to = "nMatrix")[]\T1/ptm/m/n/10 : N ote that these co-er-cions [2414] Underfull \hbox (badness 1867) in paragraph at lines 8586--8588 []\T1/ptm/m/n/10 fast sim- [2415] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignored \relax l.8626 \HeaderA{norm}{Matrix Norms}{norm} [2416] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8720--8720 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8721--8721 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8867--8877 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][][]\T1/pcr/m/n /10 TsparseMatrix[][][][]\T1/ptm/m/n/10 , sub-classes []\T1/pcr/m/n/10 ngTMatri x[]\T1/ptm/m/n/10 , [2417] Underfull \hbox (badness 3179) in paragraph at lines 8938--8941 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cal ly equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2418] Underfull \hbox (badness 10000) in paragraph at lines 9036--9039 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2419] Underfull \hbox (badness 10000) in paragraph at lines 9118--9121 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/pcr/m/n/10 t[][][]() []\T1/ptm/m/n /10 and co-er-cion meth-ods (for [][][]\T1/pcr/m/n/10 as[][][](.)[]\T1/ptm/m/n/ 10 ; use, e.g., [2420] [2421] Underfull \hbox (badness 10000) in paragraph at lines 9213--9214 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9214--9215 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9215--9216 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9216--9217 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9217--9218 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9218--9219 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9219--9220 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9220--9221 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9221--9222 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9222--9223 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9223--9224 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9224--9225 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9225--9226 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9226--9227 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9227--9228 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9228--9229 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9229--9230 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "missing", drop = [2422] Underfull \hbox (badness 10000) in paragraph at lines 9230--9231 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "missing", drop = Underfull \hbox (badness 10000) in paragraph at lines 9231--9232 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "missing", dro p = Underfull \hbox (badness 10000) in paragraph at lines 9232--9233 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "missing", dr op = Underfull \hbox (badness 10000) in paragraph at lines 9233--9234 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9234--9235 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9235--9236 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9236--9237 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9237--9238 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "NULL", drop = Underfull \hbox (badness 10000) in paragraph at lines 9238--9239 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "missing", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9239--9240 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "NULL", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9240--9241 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "index", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9241--9242 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "matrix", j = "index", drop = Underfull \hbox (badness 10000) in paragraph at lines 9242--9243 []\T1/pcr/m/n/10 signature(x = "packedMatrix", i = "lMatrix", j = "index", drop = [2423] Underfull \hbox (badness 10000) in paragraph at lines 9332--9334 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") []\T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 5008) in paragraph at lines 9334--9337 []\T1/pcr/m/n/10 signature(from = "integer", to = "pMatrix")[]\T1/ptm/m/n/10 : This is en-ables typ-i-cal [2424] Underfull \hbox (badness 4954) in paragraph at lines 9340--9347 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "matrix")[]\T1/ptm/m/n/10 : c o-er-cion to a tra-di-tional Underfull \hbox (badness 1558) in paragraph at lines 9350--9354 []\T1/pcr/m/n/10 signature(x = "pMatrix", logarithm="logical")[]\T1/ptm/m/n/10 : Since per-mu-ta- Underfull \hbox (badness 3229) in paragraph at lines 9354--9358 \T1/ptm/m/n/10 trix; note that []\T1/pcr/m/n/10 solve(P) []\T1/ptm/m/n/10 is id en-ti-cal to []\T1/pcr/m/n/10 t(P) []\T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-c es. See [2425] Overfull \hbox (36.78088pt too wide) in paragraph at lines 9433--9433 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9436--9436 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9438--9438 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9442--9442 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9443--9443 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] [2426] Underfull \hbox (badness 3989) in paragraph at lines 9468--9478 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of [] \T1/pcr/m/n/10 x []\T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9468--9478 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2427] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.9569 \aliasA{qr}{qr-methods}{qr} [2428] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9641--9641 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9652--9652 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] [2429] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9671--9671 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9679--9679 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2430] Underfull \hbox (badness 2005) in paragraph at lines 9736--9742 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/pcr/m/n/10 qr[][][](x, tol, Underfull \hbox (badness 10000) in paragraph at lines 9753--9756 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense []\T1/pcr/m/n/10 x[]\ T1/ptm/m/n/10 , it cor-re-sponds to [2431] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9852--9852 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9868--9868 []\T1/pcr/m/n/9 sapply(meths, function(.m.) rankMatrix(M15, method = .m., tol = 1e-7)) # all 14[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9874--9874 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9875--9875 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] [2432] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9893 ... the Reciprocal Condition Number}{rcond} [2433] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10011--10011 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2434] [2435] [2436] Underfull \hbox (badness 2150) in paragraph at lines 10202--10210 \T1/ptm/m/n/10 dices, if not []\T1/pcr/m/n/10 symmetric [][]sample.int[][][](nr ow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/pcr/m/n/10 rand.x []\T1/ptm/m/n /10 is not [2437] [2438] Underfull \hbox (badness 1558) in paragraph at lines 10342--10345 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class []\T1/pcr/m/n /10 "Matrix"[]\T1/ptm/m/n/10 ) or tra-di-tional [2439] Overfull \hbox (52.98038pt too wide) in paragraph at lines 10404--10404 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10408--10408 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2440] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.10470 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (48.78088pt too wide) in paragraph at lines 10572--10572 []\T1/pcr/m/n/10 ## solve(a, b, ...) # the two-argument version, almost always preferred to [2441] Overfull \hbox (90.78088pt too wide) in paragraph at lines 10584--10584 []\T1/pcr/m/n/10 solve(a, b, system = c("A", "LDLt", "LD", "DLt", "L", "Lt", " D", "P", "Pt"), ...)[] Underfull \hbox (badness 1616) in paragraph at lines 10619--10631 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 solve []\T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 10636--10639 []\T1/ptm/m/n/10 (for all []\T1/pcr/m/n/10 b[]\T1/ptm/m/n/10 ) work via []\T1/p cr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10645--10652 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( [2442] Underfull \hbox (badness 10000) in paragraph at lines 10658--10668 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list []\T1/pcr/m/n/10 ( Underfull \hbox (badness 3657) in paragraph at lines 10658--10668 \T1/pcr/m/n/10 sparse=FALSE, tol = .Machine$double.eps ) []\T1/ptm/m/n/10 : Che cks if []\T1/pcr/m/n/10 a []\T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10685--10689 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10692--10694 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10715--10716 []\T1/ptm/m/n/10 works via []\T1/pcr/m/n/10 as(b, Underfull \hbox (badness 10000) in paragraph at lines 10721--10723 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10725--10726 []\T1/ptm/m/n/10 all work via []\T1/pcr/m/n/10 as(a, Underfull \hbox (badness 10000) in paragraph at lines 10733--10736 [][][]\T1/pcr/m/n/10 solve[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lu[][][ ][]\T1/ptm/m/n/10 , and class doc-u-men-ta-tions [][][]\T1/pcr/m/n/10 CHMfactor [][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 sparseLU[][][][]\T1/ptm/m/n/10 , and [2443] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10751--10751 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10755--10755 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] Underfull \hbox (badness 10000) in paragraph at lines 10776--10779 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Overfull \hbox (6.78088pt too wide) in paragraph at lines 10793--10793 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10795--10795 [] \T1/pcr/m/n/10 drop.unused.levels = TRUE, repr = c("C", "R", "T"), giveCs parse,[] [2444] Underfull \hbox (badness 1648) in paragraph at lines 10804--10806 []\T1/ptm/m/n/10 a data frame cre-ated with [][][]\T1/pcr/m/n/10 model.frame[][ ][][]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10812--10815 []\T1/ptm/m/n/10 character string or []\T1/pcr/m/n/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10812--10815 []\T1/pcr/m/n/10 "[][]sparseMatrix[][][]"[]\T1/ptm/m/n/10 , spec-i-fy-ing the c on-trasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10823--10827 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10823--10827 []\T1/pcr/m/n/10 sparse.model.matrix []\T1/ptm/m/n/10 has been changed to []\T1 /pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 1668) in paragraph at lines 10838--10843 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10918--10918 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10919--10919 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10920--10920 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2446] [2447] [2448] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11107--11107 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Underfull \hbox (badness 1668) in paragraph at lines 11149--11154 [][][]\T1/pcr/m/n/10 character[][][] []\T1/ptm/m/n/10 string, one of []\T1/pcr/ m/n/10 "C"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "T"[]\T1/ptm/m/n/10 , or []\T1/pc r/m/n/10 "R"[]\T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2449] Underfull \hbox (badness 10000) in paragraph at lines 11234--11237 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][][]\T1/pcr/m/n/10 xtabs[][][ ](*, sparse=TRUE)[]\T1/ptm/m/n/10 , for sparse ta-bles and [2450] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11246--11246 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11250--11250 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11251--11251 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11256--11256 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11259--11259 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 11282--11282 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 11283--11283 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Underfull \vbox (badness 10000) has occurred while \output is active [2451] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11309--11309 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 11311--11311 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11313--11313 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2452] Underfull \hbox (badness 6842) in paragraph at lines 11411--11414 []\T1/pcr/m/n/10 (x = "sparseMatrix", logarithm=TRUE)[]\T1/ptm/m/n/10 : [][][]\ T1/pcr/m/n/10 determinant[][][]() []\T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 11446--11450 [][][]\T1/pcr/m/n/10 sparseMatrix[][][][]\T1/ptm/m/n/10 , and its ref-er-ences, such as [][][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)[]\T1/ptm/m/n/10 , or [2453] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11486 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2454] Underfull \hbox (badness 10000) in paragraph at lines 11616--11618 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")[]\T1/ptm/m/n/10 : For []\ T1/pcr/m/n/10 solve(a,b)[]\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11644--11644 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2455] Underfull \hbox (badness 5036) in paragraph at lines 11672--11674 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2456] Underfull \hbox (badness 2970) in paragraph at lines 11783--11789 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class []\T1/pcr/m/ n/10 "sparseVector" []\T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11783--11789 \T1/ptm/m/n/10 tual daugh-ter classes []\T1/pcr/m/n/10 "dsparseVector"[]\T1/ptm /m/n/10 , []\T1/pcr/m/n/10 "isparseVector"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 " lsparseVector"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 11834--11837 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m/ n/10 co-erces sparse [2457] Underfull \hbox (badness 10000) in paragraph at lines 11874--11879 []\T1/pcr/m/n/10 (x = "nsparseVector")[]\T1/ptm/m/n/10 : re-turn [][][]\T1/pcr/ m/n/10 logical[][][] []\T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11889--11891 [][][]\T1/pcr/m/n/10 sparseVector[][][]() []\T1/ptm/m/n/10 for friendly con-str uc-tion of sparse vec-tors (apart from []\T1/pcr/m/n/10 as(*, [2458] Underfull \vbox (badness 10000) has occurred while \output is active [2459] Underfull \hbox (badness 2310) in paragraph at lines 12014--12020 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) []\T1/ptm/m/n/10 for the more usual con-struc-tor of such ma-tri-ces. Then, [2460] [2461] Underfull \hbox (badness 6188) in paragraph at lines 12105--12107 []\T1/pcr/m/n/10 signature(from = "ddiMatrix", to = "symmetricMatrix")[]\T1/ptm /m/n/10 : and many Underfull \hbox (badness 2591) in paragraph at lines 12131--12136 \T1/ptm/m/n/10 Classes [][][]\T1/pcr/m/n/10 triangularMatrix[][][][]\T1/ptm/m/n /10 , and, e.g., [][][]\T1/pcr/m/n/10 dsyMatrix[][][] []\T1/ptm/m/n/10 for nu-m eric \T1/ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2462] Underfull \hbox (badness 2057) in paragraph at lines 12207--12209 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2463] Underfull \hbox (badness 6641) in paragraph at lines 12294--12297 []\T1/ptm/m/n/10 Currently, [][][]\T1/pcr/m/n/10 Schur[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 isSymmetric[][][] []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 as () []\T1/ptm/m/n/10 (i.e. [][][]\T1/pcr/m/n/10 coerce[][][][]\T1/ptm/m/n/10 ) h ave meth-ods with [2464] Underfull \hbox (badness 5133) in paragraph at lines 12338--12342 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 "TsparseMatrix" []\T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 12338--12342 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2465] Underfull \hbox (badness 7649) in paragraph at lines 12445--12447 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2466] [2467] Underfull \hbox (badness 10000) in paragraph at lines 12563--12565 []\T1/ptm/m/n/10 typically a []\T1/pcr/m/n/10 "packedMatrix"[]\T1/ptm/m/n/10 , though [2468] Underfull \hbox (badness 1668) in paragraph at lines 12692--12695 [][][]\T1/pcr/m/n/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/pcr/m/n/10 unpac k[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/pcr/m/n/10 "[][]pac kedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [2469] Underfull \hbox (badness 7362) in paragraph at lines 12743--12745 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2470] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12781--12781 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12782--12782 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2471] [2472] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12936--12936 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C1, nWC, 1/ x))$modulus))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12941--12941 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2473] Underfull \hbox (badness 6910) in paragraph at lines 13147--13149 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2474] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 13194. [2475] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 L. <- L; L.[1:2,1] <- TRUE; L.@x[1:2] <- FALSE; L. # has "zero s" to drop0()[] [2476] [2477]) (./boot-pkg.tex [2478] Chapter 18. [2479] [2480] [2481] [2482] [2483] [2484] [2485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 532--532 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2486] Underfull \hbox (badness 1325) in paragraph at lines 570--577 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 585--590 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2487] [2488] [2489] Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 853--857 [][][]\T1/pcr/m/n/10 boot.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 bo ot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 censboot[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 empinf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 j ack.after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 tilt.boot[][][][]\T 1/ptm/m/n/10 , [2490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 887--887 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2491] [2492] [2493] Underfull \hbox (badness 1496) in paragraph at lines 1084--1093 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1084--1093 \T1/ptm/m/n/10 is not sup-plied and []\T1/pcr/m/n/10 length(index) []\T1/ptm/m/ n/10 is 2 then []\T1/pcr/m/n/10 var.t0 []\T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2494] [2495] [2496] [2497] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2498] [2499] [2500] [2501] [2502] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1738--1738 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2503] [2504] [2505] Underfull \vbox (badness 10000) has occurred while \output is active [2506] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2013--2013 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2507] Underfull \hbox (badness 6268) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2508] [2509] [2510] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2511] Underfull \hbox (badness 4595) in paragraph at lines 2363--2368 \T1/ptm/m/n/10 are passed un-changed ev-ery time []\T1/pcr/m/n/10 boot.out$stat istic []\T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2440--2441 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 empinf[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 k3.linear[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 linear.approx[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 saddle.distn[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.spline[][][][] \T1/ptm/m/n/10 , [2512] [2513] Underfull \hbox (badness 1077) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/pcr/m /n/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/pcr/m/n/10 n []\T1/ptm/m/n/1 0 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/pcr/m/n/10 unbiased []\T1/ptm/m/n/10 is []\T1/pcr /m/n/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/pcr/m/n/10 1/n []\T 1/ptm/m/n/10 is used. This is mul-ti-plied by [2514] [2515] [2516] [2517] [2518] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2895--2895 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2897--2897 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2519] [2520] [2521] Underfull \hbox (badness 3861) in paragraph at lines 3105--3108 [][][]\T1/pcr/m/n/10 boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.arr ay[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 boot.ci[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 control[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 jack .after.boot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 linear.approx[][][][]\ T1/ptm/m/n/10 , [2522] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3158--3158 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2523] [2524] [2525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2526] [2527] [2528] [2529] [2530] [2531] [2532] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2533] [2534] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2535] [2536] [2537] [2538] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2539] [2540] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is sup-plied but nei-the r []\T1/pcr/m/n/10 t []\T1/ptm/m/n/10 nor []\T1/pcr/m/n/10 L []\T1/ptm/m/n/10 a re sup-plied then []\T1/pcr/m/n/10 t0 []\T1/ptm/m/n/10 is set to [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2550] [2551] [2552] [2553] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2555] [2556] [2557] [2558] [2559] [2560] [2561] [2562] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2563] Underfull \hbox (badness 1127) in paragraph at lines 5988--6006 []\T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less than []\T1/pcr/m/n/10 min(alpha)/10[]\T1/ptm/m/n/10 , then [2564] Underfull \hbox (badness 2837) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/pcr/m/n/10 "s addle.distn"[]\T1/ptm/m/n/10 . See the help file for [2565] [2566] [2567] [2568] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6306--6306 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2569] [2570] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6495--6495 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6497--6497 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2571] [2572] [2573] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2574] [2575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6902--6902 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2576] [2577] [2578] [2579] [2580] [2581] [2582] [2583]) (./class-pkg.tex [2584] Chapter 19. [2585] [2586] [2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600]) (./cluster-pkg.tex Chapter 20. [2601] [2602] [2603] Overfull \hbox (42.18039pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 255--255 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2604] [2605] [2606] [2607] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 523--523 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2608] [2609] Overfull \hbox (66.78088pt too wide) in paragraph at lines 638--638 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2610] Underfull \hbox (badness 3078) in paragraph at lines 691--694 []\T1/ptm/m/n/10 Setting this to []\T1/pcr/m/n/10 FALSE []\T1/ptm/m/n/10 saves mem-ory (and hence time), but dis-ables [2611] [2612] Underfull \hbox (badness 2941) in paragraph at lines 791--794 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 clara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\ T1/ptm/m/n/10 , [2613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 834--834 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] Underfull \hbox (badness 10000) in paragraph at lines 881--883 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2614] Overfull \hbox (24.78088pt too wide) in paragraph at lines 946--946 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2615] Underfull \hbox (badness 4872) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1138--1138 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Underfull \vbox (badness 10000) has occurred while \output is active [2618] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1176--1176 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1208--1212 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 nor a []\T1/pcr/m/n/10 data []\T1/ptm/m/n/10 com-po-nent, e.g., for [2619] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1284--1284 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2620] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1477--1480 Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 [][][]\T1/pcr/m/n/10 princomp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cmds cale[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 daisy[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cov.mve[][][ ][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1518--1518 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1528--1528 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2623] Underfull \hbox (badness 5741) in paragraph at lines 1568--1571 []\T1/pcr/m/n/10 coefHier() []\T1/ptm/m/n/10 di-rectly in-ter-faces to the un-d er-ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2624] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1637--1637 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2625] Underfull \hbox (badness 1552) in paragraph at lines 1686--1688 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/pcr/m/n /10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , se e Underfull \hbox (badness 1629) in paragraph at lines 1699--1703 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 3746) in paragraph at lines 1699--1703 \T1/ptm/m/n/10 (incl []\T1/pcr/m/n/10 integer[]\T1/ptm/m/n/10 ) columns of []\T 1/pcr/m/n/10 x[]\T1/ptm/m/n/10 , aka []\T1/pcr/m/n/10 "I" []\T1/ptm/m/n/10 in r e-sult []\T1/pcr/m/n/10 Types[]\T1/ptm/m/n/10 , see [2626] Underfull \hbox (badness 1540) in paragraph at lines 1775--1783 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$[]\T1/pcr/m/n/10 = [2627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1886--1886 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2628] [2629] [2630] [2631] [2632] Underfull \hbox (badness 10000) in paragraph at lines 2207--2210 Underfull \hbox (badness 3179) in paragraph at lines 2221--2227 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also the [][][]\T1/pcr/m/n/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/pcr/m/n/1 0 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2633] [2634] Underfull \hbox (badness 10000) in paragraph at lines 2379--2382 [][][]\T1/pcr/m/n/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-en ces; [][][]\T1/pcr/m/n/10 fanny.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2635] Underfull \hbox (badness 1292) in paragraph at lines 2447--2450 []\T1/ptm/m/n/10 named vec-tor with []\T1/pcr/m/n/10 iterations[]\T1/ptm/m/n/10 , the num-ber of it-er-a-tions needed and [2636] Underfull \hbox (badness 6675) in paragraph at lines 2456--2458 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2479--2482 [][][]\T1/pcr/m/n/10 fanny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.f anny[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 dissimilarity.object[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [2637] [2638] Overfull \hbox (48.78088pt too wide) in paragraph at lines 2608--2608 []\T1/pcr/m/n/10 medoids(x, clustering, diss = inherits(x, "dist"), USE.NAMES = FALSE, ...) [2639] Overfull \hbox (69.18036pt too wide) in paragraph at lines 2655--2655 [] \T1/pcr/m/n/9 stopifnot(length(cl.k) == nrow(votes.repub), 1 <= cl.k, cl.k <= k, table(cl.k) >= 2)[] [2640] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2760--2760 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2641] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2839--2839 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2642] [2643] [2644] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3068--3068 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2645] [2646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3171--3171 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2647] [2648] [2649] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3367--3367 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3368--3368 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2650] Underfull \hbox (badness 10000) in paragraph at lines 3435--3438 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via []\T1/pcr/m /n/10 pltree() []\T1/ptm/m/n/10 is pro-vided by []\T1/pcr/m/n/10 dg <- [2651] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3485--3485 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2652] [2653] [2654] Underfull \hbox (badness 10000) in paragraph at lines 3671--3674 []\T1/ptm/m/n/10 when []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 does not have a []\T1 /pcr/m/n/10 diss []\T1/ptm/m/n/10 com-po-nent as for [][][]\T1/pcr/m/n/10 pam[] [][](*, Underfull \hbox (badness 1448) in paragraph at lines 3671--3674 \T1/pcr/m/n/10 keep.diss=FALSE)[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 dist []\T1/p tm/m/n/10 must be the dis-sim-i-lar-ity if a clus-plot is [2655] Underfull \hbox (badness 10000) in paragraph at lines 3734--3739 [][][]\T1/pcr/m/n/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 clusplot.de fault[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pam[][][][]\T1/ptm/m/n/10 , [2656] Underfull \hbox (badness 1748) in paragraph at lines 3796--3801 \T1/ptm/m/n/10 dis-patches to [][][]\T1/pcr/m/n/10 plot.hclust[][][](..)[]\T1/p tm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/pcr/m/n/10 xx <- Underfull \hbox (badness 6268) in paragraph at lines 3808--3811 [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 agnes.o bject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 diana.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/1 0 hclust[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 par[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.agnes[][][][]\T1/ptm/m/n/10 , [2657] [2658] [2659] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 [][][]\T1/pcr/m/n/10 summary.agnes[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 agnes[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ag nes.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4024--4027 [][][]\T1/pcr/m/n/10 summary.clara[][][] []\T1/ptm/m/n/10 pro-duc-ing more out- put; [][][]\T1/pcr/m/n/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cl ara.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print[][][][]\T1/ptm/m/ n/10 , [2660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] [2661] Underfull \hbox (badness 2035) in paragraph at lines 4088--4090 []\T1/ptm/m/n/10 a []\T1/pcr/m/n/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/pcr/m/n/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2662] [2663] [2664] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2665] [2666] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4426--4426 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4435--4435 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4437--4437 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4440--4440 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4442--4442 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4449--4449 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2667] [2668] [2669] [2670] [2671] [2672] [2673] Underfull \hbox (badness 10000) in paragraph at lines 4823--4829 []\T1/ptm/m/n/10 Our ver-sion of the []\T1/pcr/m/n/10 xclara []\T1/ptm/m/n/10 i s slightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4839--4841 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4854--4854 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4864--4864 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2674] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4868--4868 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2675]) (./codetools-pkg.tex [2676] Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2677] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 checkUsage Package []\T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2678] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2679] [2680] [2681]) (./foreign-pkg.tex [2682] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 33--37 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2683] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a [2684] [2685] Underfull \hbox (badness 3601) in paragraph at lines 237--245 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude []\T1/pcr/m /n/10 "datalabel"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "time.stamp"[]\T1/ptm/m/n/ 10 , [2686] Overfull \hbox (12.78088pt too wide) in paragraph at lines 295--295 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2687] [2688] [2689] Overfull \hbox (48.78088pt too wide) in paragraph at lines 461--461 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2690] Overfull \hbox (30.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] Underfull \hbox (badness 2846) in paragraph at lines 505--514 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 3746) in paragraph at lines 505--514 \T1/ptm/m/n/10 els. For []\T1/pcr/m/n/10 "append" []\T1/ptm/m/n/10 (the de-faul t), the first orig-i-nal value la-bel is Underfull \hbox (badness 2269) in paragraph at lines 505--514 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/p cr/m/n/10 paste0(label, Underfull \hbox (badness 10000) in paragraph at lines 515--518 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 515--518 \T1/ptm/m/n/10 pli-cated value la-bels in SPSS (de-fault []\T1/pcr/m/n/10 "_dup licated_"[]\T1/ptm/m/n/10 ) if [2691] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / learn . microsoft . com / en-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 568--574 []\T1/ptm/m/n/10 There may be at-tributes []\T1/pcr/m/n/10 "label.table" []\T1/ ptm/m/n/10 and []\T1/pcr/m/n/10 "variable.labels"[]\T1/ptm/m/n/10 . At-tribute [2692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2693] Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2694] [2695] Underfull \hbox (badness 10000) in paragraph at lines 812--813 Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2696] Underfull \hbox (badness 10000) in paragraph at lines 869--873 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\T1/p cr/m/n/10 https : / / support . Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/pcr/m/n/10 sas . com / content / dam / SAS / support / en / technical-[]pap ers / Overfull \hbox (74.28088pt too wide) in paragraph at lines 869--873 \T1/pcr/m/n/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[]s et-[]in-[]sas-[]transport-[]xport-[]format . [2697] Overfull \hbox (24.78088pt too wide) in paragraph at lines 900--900 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2698] Overfull \hbox (0.78088pt too wide) in paragraph at lines 964--964 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) [2699] [2700] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2701] [2702] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/pcr/m/n/10 foreig n:::writeForeignStata[]\T1/ptm/m/n/10 , [2703] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 package="SPSS"[]\T1/ptm/m/n/10 , as a sid e ef-fect, the dec-i-mal in-di-ca-tor is al-ways set by []\T1/pcr/m/n/10 SET [2704]) (./lattice-pkg.tex Chapter 23. [2705] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\T1/pcr/m/n/10 http : / / web . archive . org / Underfull \hbox (badness 10000) in paragraph at lines 117--121 \T1/pcr/m/n/10 web / 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / [2706] [2707] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2708] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2709] [2710] [2711] [2712] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2713] [2714] [2715] [2716] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2717] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 sho uld be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2718] [2719] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2720] [2721] [2722] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][][]\T1/pcr/m/ n/10 plot.trellis[][][][]\T1/ptm/m/n/10 , [2723] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][][]\T1/pcr/m/n/10 panel.dotplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.superpose[] [][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 panel.loess[][][][]\T1/ptm/m/n/10 , [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/pcr/m/n/10 xyplot[] [][][]\T1/ptm/m/n/10 , which may pass them on to [2726] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard []\T1/pcr/m/n/10 col[]\T 1/ptm/m/n/10 , []\T1/pcr/m/n/10 lty[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 lwd[]\T1 /ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2727] [2728] [2729] [2730] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2731] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When []\T1/pcr/m/n/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fie d, the value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 []\T1/pcr/m/n/10 lattice.getOption("histogram.breaks") []\T1/ptm/m/n/10 is firs t checked. If [2732] [2733] [2734] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2735] [2736] [2737] [2738] [2739] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2740] [2741] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2742] Underfull \hbox (badness 6758) in paragraph at lines 2919--2923 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2919--2923 \T1/ptm/m/n/10 ren-dered as a raster im-age us-ing [][][]\T1/pcr/m/n/10 grid.ra ster[][][][]\T1/ptm/m/n/10 . See also Underfull \hbox (badness 10000) in paragraph at lines 2925--2927 []\T1/ptm/m/n/10 Logical flag, passed to [][][]\T1/pcr/m/n/10 rasterGrob[][][] []\T1/ptm/m/n/10 when Underfull \hbox (badness 1609) in paragraph at lines 2977--2983 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- Underfull \hbox (badness 1400) in paragraph at lines 2977--2983 \T1/ptm/m/n/10 fec-tively, set-ting this to []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n /10 changes the de-fault panel func-tion from [2743] Underfull \hbox (badness 2486) in paragraph at lines 3001--3005 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2744] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3104--3104 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3105--3105 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3106--3106 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] [2745] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3117--3117 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3129--3129 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2746] Underfull \hbox (badness 2913) in paragraph at lines 3187--3194 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when []\T1/ pcr/m/n/10 x []\T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3187--3194 []\T1/pcr/m/n/10 row.values []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 column.values []\T1/ptm/m/n/10 must have the same lengths as [2747] [2748] [2749] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3475 \aliasA{parallel}{B\_08\_splom}{parallel} [2750] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3517--3517 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3540--3540 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2751] [2752] [2753] [2754] [2755] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3876--3876 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2756] [2757] Underfull \hbox (badness 2277) in paragraph at lines 3970--3974 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by Underfull \hbox (badness 2435) in paragraph at lines 3970--3974 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2758] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4100--4100 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4109--4113 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in [2759] Underfull \hbox (badness 3219) in paragraph at lines 4136--4138 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when Underfull \hbox (badness 1728) in paragraph at lines 4153--4157 []\T1/pcr/m/n/10 theme[]\T1/ptm/m/n/10 ). These are used to mod-ify the cur-ren t set-tings (ob-tained by [2760] Underfull \hbox (badness 5161) in paragraph at lines 4218--4222 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in []\T1/pcr/m/n/10 trell is.settings []\T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4218--4222 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2761] [2762] Underfull \hbox (badness 1067) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/pcr/m/n/10 col []\T1/ptm/m/n/ 10 is used for com-po-nents []\T1/pcr/m/n/10 "plot.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "plot.line"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "plot.polygon"[ ]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.line"[]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 "super pose.polygon"[]\T1/ptm/m/n/10 . []\T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4336--4346 []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col[]\T1/ptm/m/n/10 , but is used only for []\T1/pcr/m/n/10 "plot.symbol" []\T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4336--4346 []\T1/pcr/m/n/10 "superpose.symbol"[]\T1/ptm/m/n/10 . Sim-i-larly, []\T1/pcr/m/ n/10 col.line []\T1/ptm/m/n/10 over-rides []\T1/pcr/m/n/10 col []\T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4361--4364 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 pl ot.symbol[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4364--4366 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/pcr/m/n/10 plot.polygon []\T1/ptm/m/n/10 and [2763] [2764] [2765] [2766] [2767] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4768--4768 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2768] [2769] Underfull \vbox (badness 1092) has occurred while \output is active [2770] Underfull \hbox (badness 10000) in paragraph at lines 4955--4958 []\T1/ptm/m/n/10 An ob-ject of class []\T1/pcr/m/n/10 trellis[]\T1/ptm/m/n/10 , by de-fault plot-ted by []\T1/pcr/m/n/10 print.trellis[]\T1/ptm/m/n/10 . [2771] [2772] Underfull \hbox (badness 1442) in paragraph at lines 5087--5090 []\T1/pcr/m/n/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gle s via rect-an-gles. []\T1/pcr/m/n/10 print.shingle []\T1/ptm/m/n/10 and [2773] [2774] [2775] [2776] [2777] Underfull \hbox (badness 3646) in paragraph at lines 5426--5429 [][][]\T1/pcr/m/n/10 Lattice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 draw. key[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 trellis.par.get[][][][]\T1/ptm /m/n/10 , and [][][]\T1/pcr/m/n/10 xyplot[][][][]\T1/ptm/m/n/10 , specif-i-call y the en-try for Overfull \hbox (36.78088pt too wide) in paragraph at lines 5456--5456 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5457--5457 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2778] Underfull \hbox (badness 10000) in paragraph at lines 5545--5548 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5545--5548 []\T1/pcr/m/n/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on the left of pan-els us-ing [2779] Underfull \hbox (badness 1635) in paragraph at lines 5571--5576 []\T1/pcr/m/n/10 strip.default []\T1/ptm/m/n/10 is called for its side-effect, which is to draw a strip ap-pro-pri-ate for [2780] [2781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5722--5722 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5736--5736 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5737--5737 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5740--5740 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5743--5743 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5745--5745 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5751--5751 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5752--5752 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5753--5753 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] [2782] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5754--5754 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5755--5755 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5771--5773 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of Underfull \hbox (badness 2376) in paragraph at lines 5782--5784 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2783] Underfull \hbox (badness 2538) in paragraph at lines 5907--5911 \T1/ptm/m/n/10 For []\T1/pcr/m/n/10 trellis.focus[]\T1/ptm/m/n/10 , the de-faul t is []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 in in-ter-ac-tive mode, and Underfull \hbox (badness 4205) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 For []\T1/pcr/m/n/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , e x-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5918--5925 []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 trellis.switchFocus[]\T1/ptm/m/n/10 , the se are used (in com-bi-na-tion with [2784] [2785] Underfull \hbox (badness 10000) in paragraph at lines 6071--6075 [][][]\T1/pcr/m/n/10 identify[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Latt ice[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.trellis[][][][]\T1/ptm/m /n/10 , [][][]\T1/pcr/m/n/10 trellis.currentLayout[][][][]\T1/ptm/m/n/10 , [2786] Underfull \vbox (badness 10000) has occurred while \output is active [2787] [2788] Underfull \hbox (badness 4242) in paragraph at lines 6218--6223 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2789] [2790] Underfull \hbox (badness 3601) in paragraph at lines 6334--6339 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/pcr/m/n/10 x []\T1/ptm/m /n/10 for ev-ery level of []\T1/pcr/m/n/10 y []\T1/ptm/m/n/10 (or the other way round Underfull \hbox (badness 2486) in paragraph at lines 6334--6339 \T1/ptm/m/n/10 if []\T1/pcr/m/n/10 horizontal=FALSE[]\T1/ptm/m/n/10 ). By de-fa ult, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2791] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6421--6421 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2792] [2793] Underfull \hbox (badness 1888) in paragraph at lines 6553--6560 []\T1/pcr/m/n/10 at []\T1/ptm/m/n/10 can be a nu-meric vec-tor, []\T1/pcr/m/n/1 0 col.regions []\T1/ptm/m/n/10 a vec-tor of col-ors, and [2794] Underfull \hbox (badness 10000) in paragraph at lines 6610--6613 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6610--6613 []\T1/pcr/m/n/10 shade.colors.palette []\T1/ptm/m/n/10 func-tion should re-turn a valid color. The [2795] [2796] [2797] [2798] [2799] Underfull \hbox (badness 1320) in paragraph at lines 7016--7023 []\T1/pcr/m/n/10 panel.levelplot.raster []\T1/ptm/m/n/10 is an al-ter-na-tive p anel func-tion that uses the raster draw- Underfull \hbox (badness 1715) in paragraph at lines 7016--7023 \T1/ptm/m/n/10 can only ren-der data on an eq-ui-s-paced grid), but can be more ef-fi-cient. When us-ing [2800] [2801] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7086--7086 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] Underfull \hbox (badness 10000) in paragraph at lines 7116--7120 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7116--7120 []\T1/pcr/m/n/10 diag.panel.splom []\T1/ptm/m/n/10 to know what ar-gu-ments thi s func-tion is passed [2802] [2803] Underfull \hbox (badness 10000) in paragraph at lines 7221--7224 \T1/ptm/m/n/10 and []\T1/pcr/m/n/10 diag.panel []\T1/ptm/m/n/10 from []\T1/pcr/ m/n/10 panel.pairs[]\T1/ptm/m/n/10 . Cur-rently ig-nored by [2804] [2805] Underfull \hbox (badness 2012) in paragraph at lines 7387--7390 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7433--7433 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2807] [2808] Underfull \hbox (badness 2644) in paragraph at lines 7574--7578 []\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed o n to Underfull \hbox (badness 2772) in paragraph at lines 7587--7590 []\T1/ptm/m/n/10 Most gen-er-ally, []\T1/pcr/m/n/10 grid []\T1/ptm/m/n/10 can b e a list of ar-gu-ments to be sup-plied to [2809] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7657--7657 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2810] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7728--7728 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7733--7733 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2811] [2812] [2813] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7918--7918 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] Underfull \hbox (badness 1436) in paragraph at lines 7973--7979 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/pcr/m/n/10 panel.super pose Underfull \hbox (badness 10000) in paragraph at lines 8531--8534 []\T1/ptm/m/n/10 from []\T1/pcr/m/n/10 panel.superpose.2[]\T1/ptm/m/n/10 , and to []\T1/pcr/m/n/10 panel.groups []\T1/ptm/m/n/10 from [2822] [2823] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8706--8706 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8707--8707 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] [2824] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8719--8719 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] Underfull \hbox (badness 3118) in paragraph at lines 8738--8741 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/pcr/m/n/10 type [ ]\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in [2825] Underfull \hbox (badness 1515) in paragraph at lines 8814--8818 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2826] [2827] Underfull \hbox (badness 6316) in paragraph at lines 8920--8925 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2828] Overfull \hbox (47.58038pt too wide) in paragraph at lines 9030--9030 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2829] [2830] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9169--9169 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2831] Underfull \hbox (badness 1028) in paragraph at lines 9228--9232 \T1/pcr/m/n/10 condition []\T1/ptm/m/n/10 for 2-D, and []\T1/pcr/m/n/10 left, r ight.x, right.y, left.name, right.x.name, [2832] [2833] [2834] [2835] [2836] [2837] [2838] Underfull \hbox (badness 7238) in paragraph at lines 9692--9696 []\T1/ptm/m/n/10 Factor with lev-els []\T1/pcr/m/n/10 "Svansota"[]\T1/ptm/m/n/1 0 , []\T1/pcr/m/n/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Manchuria"[] \T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 475"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9692--9696 []\T1/pcr/m/n/10 "Velvet"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Peatland"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "Glabron"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "No. 4 57"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "Wisconsin No. 38"[]\T1/ptm/m/n/10 , [2839] [2840] [2841] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.9923 \aliasA{melanoma}{H\_melanoma}{melanoma} [2842] [2843] [2844] Underfull \hbox (badness 10000) in paragraph at lines 10085--10090 \T1/pcr/m/n/10 diseases[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Diabetes[]\T1/ptm/m/ n/10 , []\T1/pcr/m/n/10 Flu and pneumonia[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 He art disease[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 Lower Overfull \hbox (9.78043pt too wide) in paragraph at lines 10158--10158 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2845] [2846]) (./mgcv-pkg.tex Chapter 24. [2847] [2848] Overfull \hbox (6.78088pt too wide) in paragraph at lines 160--160 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 163--163 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2849] Overfull \hbox (72.78088pt too wide) in paragraph at lines 165--165 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 184--188 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 209--214 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2850] [2851] [2852] [2853] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][]\T1 /pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2854] Overfull \hbox (4.38043pt too wide) in paragraph at lines 422--422 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2855] [2856] [2857] Underfull \hbox (badness 2922) in paragraph at lines 634--635 []\T1/ptm/m/n/10 The link func-tion: one of []\T1/pcr/m/n/10 "logit"[]\T1/ptm/m /n/10 , []\T1/pcr/m/n/10 "probit"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "cloglog" []\T1/ptm/m/n/10 and [2858] [2859] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [2860] [2861] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2862] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2863] Underfull \vbox (badness 10000) has occurred while \output is active [2864] [2865] [2866] [2867] [2868] [2869] [2870] [2871] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1337--1337 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1338--1338 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1355--1355 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1367--1367 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1376--1376 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1378--1378 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1409--1409 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2873] [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1492--1492 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1503--1503 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Underfull \vbox (badness 10000) has occurred while \output is active [2875] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1542--1542 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2876] [2877] [2878] [2879] [2880] [2881] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1937--1937 []\T1/pcr/m/n/9 bd <- bam(y~s(x0)+ s(x1) + s(x1,fac,bs="sz",k=5)+s(x2,k=20),di screte=TRUE)[] [2882] [2883] [2884] [2885] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2162--2162 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2886] [2887] [2888] [2889] [2890] [2891] [2892] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2567--2567 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2579--2582 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][][]\T1/pcr/m/n /10 formula.gam[][][] []\T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2592--2596 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2618--2624 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2893] [2894] [2895] Underfull \hbox (badness 1043) in paragraph at lines 2787--2793 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2896] [2897] Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gamObject[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][] [][]predict. gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2923--2929 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 g am.side[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.selection[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][][]\T1/ptm /m/n/10 , [2898] Underfull \vbox (badness 10000) has occurred while \output is active [2899] Underfull \vbox (badness 10000) has occurred while \output is active [2900] Underfull \vbox (badness 10000) has occurred while \output is active [2901] [2902] [2903] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3240--3240 []\T1/pcr/m/n/10 gam.control(nthreads=1,ncv.threads=1,irls.reg=0.0,epsilon = 1 e-07, maxit = 200, [2904] [2905] [2906] [2907] [2908] [2909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3581--3581 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3584--3584 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3585--3585 [] \T1/pcr/m/n/10 pearson.extra=0,dev.extra=0,n.true=-1,Sl=NULL,nei=NU LL,...)[] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] Underfull \hbox (badness 5189) in paragraph at lines 4063--4067 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/pcr/m/n/10 gam []\T1/ptm /m/n/10 mod-els us-ing []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms ( see [2918] [2919] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4180--4180 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2920] [2921] [2922] Underfull \hbox (badness 1184) in paragraph at lines 4350--4354 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2923] [2924] [2925] [2926] [2927] [2928] [2929] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4796--4796 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2930] [2931] [2932] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2933] [2934] Underfull \hbox (badness 1142) in paragraph at lines 5073--5077 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2935] Underfull \hbox (badness 10000) in paragraph at lines 5145--5154 []\T1/ptm/m/n/10 In the event of []\T1/pcr/m/n/10 lme []\T1/ptm/m/n/10 con-ver- gence fail-ures, con-sider mod-i-fy-ing [2936] [2937] Underfull \hbox (badness 5970) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 magic[][][] []\T1/ptm/m/n/10 for an al-ter-na-tive for cor -re-lated data, [][][]\T1/pcr/m/n/10 te[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gam[][][][]\T1/ptm /m/n/10 , [][][]\T1/pcr/m/n/10 plot.gam[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 5262--5268 [][][]\T1/pcr/m/n/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 n egbin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 vis.gam[][][][]\T1/ptm/m/n/1 0 ,[][][]\T1/pcr/m/n/10 pdTens[][][][]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 gamm4 [ ]\T1/ptm/m/n/10 ( [][]$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2938] Underfull \vbox (badness 10000) has occurred while \output is active [2939] [2940] [2941] [2942] Underfull \hbox (badness 1577) in paragraph at lines 5614--5617 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] [][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5621--5622 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2943] [2944] [2945] [2946] [2947] [2948] [2949] Underfull \hbox (badness 6708) in paragraph at lines 6010--6011 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/pcr/m/n/10 gam(.. .,fit=FALSE) []\T1/ptm/m/n/10 or [2950] [2951] Overfull \hbox (58.38037pt too wide) in paragraph at lines 6059--6059 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6084--6084 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6113--6113 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2953] [2954] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6235--6235 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2955] [2956] [2957] [2958] [2959] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6572--6572 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2960] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6574--6574 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6595--6599 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2961] [2962] [2963] Underfull \vbox (badness 10000) has occurred while \output is active [2964] [2965] [2966] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6914--6914 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Underfull \vbox (badness 10000) has occurred while \output is active [2972] [2973] [2974] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7346--7346 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7373--7373 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2975] [2976] [2977] [2978] [2979] [2980] [2981] [2982] [2983] Underfull \hbox (badness 1242) in paragraph at lines 7916--7917 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2984] [2985] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8003--8003 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2986] [2987] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8066--8066 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8085--8085 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2988] [2989] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] Underfull \vbox (badness 10000) has occurred while \output is active [3006] [3007] Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/pcr/m/n/10 Dim .pdIndot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 logDet.pd Idnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdConstruct.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 9310--9313 []\T1/pcr/m/n/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdMatrix.p dIdnot[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 solve.pdIdnot[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 summary.pdIdnot[]\T1/ptm/m/n/10 . [3008] Underfull \hbox (badness 10000) in paragraph at lines 9366--9369 []\T1/ptm/m/n/10 These func-tions ([]\T1/pcr/m/n/10 pdTens[]\T1/ptm/m/n/10 , [] \T1/pcr/m/n/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 pdFactor.p dTens[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9366--9369 []\T1/pcr/m/n/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 coef.pdTens []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 summary.pdTens[]\T1/ptm/m/n/10 ) would n ot nor-mally be [3009] [3010] [3011] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9586--9586 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9587--9587 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 9590--9590 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [3012] [3013] [3014] Underfull \hbox (badness 1629) in paragraph at lines 9748--9753 []\T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [3015] [3016] [3017] [3018] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9960--9960 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,gc.level=0,...)[] Underfull \hbox (badness 1062) in paragraph at lines 9997--10001 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 type=="terms" []\T1/ptm/m/n/10 or []\T1/pc r/m/n/10 type="iterms" []\T1/ptm/m/n/10 then terms (smooth or para- [3019] [3020] [3021] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10130--10130 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [3022] [3023] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10291--10291 []\T1/pcr/m/n/9 x1 <- seq(.2,.8,length=m1);x2 <- seq(.2,.8,length=m2) ## margi nal grid points[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10292--10292 []\T1/pcr/m/n/9 df <- data.frame(x0=rep(.5,n),x1=rep(x1,m2),x2=rep(x2,each=m1) ,x3=rep(0,n))[] [3024] Underfull \vbox (badness 10000) has occurred while \output is active [3025] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10411--10411 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [3026] Underfull \hbox (badness 1205) in paragraph at lines 10449--10451 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10449--10451 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10455--10460 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3027] Underfull \hbox (badness 1205) in paragraph at lines 10539--10541 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10539--10541 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3028] Underfull \hbox (badness 10000) in paragraph at lines 10608--10611 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 10608--10611 [][][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][][]\T1/ptm/m/n/10 , al -though el-e-ments []\T1/pcr/m/n/10 X []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 S [ ]\T1/ptm/m/n/10 are not needed, [3029] [3030] [3031] Underfull \hbox (badness 1253) in paragraph at lines 10738--10740 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 1946) in paragraph at lines 10991--10998 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10991--10998 \T1/ptm/m/n/10 can be used with [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 by mak-ing use of []\T1/pcr/m/n/10 s(...,bs="re") []\T1/ptm/m/n/10 terms in a model: see Underfull \hbox (badness 2846) in paragraph at lines 10999--11002 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/pcr/m/n /10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/pcr/m/n/10 gam[][][] []\T1 /ptm/m/n/10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10999--11002 \T1/ptm/m/n/10 see [][][]\T1/pcr/m/n/10 gam.models[][][][]\T1/ptm/m/n/10 . If s mooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3037] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11065--11065 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11075--11075 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [3038] Underfull \hbox (badness 10000) in paragraph at lines 11106--11109 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/pcr/m/n/ 10 "deviance"[]\T1/ptm/m/n/10 , [3039] [3040] [3041] [3042] [3043] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11408--11408 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [3044] [3045] [3046] [3047] [3048] [3049] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11782--11782 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11796--11796 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] Underfull \vbox (badness 10000) has occurred while \output is active [3050] [3051] Underfull \hbox (badness 3861) in paragraph at lines 11898--11901 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 11907--11907 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [3052] Underfull \hbox (badness 10000) in paragraph at lines 11924--11928 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- Underfull \hbox (badness 10000) in paragraph at lines 11964--11968 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 inverse==TRUE []\T1/ptm/m/n/10 and []\T1/p cr/m/n/10 both.sides==FALSE []\T1/ptm/m/n/10 then the re- [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 12108--12108 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 12119--12124 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3056] Underfull \hbox (badness 1803) in paragraph at lines 12196--12200 \T1/ptm/m/n/10 The last en-try will be the []\T1/pcr/m/n/10 by []\T1/ptm/m/n/10 vari-able, if []\T1/pcr/m/n/10 object$by []\T1/ptm/m/n/10 is not []\T1/pcr/m/n /10 "NA"[]\T1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 12208--12220 []\T1/pcr/m/n/10 cs.smooth.spec []\T1/ptm/m/n/10 (cu-bic re-gres-sion splines w ith shrinkage-to-zero); []\T1/pcr/m/n/10 cc.smooth.spec [3057] Underfull \hbox (badness 2401) in paragraph at lines 12225--12229 []\T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able . Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 12225--12229 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for []\T1/pc r/m/n/10 mgcv:::plot.sos.smooth[]\T1/ptm/m/n/10 , [3058] [3059] [3060] Underfull \hbox (badness 6876) in paragraph at lines 12420--12426 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of on e or two vari-ables, spec-i-fied via terms like [3061] Underfull \hbox (badness 10000) in paragraph at lines 12461--12462 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 12579--12580 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3064] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12633--12633 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12645--12645 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3065] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12657--12657 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12662--12662 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12668--12668 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (3.70428pt too wide) in paragraph at lines 12669--12669 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/cmtt/m/n/9 `\T1 /pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3066] Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 12738--12740 \T1/ptm/m/n/10 term []\T1/pcr/m/n/10 s(...,bs="cr",...)[]\T1/ptm/m/n/10 , []\T1 /pcr/m/n/10 s(...,bs="cs",...) []\T1/ptm/m/n/10 or [3067] [3068] Underfull \hbox (badness 10000) in paragraph at lines 12868--12869 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3069] [3070] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12949--12949 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12950--12950 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [3071] [3072] Underfull \hbox (badness 10000) in paragraph at lines 13103--13104 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3073] [3074] [3075] [3076] [3077] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13353--13353 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3078] Underfull \hbox (badness 10000) in paragraph at lines 13414--13416 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3079] [3080] Underfull \hbox (badness 10000) in paragraph at lines 13573--13576 []\T1/ptm/m/n/10 For the []\T1/pcr/m/n/10 smooth.construct []\T1/ptm/m/n/10 met hod a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13573--13576 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term []\T1/pcr/m/n/10 s(x,...,bs ="re",)[]\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 13573--13576 []\T1/pcr/m/n/10 predict.Matrix []\T1/ptm/m/n/10 method an ob-ject of class []\ T1/pcr/m/n/10 "random.effect" [3081] [3082] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13659--13659 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3083] Underfull \hbox (badness 10000) in paragraph at lines 13704--13710 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 13704--13710 []\T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/pcr/m/n/10 gam []\T1/ptm/m/n/10 for- [3084] [3085] [3086] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13918--13918 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [3087] Underfull \vbox (badness 10000) has occurred while \output is active [3088] Underfull \hbox (badness 10000) in paragraph at lines 14021--14029 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths on th e sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 14047--14048 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3089] [3090] [3091] Underfull \hbox (badness 7613) in paragraph at lines 14192--14195 []\T1/ptm/m/n/10 method an ob-ject of class []\T1/pcr/m/n/10 "sz.interaction" [ ]\T1/ptm/m/n/10 pro-duced by the [3092] Underfull \hbox (badness 1546) in paragraph at lines 14213--14214 []\T1/ptm/m/n/10 The terms can have a smooth-ing pa-ram-e-ter per smooth, or a sin-gle smooth-ing pa-ram-e- Overfull \hbox (128.58029pt too wide) in paragraph at lines 14259--14259 []\T1/pcr/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3093] [3094] [3095] Underfull \hbox (badness 3396) in paragraph at lines 14405--14408 [][][]\T1/pcr/m/n/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of an y num-ber of vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 14450--14452 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3096] [3097] [3098] [3099] [3100] [3101] Underfull \hbox (badness 10000) in paragraph at lines 14741--14743 []\T1/pcr/m/n/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 te[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][][]\T1/ptm/m/n/10 ,[ ][][]\T1/pcr/m/n/10 Duchon.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cubic.regression.spline[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 p.spline[][ ][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 soap[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Spherical.Spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14771--14775 [][][]\T1/pcr/m/n/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/ m/n/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [3102] [3103] [3104] [3105] [3106] Underfull \hbox (badness 2158) in paragraph at lines 15061--15061 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3107] [3108] Overfull \hbox (48.78088pt too wide) in paragraph at lines 15140--15140 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3109] [3110] Overfull \hbox (12.78088pt too wide) in paragraph at lines 15274--15274 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3111] [3112] Underfull \hbox (badness 4846) in paragraph at lines 15405--15408 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3113] [3114] [3115] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] Overfull \hbox (120.78088pt too wide) in paragraph at lines 16623--16623 []\T1/pcr/m/n/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL, unconditional=FALSE, ...)[] [3133] Underfull \hbox (badness 1715) in paragraph at lines 16645--16646 []\T1/ptm/m/n/10 Basically, just ex-tracts []\T1/pcr/m/n/10 object$Ve[]\T1/ptm/ m/n/10 , []\T1/pcr/m/n/10 object$Vp []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 object $Vc []\T1/ptm/m/n/10 (if avail-able) from a [3134] [3135] [3136] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16835--16835 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16837--16837 []\T1/pcr/m/n/10 XWyd(X,w,y,k,ks,ts,dt,v,qc,drop=NULL,ar.stop=-1,ar.row=-1,ar. w=-1,lt=NULL)[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16839--16839 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3137] Underfull \hbox (badness 10000) in paragraph at lines 16859--16860 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16859--16860 []\T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] []\T1/ptm/m/n/10 of the rows se-le cted by []\T1/pcr/m/n/10 ar.row [3138] Underfull \vbox (badness 10000) has occurred while \output is active [3139] [3140] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17047--17047 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17048--17048 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] [3141] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17060--17060 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3142] [3143] [3144]) (./nlme-pkg.tex Chapter 25. [3145] Underfull \hbox (badness 1009) in paragraph at lines 84--93 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3146] Underfull \hbox (badness 1009) in paragraph at lines 174--183 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3147] [3148] [3149] [3150] [3151] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3152] [3153] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3162] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `[]\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel .htm[]\T1/ptm/m/n/10 ', the first edi-tion of [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 fixed. effects.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 ranef.lmList[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.ranef.lmList[][][][]\T1/ptm/m/n/10 , [3170] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3171] [3172] [3173] [3174] [3175] Underfull \hbox (badness 2042) in paragraph at lines 1996--2002 \T1/ptm/m/n/10 is in-ner to the []\T1/pcr/m/n/10 displayLevel []\T1/ptm/m/n/10 group-ing fac-tor. If equal to []\T1/pcr/m/n/10 TRUE[]\T1/ptm/m/n/10 , [3176] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2058--2058 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3177] Underfull \hbox (badness 1132) in paragraph at lines 2147--2149 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3178] [3179] Underfull \hbox (badness 4168) in paragraph at lines 2258--2264 [][][]\T1/pcr/m/n/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corAR MA[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2283--2283 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 2849--2853 [][][]\T1/pcr/m/n/10 corFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cor Matrix.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 recalc.corStruct[ ][][][]\T1/ptm/m/n/10 , [3189] [3190] [3191] [3192] [3193] [3194 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix .corCompSymm}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3195] [3196] [3197] [3198] [3199] [3200] Underfull \hbox (badness 6493) in paragraph at lines 3585--3593 [][][]\T1/pcr/m/n/10 corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corGau s[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corLin[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 corSp her[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T 1/ptm/m/n/10 , [3201] [3202] [3203] [3204] [3205] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/p cr/m/n/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [3225] [3226] [3227] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 5597--5600 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 getGroups .gls[][][][]\T1/ptm/m/n/10 , [3232] [3233] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 2799) in paragraph at lines 6103--6109 \T1/ptm/m/n/10 covariance ma-trix, ei-ther []\T1/pcr/m/n/10 "random.effects" [] \T1/ptm/m/n/10 for the random-effects [3241] Underfull \hbox (badness 7133) in paragraph at lines 6164--6168 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3242] Underfull \hbox (badness 2057) in paragraph at lines 6253--6264 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gl sControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 glsObject[][][][]\T1/ptm/ m/n/10 , [][][]\T1/pcr/m/n/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.gls[][][][] \T1/ptm/m/n/10 , [3243] Underfull \hbox (badness 10000) in paragraph at lines 6317--6319 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3244] [3245] [3246] [3247] Underfull \hbox (badness 7133) in paragraph at lines 6566--6570 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in [ ]\T1/pcr/m/n/10 model[]\T1/ptm/m/n/10 , [3248] Underfull \hbox (badness 10000) in paragraph at lines 6665--6671 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gn lsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsObject[][][][]\T1/pt m/m/n/10 , [][][]\T1/pcr/m/n/10 gnlsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pc r/m/n/10 predict.gnls[][][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3249] Underfull \hbox (badness 10000) in paragraph at lines 6730--6732 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3250] [3251] [3252] [3253] Underfull \hbox (badness 10000) in paragraph at lines 7002--7009 [][][]\T1/pcr/m/n/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gappl y[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 gsummary[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nff GroupedData[][][][]\T1/ptm/m/n/10 , [3254] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7020--7020 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7025--7025 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7047--7049 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a []\T1/pcr/m/n/10 gr oupedData []\T1/ptm/m/n/10 ob-ject or a [3255] [3256] [3257] Underfull \hbox (badness 10000) in paragraph at lines 7262--7267 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr /m/n/10 Initialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initi alize.glsStruct[][][][]\T1/ptm/m/n/10 , [3258] [3259] [3260] Underfull \hbox (badness 1997) in paragraph at lines 7414--7422 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza-tion and op-ti- Underfull \hbox (badness 2205) in paragraph at lines 7414--7422 \T1/ptm/m/n/10 miza-tion al-go-rithms used in []\T1/pcr/m/n/10 lme[]\T1/ptm/m/n /10 . De-faults to []\T1/pcr/m/n/10 list(niterEM=20, Underfull \hbox (badness 3118) in paragraph at lines 7437--7440 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initializ e.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.corStruct[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Initialize.varFunc[][][][]\T1/ptm/m/ n/10 , [3261] [3262] [3263] Underfull \hbox (badness 3354) in paragraph at lines 7653--7655 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when []\T1/pcr/m/n/ 10 which []\T1/ptm/m/n/10 is not equal to [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lm e.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lme.groupedData[][][][]\T 1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T 1/pcr/m/n/10 lmeObject[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8170--8187 [][][]\T1/pcr/m/n/10 lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 lmL ist[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/pcr/m/n/10 plot.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 predict.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 qqnorm.lme[][][][]\T1/ ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8213--8213 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] [3272] Underfull \hbox (badness 1642) in paragraph at lines 8222--8244 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3273] [3274] [3275] [3276] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8487--8487 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8535--8537 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3277] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8579--8579 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] [3289] Underfull \hbox (badness 10000) in paragraph at lines 9336--9343 [][][]\T1/pcr/m/n/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/pcr/m/n/10 gls[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9347--9347 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3290] [3291] [3292] [3293] [3294] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9698 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3295] Underfull \hbox (badness 10000) in paragraph at lines 9718--9721 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9762--9765 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9762--9765 \T1/ptm/m/n/10 ma-trix rep-re-sented by []\T1/pcr/m/n/10 object[]\T1/ptm/m/n/10 . Must have the same di-men-sions as [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] [3304] [3305] [3306] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10442--10442 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3307] Underfull \hbox (badness 1596) in paragraph at lines 10471--10497 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3308] [3309] [3310] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10647--10647 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3311] [3312] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10798--10798 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10809--10814 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][][]\T1/pcr/m/n/10 nlmi nb[][][] []\T1/ptm/m/n/10 ([]\T1/pcr/m/n/10 iter.max[]\T1/ptm/m/n/10 ) or the [ ][][]\T1/pcr/m/n/10 nlm[][][] [3313] Underfull \hbox (badness 6961) in paragraph at lines 10831--10835 []\T1/ptm/m/n/10 a log-i-cal value passed as the []\T1/pcr/m/n/10 trace []\T1/p tm/m/n/10 to [][][]\T1/pcr/m/n/10 nlminb[][][](.., control= Underfull \hbox (badness 10000) in paragraph at lines 10850--10852 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3314] [3315] [3316] [3317] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11141--11141 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 11142--11142 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3318] [3319] [3320] [3321] [3322] [3323] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11532--11532 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3324] [3325] [3326] [3327] [3328] [3329] Underfull \hbox (badness 6268) in paragraph at lines 11919--11929 [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdMatrix[][][][]\T1/ptm/m/n/10 , [3330] [3331] [3332] [3333] Underfull \hbox (badness 10000) in paragraph at lines 12180--12186 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 coef.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdBlocked[][][][]\T1 /ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/ pcr/m/n/10 pdConstruct[][][][]\T1/ptm/m/n/10 , [3334] [3335] [3336] [3337] [3338] Underfull \hbox (badness 6876) in paragraph at lines 12502--12504 []\T1/ptm/m/n/10 If []\T1/pcr/m/n/10 value []\T1/ptm/m/n/10 is an \T1/ptm/m/it/ 10 ini-tial-ized []\T1/pcr/m/n/10 pdMat []\T1/ptm/m/n/10 ob-ject, []\T1/pcr/m/n /10 object []\T1/ptm/m/n/10 will be con-structed from [3339] [3340] Underfull \hbox (badness 2452) in paragraph at lines 12658--12665 [][][]\T1/pcr/m/n/10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdC ompSymm[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdDiag[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/pcr/m/n/10 pdIdent[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdNatural[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdSymm[][][][]\T1/ptm/m/ n/10 , [][][]\T1/pcr/m/n/10 reStruct[][][][]\T1/ptm/m/n/10 , [3341] Underfull \hbox (badness 10000) in paragraph at lines 12723--12729 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 pdClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdFactor[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 pdMatrix.reStruct[][][][]\T1/ptm/m/n/10 , [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13312--13312 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3351] [3352] [3353] [3354] [3355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13677--13677 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13704--13707 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nffGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3357] Underfull \hbox (badness 1838) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/pcr/m/ n/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13747--13754 []\T1/ptm/m/n/10 or []\T1/pcr/m/n/10 innerGroups []\T1/ptm/m/n/10 are non-[]\T1 /pcr/m/n/10 NULL[]\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent []\T1/pcr/m/n/ 10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13804--13804 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3358] Underfull \hbox (badness 10000) in paragraph at lines 13811--13814 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nfnGroupe dData[]\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13811--13814 []\T1/pcr/m/n/10 groupedData []\T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-vari-ate and a sin-gle [3359] Underfull \hbox (badness 10000) in paragraph at lines 13919--13922 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 nmGrouped Data[]\T1/ptm/m/n/10 , rep-re-sent-ing a [3360] [3361] Underfull \hbox (badness 10000) in paragraph at lines 14013--14015 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 c ollapse.groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 plot.nfnGroupe dData[][][][]\T1/ptm/m/n/10 , [3362] [3363] [3364] [3365] [3366] [3367] [3368] [3369] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14537--14537 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3370] [3371] [3372] [3373] [3374] [3375] [3376] [3377] [3378] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15190 ...Extract Random Effects}{random.effects} [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] Underfull \hbox (badness 2126) in paragraph at lines 15830--15834 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3389] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15838--15838 []\T1/pcr/m/n/9 plot(Remifentanil, type = "l", lwd = 2) # shows the 65 patient s\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 remi profiles Overfull \hbox (31.3804pt too wide) in paragraph at lines 15857--15857 [] \T1/pcr/m/n/9 stopifnot(all.equal(BSA, Wt^{0.425} * Ht^{0.725} * 0.00718 4, tol = 1.5e-5),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15858--15858 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3390] Underfull \hbox (badness 1009) in paragraph at lines 15888--15897 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3391] [3392] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16035--16035 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3393] [3394] [3395] [3396] [3397] Underfull \hbox (badness 10000) in paragraph at lines 16370--16376 [][][]\T1/pcr/m/n/10 groupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 l me[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 pdMat[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/pcr/m/n/10 solve.reStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 summary.reStruct[][][][]\T1/ptm/m/n/10 , [3398] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16401--16401 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3399] [3400] [3401] [3402] [3403] [3404] [3405] Underfull \hbox (badness 1728) in paragraph at lines 16889--16892 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3406] [3407] [3408] [3409] [3410] Underfull \hbox (badness 1803) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 of an Identity" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdIdent[]\ T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Positive-Definite, Underfull \hbox (badness 10000) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Natural Parametrization" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 p dNatural[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "General Underfull \hbox (badness 7888) in paragraph at lines 17223--17232 \T1/pcr/m/n/10 Positive-Definite" []\T1/ptm/m/n/10 for []\T1/pcr/m/n/10 pdSymm[ ]\T1/ptm/m/n/10 , and []\T1/pcr/m/n/10 data.class(object) [3411] Underfull \hbox (badness 10000) in paragraph at lines 17294--17295 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17295--17296 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3412] [3413] [3414] [3415] Underfull \hbox (badness 10000) in paragraph at lines 17545--17553 [][][]\T1/pcr/m/n/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varCo nstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varConstProp[][][][]\T1/p tm/m/n/10 , [][][]\T1/pcr/m/n/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 varIdent[][][][]\T1 /ptm/m/n/10 , [3416] [3417] [3418] [3419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17817--17817 []\T1/pcr/m/n/9 # Generate some synthetic data using the two-component error m odel and use Overfull \hbox (25.98041pt too wide) in paragraph at lines 17819--17819 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3420] [3421] [3422] [3423] [3424] [3425] Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n /10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rLin[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18255--18265 [][][]\T1/pcr/m/n/10 Variogram.corRatio[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m /n/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogr am.corSpher[][][][]\T1/ptm/m/n/10 , [3426] Underfull \hbox (badness 3579) in paragraph at lines 18293--18298 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3427] Underfull \hbox (badness 3579) in paragraph at lines 18357--18362 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3428] Underfull \hbox (badness 3579) in paragraph at lines 18420--18425 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3429] Underfull \hbox (badness 1577) in paragraph at lines 18481--18483 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class []\T1/pcr/m/n/10 "[][]corR atio[][][]"[]\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18483--18488 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3430] Underfull \hbox (badness 3579) in paragraph at lines 18546--18551 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Va riogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.default[][][][]\ T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18579--18588 [][][]\T1/pcr/m/n/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/ n/10 Variogram.corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Variogram.co rRatio[][][][]\T1/ptm/m/n/10 , [3431] Underfull \hbox (badness 3579) in paragraph at lines 18618--18623 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to []\T1/pcr/m/n/10 NULL[]\T1/p tm/m/n/10 , in which case a se-quence [3432] [3433] Underfull \hbox (badness 1009) in paragraph at lines 18764--18773 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3434] [3435] Underfull \hbox (badness 1009) in paragraph at lines 18896--18905 []\T1/pcr/m/n/10 "response"[]\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fit-ted) are used; else, if [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3445] Overfull \hbox (12.78088pt too wide) in paragraph at lines 71--71 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3446] [3447] [3448] Overfull \hbox (15.18042pt too wide) in paragraph at lines 371--371 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 428--428 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 431--431 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3450] [3451] Overfull \hbox (15.18042pt too wide) in paragraph at lines 511--511 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3452]) (./rpart-pkg.tex Chapter 27. [3453] [3454] [3455] [3456] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3457] [3458] [3459] [3460] Underfull \hbox (badness 1442) in paragraph at lines 592--598 []\T1/ptm/m/n/10 if []\T1/pcr/m/n/10 FALSE[]\T1/ptm/m/n/10 , the leaf nodes wil l be at the hor-i-zon-tal plot co-or-di-nates of [3461] [3462] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 (de-fault), adds to the la-bel Underfull \hbox (badness 1142) in paragraph at lines 771--775 \T1/pcr/m/n/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method [ ]\T1/pcr/m/n/10 class[]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 n [3463] [3464] [3465] Overfull \hbox (25.98041pt too wide) in paragraph at lines 915--915 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 934--934 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3466] [3467] [3468] [3469] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1180--1180 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1181--1181 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1243--1245 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the []\T1/pcr/m/n /10 rpart []\T1/ptm/m/n/10 al-go-rithm. See [3470] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1287--1287 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1303--1303 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1304--1304 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3471] [3472] [3473] [3474] [3475] [3476] [3477] Underfull \hbox (badness 1565) in paragraph at lines 1760--1763 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `[]\T1/pcr/m/n/10 diploid[]\T1/ptm/m/n/10 ', [3478] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1854--1854 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3479] [3480] [3481]) (./spatial-pkg.tex [3482] Chapter 28. [3483] [3484] [3485] [3486] [3487] [3488] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501]) (./survival-pkg.tex [3502] Chapter 29. [3503] [3504] Overfull \hbox (31.3804pt too wide) in paragraph at lines 173--173 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 192--192 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 195--195 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3505] [3506] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3507] [3508] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3509] Overfull \hbox (9.78043pt too wide) in paragraph at lines 485--485 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 487--487 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3510] Overfull \hbox (6.78088pt too wide) in paragraph at lines 524--524 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3511] [3512] [3513] Overfull \hbox (20.58041pt too wide) in paragraph at lines 769--769 []\T1/pcr/m/n/9 py <- pseudo(survfit(Surv(time, status) ~1, lung), time=730) # 2 year survival [3514] Overfull \hbox (48.78088pt too wide) in paragraph at lines 792--792 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3515] [3516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 935--935 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3517] [3518] [3519] Underfull \hbox (badness 1097) in paragraph at lines 1106--1108 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 1126--1126 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3520] [3521] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1241--1241 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3522] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1302--1302 []\T1/pcr/m/n/9 marginal.model <- coxph(Surv(time, status) ~ rx, data= rats, c luster=litter, pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1308 ...erapy for Stage B/C colon cancer}{colon} [3523] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1407--1407 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1408--1408 [] \T1/pcr/m/n/10 influence=0, ranks = FALSE, reverse=FALSE, timefix=TRUE, ke epstrata=10, ...)[] [3524] [3525] [3526] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1598--1598 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1647--1647 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3527] [3528] [3529] [3530] [3531] Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 []\T1/ptm/m/n/10 One user mis-take that has re-cently arisen is to slav-ishly f ol-low the ad-vice of Underfull \hbox (badness 7486) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 some cod-ing guides and prepend []\T1/pcr/m/n/10 survival:: []\T 1/ptm/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1964--1979 \T1/ptm/m/n/10 cial terms, e.g., []\T1/pcr/m/n/10 survival::coxph(survival:Surv (time, status) ~ age + [3532] Underfull \hbox (badness 3861) in paragraph at lines 2048--2052 [][][]\T1/pcr/m/n/10 coxph.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxphms.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 coxph.control[][][] []\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 cluster[][][][]\T1/ptm/m/n/10 , [][][]\ T1/pcr/m/n/10 strata[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 Surv[][][][]\ T1/ptm/m/n/10 , [3533] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2103--2103 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3534] [3535] [3536] [3537] [3538] [3539] [3540] [3541] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2717--2717 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3542] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2744--2744 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3543] [3544] [3545] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2976--2976 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3546] [3547] [3548] [3549] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3317--3317 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3551] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3352--3352 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 3366--3368 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with Overfull \hbox (12.78088pt too wide) in paragraph at lines 3377--3377 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3552] [3553] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3554] [3555] Overfull \hbox (467.89665pt too wide) in alignment at lines 3652--3652 [] [] [3556] [3557] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3774--3774 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3558] [3559] [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4210--4210 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3565] [3566] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4360--4360 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4365--4365 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4369--4369 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3568] [3569] [3570] [3571] [3572] [3573] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4786--4786 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3574] [3575] [3576] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5016--5016 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3577] [3578] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5142--5142 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5150--5150 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3579] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5236--5236 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3580] [3581] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5314--5314 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3582] Underfull \hbox (badness 1852) in paragraph at lines 5386--5388 []\T1/ptm/m/n/10 an ob-ject of class []\T1/pcr/m/n/10 "summary.survfit"[]\T1/pt m/m/n/10 , which is the re-sult of the [3583] [3584] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5512--5512 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3585] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5615--5615 []\T1/pcr/m/n/9 rhat <- predict(rfit, newdata=expand.grid(ph.ecog=0:3, sex=1:2 ), se.fit=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5627--5627 []\T1/pcr/m/n/9 # the estimate for ph.ecog=3 is very unstable (n=1), pseudoval ues smooth it.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5629--5629 []\T1/pcr/m/n/9 # In all the above we should be using the robust variance, e.g ., svyglm, but[] [3586] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5653--5653 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5654--5654 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3587] [3588] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3589] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5920--5920 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5941--5941 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5943--5943 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3590] [3591] [3592] [3593] [3594] [3595] [3596] [3597] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6462--6462 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3598] [3599] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6642--6642 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] [3600] Underfull \hbox (badness 1043) in paragraph at lines 6654--6657 []\T1/pcr/m/n/10 "dfbetas"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "working"[]\T1/pt m/m/n/10 , []\T1/pcr/m/n/10 "ldcase"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "lsresp "[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "ldshape"[]\T1/ptm/m/n/10 , and [3601] [3602] [3603] [3604] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6962--6962 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), lung)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6963--6963 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3605] [3606] [3607] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7135--7135 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3608] Overfull \hbox (42.18039pt too wide) in paragraph at lines 7216--7216 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicate times[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7220--7220 []\T1/pcr/m/n/9 wt2 <- rttright(Surv(dtime, death) ~ hormon, rotterdam, times= 365*c(3, 5))[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7224 ...ata from a soldering experiment}{solder} [3609] [3610] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7330--7330 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3611] [3612] [3613] [3614] [3615] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7694--7694 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7695--7695 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3616] [3617] [3618] [3619] Overfull \hbox (54.78088pt too wide) in paragraph at lines 8013--8013 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3620] [3621] [3622] [3623] Underfull \hbox (badness 1253) in paragraph at lines 8302--8305 []\T1/ptm/m/n/10 The []\T1/pcr/m/n/10 median[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 quantile []\T1/ptm/m/n/10 and []\T1/pcr/m/n/10 plot []\T1/ptm/m/n/10 meth-ods first con-struct a sur-vival curve us-ing [3624] [3625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8432--8432 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3626] [3627] [3628] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8662--8662 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8680--8680 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] [3629] Underfull \hbox (badness 1038) in paragraph at lines 8722--8728 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8774--8774 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8860--8860 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3632] [3633] [3634] Underfull \hbox (badness 10000) in paragraph at lines 9080--9085 [][][]\T1/pcr/m/n/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/ 10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 survfit.object[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/pcr/m/n/10 print.survfit[][][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 9100--9100 [] \T1/pcr/m/n/10 se.fit=TRUE, conf.int=.95, individual=FALSE, stype=2, ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 se.fit=FALSE, conf.int=.95, individual=FALSE, stype=2 , ctype,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9107--9107 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3635] [3636] [3637] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9321--9321 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3638] Underfull \hbox (badness 2653) in paragraph at lines 9454--9459 \T1/pcr/m/n/10 ctype=1[]\T1/ptm/m/n/10 , "fleming-harrington" which is equiv-a- lent to []\T1/pcr/m/n/10 stype=2, [3639] [3640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9594--9594 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3641] [3642] [3643] [3644] [3645] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9979--9979 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3646] Underfull \hbox (badness 1354) in paragraph at lines 10020--10024 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3647] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10066--10066 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3648] [3649] Underfull \hbox (badness 2035) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][][]\T1/pcr/m/n/10 su rvreg.distributions[][][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10230--10237 \T1/ptm/m/n/10 These in-clude []\T1/pcr/m/n/10 "weibull"[]\T1/ptm/m/n/10 , []\T 1/pcr/m/n/10 "exponential"[]\T1/ptm/m/n/10 , []\T1/pcr/m/n/10 "gaussian"[]\T1/p tm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10230--10237 []\T1/pcr/m/n/10 "logistic"[]\T1/ptm/m/n/10 ,[]\T1/pcr/m/n/10 "lognormal" []\T1 /ptm/m/n/10 and []\T1/pcr/m/n/10 "loglogistic"[]\T1/ptm/m/n/10 . Oth-er-wise, i t is [3650] [3651] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10320--10320 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3652] [3653] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10477--10477 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3654] [3655] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10609--10609 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10612--10612 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3656] [3657] [3658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10772--10772 []\T1/pcr/m/n/9 pfit2 <- pyears(Surv(years, death) ~ fgrp + agegrp, scale =100 0, data=test)[] [3659] [3660] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10930--10930 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10931--10931 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10937--10937 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10939--10939 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3661] [3662] [3663] [3664] [3665] [3666] [3667] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11380--11380 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3668] [3669] [3670]) (./fullrefman.ind [3671] [3672] [3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683] [3684] [3685] [3686] [3687] [3688] [3689] [3690] [3691] [3692] [3693] [3694] [3695] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2605--2607 []| \T1/pcr/m/n/10 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%*%,ndenseMatrix,ndenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 5113--5115 []\T1/pcr/m/n/10 %*%,ndenseMatrix,nsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 5115--5117 []\T1/pcr/m/n/10 %*%,nsparseMatrix,ndenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5117--5119 []\T1/pcr/m/n/10 %*%,nsparseMatrix,nsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5119--5121 []\T1/pcr/m/n/10 %*%,numLike,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5127--5129 []\T1/pcr/m/n/10 %*%,sparseMatrix,diagonalMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 5135--5137 []\T1/pcr/m/n/10 %*%,sparseVector,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5145--5147 []\T1/pcr/m/n/10 %/%,ddiMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5147--5149 []\T1/pcr/m/n/10 %/%,ddiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5149--5151 []\T1/pcr/m/n/10 %/%,ddiMatrix,ndenseMatrix-method [3717] Overfull \hbox (8.8567pt too wide) in paragraph at lines 5153--5155 []\T1/pcr/m/n/10 %/%,ldiMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5155--5157 []\T1/pcr/m/n/10 %/%,ldiMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 5157--5159 []\T1/pcr/m/n/10 %/%,ldiMatrix,ndenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5163--5165 []\T1/pcr/m/n/10 %%,ddiMatrix,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5165--5167 []\T1/pcr/m/n/10 %%,ddiMatrix,ldenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5167--5169 []\T1/pcr/m/n/10 %%,ddiMatrix,ndenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 5171--5173 []\T1/pcr/m/n/10 %%,ldiMatrix,ddenseMatrix-method Overfull 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Arith,numeric,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 5980--5982 []\T1/pcr/m/n/10 Arith,numeric,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5990--5992 []\T1/pcr/m/n/10 Arith,sparseVector,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 5992--5994 []\T1/pcr/m/n/10 Arith,sparseVector,dgeMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 5994--5996 []\T1/pcr/m/n/10 Arith,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 5996--5998 []\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method [3723] Overfull \hbox (2.8567pt too wide) in paragraph at lines 6278--6280 []\T1/pcr/m/n/10 as.logical,diagonalMatrix-method [3724] Overfull \hbox (2.8567pt too wide) in paragraph at lines 6360--6362 []\T1/pcr/m/n/10 as.numeric,diagonalMatrix-method [3725] Overfull \hbox (32.8567pt too wide) in paragraph at lines 6526--6528 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file [3726] Overfull \hbox (46.01662pt too wide) in paragraph at lines 6696--6698 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3727] [3728] [3729] Overfull \hbox (26.8567pt too wide) in paragraph at lines 7352--7354 []\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7354--7356 []\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7356--7358 []\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7358--7360 []\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 7362--7364 []\T1/pcr/m/n/10 cbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7364--7366 []\T1/pcr/m/n/10 cbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7366--7368 []\T1/pcr/m/n/10 cbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7368--7370 []\T1/pcr/m/n/10 cbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7370--7372 []\T1/pcr/m/n/10 cbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7372--7374 []\T1/pcr/m/n/10 cbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7378--7380 []\T1/pcr/m/n/10 cbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 7382--7384 []\T1/pcr/m/n/10 cbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7392--7394 []\T1/pcr/m/n/10 cbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7396--7398 []\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7398--7400 []\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7400--7402 []\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7402--7404 []\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7404--7406 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3730] [3731] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7660--7662 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3732] [3733] [3734] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8168--8170 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8170--8172 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8172--8174 []\T1/pcr/m/n/10 coerce,CHMfactor,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8176--8178 []\T1/pcr/m/n/10 coerce,CHMfactor,dsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8182--8184 []\T1/pcr/m/n/10 coerce,CHMfactor,RsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8184--8186 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8186--8188 []\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 8188--8190 []\T1/pcr/m/n/10 coerce,CHMfactor,TsparseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8190--8192 []\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8192--8194 []\T1/pcr/m/n/10 coerce,CsparseMatrix,generalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8194--8196 []\T1/pcr/m/n/10 coerce,CsparseMatrix,matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8196--8198 []\T1/pcr/m/n/10 coerce,CsparseMatrix,packedMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8198--8200 []\T1/pcr/m/n/10 coerce,CsparseMatrix,RsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8200--8202 []\T1/pcr/m/n/10 coerce,CsparseMatrix,sparseVector-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 8202--8204 []\T1/pcr/m/n/10 coerce,CsparseMatrix,TsparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 8204--8206 []\T1/pcr/m/n/10 coerce,CsparseMatrix,unpackedMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8206--8208 []\T1/pcr/m/n/10 coerce,CsparseMatrix,vector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8208--8210 []\T1/pcr/m/n/10 coerce,ddenseMatrix,dgeMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8210--8212 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coerce,ddiMatrix,dtCMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8228--8230 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtRMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8230--8232 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtrMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8232--8234 []\T1/pcr/m/n/10 coerce,ddiMatrix,dtTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8234--8236 []\T1/pcr/m/n/10 coerce,ddiMatrix,ldiMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8236--8238 []\T1/pcr/m/n/10 coerce,denseMatrix,CsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 8238--8240 []\T1/pcr/m/n/10 coerce,denseMatrix,ddenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 8240--8242 []\T1/pcr/m/n/10 coerce,denseMatrix,dMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8242--8244 []\T1/pcr/m/n/10 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in paragraph at lines 10447--10449 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,ANY-method [3755] Overfull \hbox (44.8567pt too wide) in paragraph at lines 10449--10451 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,Matrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 10451--10453 []\T1/pcr/m/n/10 crossprod,symmetricMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 10453--10455 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,ANY-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 10455--10457 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,Matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 10457--10459 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,missing-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 10459--10461 []\T1/pcr/m/n/10 crossprod,TsparseMatrix,TsparseMatrix-method Overfull \hbox (46.01662pt too wide) in paragraph at lines 10496--10498 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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wide) in paragraph at lines 10941--10943 []\T1/pcr/m/n/10 determinant,dsRMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10943--10945 []\T1/pcr/m/n/10 determinant,dsTMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 10945--10947 []\T1/pcr/m/n/10 determinant,dsyMatrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10947--10949 []\T1/pcr/m/n/10 determinant,Matrix,logical-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 10949--10951 []\T1/pcr/m/n/10 determinant,Matrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 determinant,MatrixFactorization,missing-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 10951--10953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 10953--10955 []\T1/pcr/m/n/10 determinant,pMatrix,logical-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 10955--10957 []\T1/pcr/m/n/10 determinant,triangularMatrix,logical-method [3758] Overfull \hbox (10.01662pt too wide) in paragraph at lines 11229--11231 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3759] Overfull \hbox (8.8567pt too wide) in paragraph at lines 11297--11299 []\T1/pcr/m/n/10 dimnames<-,compMatrix,list-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 11299--11301 []\T1/pcr/m/n/10 dimnames<-,compMatrix,NULL-method [3760] Overfull \hbox (46.01662pt too wide) in paragraph at lines 11643--11645 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3761] [3762] Overfull \hbox (8.8567pt too wide) in paragraph at lines 11963--11965 []\T1/pcr/m/n/10 expand,MatrixFactorization-method [3763] [3764] Overfull \hbox (80.8567pt too wide) in paragraph at lines 12523--12525 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12525--12527 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 12527--12529 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 12529--12531 []\T1/pcr/m/n/10 forceSymmetric,diagonalMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 12531--12533 []\T1/pcr/m/n/10 forceSymmetric,indMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 12533--12535 []\T1/pcr/m/n/10 forceSymmetric,indMatrix,missing-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 12535--12537 []\T1/pcr/m/n/10 forceSymmetric,matrix,character-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 12537--12539 []\T1/pcr/m/n/10 forceSymmetric,matrix,missing-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 12539--12541 []\T1/pcr/m/n/10 forceSymmetric,packedMatrix,character-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 12541--12543 []\T1/pcr/m/n/10 forceSymmetric,packedMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 12543--12545 []\T1/pcr/m/n/10 forceSymmetric,RsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12545--12547 []\T1/pcr/m/n/10 forceSymmetric,RsparseMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 12547--12549 []\T1/pcr/m/n/10 forceSymmetric,TsparseMatrix,character-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 12549--12551 []\T1/pcr/m/n/10 forceSymmetric,TsparseMatrix,missing-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 12551--12553 []\T1/pcr/m/n/10 forceSymmetric,unpackedMatrix,character-method [3765] Overfull \hbox (74.8567pt too wide) in paragraph at lines 12553--12555 []\T1/pcr/m/n/10 forceSymmetric,unpackedMatrix,missing-method [3766] [3767] [3768] Overfull \hbox (46.01662pt too wide) in paragraph at lines 13498--13500 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3769] [3770] Overfull \hbox (20.8567pt too wide) in paragraph at lines 13866--13868 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [3771] [3772] [3773] [3774] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14669--14671 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14685--14687 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method [3775] [3776] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14873--14875 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14885--14887 []\T1/pcr/m/n/10 isDiagonal,unpackedMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14955--14957 []\T1/pcr/m/n/10 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kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15133--15135 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 15135--15137 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15137--15139 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 15139--15141 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15141--15143 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15143--15145 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15145--15147 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 15149--15151 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15151--15153 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 15153--15155 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 15155--15157 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method [3778] Overfull \hbox (74.8567pt too wide) in paragraph at lines 15157--15159 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3779] [3780] [3781] Overfull \hbox (50.8567pt too wide) in paragraph at lines 15979--15981 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15985--15987 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15987--15989 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15989--15991 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15991--15993 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15993--15995 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15999--16001 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16007--16009 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 16009--16011 []\T1/pcr/m/n/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16011--16013 []\T1/pcr/m/n/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16013--16015 []\T1/pcr/m/n/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16015--16017 []\T1/pcr/m/n/10 Logic,ltCMatrix,ltCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16021--16023 []\T1/pcr/m/n/10 Logic,ngeMatrix,ngeMatrix-method [3782] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16031--16033 []\T1/pcr/m/n/10 Logic,nMatrix,sparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16039--16041 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16041--16043 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16043--16045 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16045--16047 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 16047--16049 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3783] [3784] [3785] [3786] Overfull 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paragraph at lines 18135--18137 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3793] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18344--18346 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 18376--18378 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3794] [3795] [3796] [3797] [3798] [3799] Overfull \hbox (46.01662pt too wide) in paragraph at lines 19692--19694 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19695--19697 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19697--19699 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19699--19701 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19701--19703 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19703--19705 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19705--19707 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19707--19709 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19709--19711 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19711--19713 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 19715--19717 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19717--19719 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 19719--19721 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19721--19723 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19723--19725 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19725--19727 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 19727--19729 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3800] [3801] Overfull \hbox (4.01662pt too wide) in paragraph at lines 20078--20080 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 20154--20156 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3802] [3803] [3804] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20629--20631 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20638--20640 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20640--20642 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20642--20644 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20644--20646 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20656--20658 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20666--20668 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method [3805] Overfull \hbox (32.8567pt too wide) in paragraph at lines 20681--20683 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20687--20689 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20811--20813 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3806] Overfull \hbox (26.8567pt too wide) in paragraph at lines 21032--21034 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21034--21036 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21036--21038 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21038--21040 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21042--21044 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21044--21046 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21046--21048 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 21048--21050 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method [3807] Overfull \hbox (56.8567pt too wide) in paragraph at lines 21050--21052 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21052--21054 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21054--21056 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21060--21062 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21064--21066 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21074--21076 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21078--21080 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 21080--21082 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 21082--21084 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 21084--21086 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 21086--21088 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21116--21118 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21118--21120 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21120--21122 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21122--21124 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21124--21126 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21126--21128 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21128--21130 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 21130--21132 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 21132--21134 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3808] [3809] [3810] [3811] [3812] Overfull \hbox (20.8567pt too wide) in paragraph at lines 22117--22119 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22121--22123 []\T1/pcr/m/n/10 Schur,generalMatrix,logical-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22129--22131 []\T1/pcr/m/n/10 Schur,symmetricMatrix,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 22131--22133 []\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method [3813] [3814] Overfull \hbox (26.8567pt too wide) in paragraph at lines 22515--22517 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 22517--22519 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , Overfull \hbox (32.8567pt too wide) in paragraph at lines 22521--22523 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22525--22527 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22535--22537 []\T1/pcr/m/n/10 show,refClassRepresentation-method [3815] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22784--22786 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3816] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22786--22788 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22789--22791 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22797--22798 []\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22806--22808 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22810--22811 []\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22811--22813 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (23.3567pt too wide) in paragraph at lines 22818--22822 []\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22823--22825 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22874--22876 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (14.8567pt too wide) in paragraph at lines 22911--22913 []\T1/pcr/m/n/10 solve,CHMfactor,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22919--22921 []\T1/pcr/m/n/10 solve,CHMfactor,sparseMatrix-method [3817] Overfull \hbox (14.8567pt too wide) in paragraph at lines 22935--22937 []\T1/pcr/m/n/10 solve,dgCMatrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22943--22945 []\T1/pcr/m/n/10 solve,dgCMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22971--22973 []\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22979--22981 []\T1/pcr/m/n/10 solve,dsCMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22997--22999 []\T1/pcr/m/n/10 solve,dtCMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22999--23001 []\T1/pcr/m/n/10 solve,dtCMatrix,dgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23001--23003 []\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23003--23005 []\T1/pcr/m/n/10 solve,dtCMatrix,dsCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23005--23007 []\T1/pcr/m/n/10 solve,dtCMatrix,dspMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23007--23009 []\T1/pcr/m/n/10 solve,dtCMatrix,dsyMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23009--23011 []\T1/pcr/m/n/10 solve,dtCMatrix,dtCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23011--23013 []\T1/pcr/m/n/10 solve,dtCMatrix,dtpMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23013--23015 []\T1/pcr/m/n/10 solve,dtCMatrix,dtrMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 23021--23023 []\T1/pcr/m/n/10 solve,dtCMatrix,sparseMatrix-method [3818] Overfull \hbox (2.8567pt too wide) in paragraph at lines 23043--23045 []\T1/pcr/m/n/10 solve,Matrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 23045--23047 []\T1/pcr/m/n/10 solve,matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 23047--23049 []\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 23049--23051 []\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 23051--23053 []\T1/pcr/m/n/10 solve,MatrixFactorization,sparseVector-method [3819] Overfull \hbox (52.01662pt too wide) in paragraph at lines 23219--23221 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3820] Overfull \hbox (44.8567pt too wide) in paragraph at lines 23670--23672 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends Overfull \hbox (44.8567pt too wide) in paragraph at lines 23672--23674 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results Overfull \hbox (44.8567pt too wide) in paragraph at lines 23674--23676 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings [3821] [3822] [3823] [3824] [3825] Overfull \hbox (20.8567pt too wide) in paragraph at lines 24509--24511 []\T1/pcr/m/n/10 tcrossprod,ANY,RsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 24511--24513 []\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24513--24515 []\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 24515--24517 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 24517--24519 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 24519--24521 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 24521--24523 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 24523--24525 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 24525--24527 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,numLike-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 24527--24529 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,CsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 24529--24531 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ddenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 24531--24533 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,dsCMatrix-method 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tcrossprod,dgeMatrix,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 24549--24551 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 24551--24553 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24553--24555 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,missing-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 24555--24557 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,numLike-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 24557--24559 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,CsparseMatrix-method Overfull \hbox (92.8567pt too wide) in paragraph at lines 24559--24561 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,diagonalMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 24561--24563 []\T1/pcr/m/n/10 tcrossprod,diagonalMatrix,missing-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 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/usr/src/tmp/R-base-buildroot/usr/lib64/R/library installing packages ... building HTML index ... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src/library' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/src' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' installing R manuals in PDF format ... make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/info /usr/libexec/rpm-build/install -p -m 644 "./dir" "/usr/src/tmp/R-base-buildroot/usr/share/info" installing R info pages ... updating '/usr/share/info/dir' ... you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually you need to adjust /usr/share/info/dir manually make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/doc/manual' make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2' + mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so ++ relative /usr/lib64/libR.so /usr/lib64/R/lib/libR.so + ln -s ../../libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so + ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so ++ relative /usr/share/doc/R-4.2 /usr/lib64/R/doc + ln -s ../../share/doc/R-4.2 /usr/src/tmp/R-base-buildroot/usr/lib64/R/doc ++ relative /usr/include/R /usr/lib64/R/include + ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/include + cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/R ++ relative /usr/lib64/R/bin/R /usr/bin/R + ln -snfv ../lib64/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R '/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib64/R/bin/R' + cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/Rscript ++ relative /usr/lib64/R/bin/Rscript /usr/bin/Rscript + ln -snfv ../lib64/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript '/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib64/R/bin/Rscript' + fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot fgrep: warning: fgrep is obsolescent; using grep -F + mkdir -p /usr/src/tmp/R-base-buildroot/etc/R + mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/ + rmdir /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc ++ relative /etc/R /usr/lib64/R/etc + ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc + mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications + cat + '[' -f /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool ']' ++ relative /usr/bin/libtool /usr/lib64/R/bin/libtool + ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool '/usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool' -> '../../../bin/libtool' + rm -fv /usr/src/tmp/R-base-buildroot/usr/share/info/dir removed '/usr/src/tmp/R-base-buildroot/usr/share/info/dir' + /usr/lib/rpm/brp-alt Cleaning files in /usr/src/tmp/R-base-buildroot (auto) mode of './usr/lib64/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop,gnuconfig) /usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -fopenmp -L${rlibdir} -lR' Checking contents of files in /usr/src/tmp/R-base-buildroot/ (default) Compressing files in /usr/src/tmp/R-base-buildroot (auto) Verifying info files in /usr/src/tmp/R-base-buildroot/usr/share/info (normal) Adjusting library links in /usr/src/tmp/R-base-buildroot ./usr/lib64: (from :0) libR.so -> libR.so ./usr/lib64/R/lib: (from :0) Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal) Splitting links to aliased files under /{,s}bin in /usr/src/tmp/R-base-buildroot Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.36906 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.2.2 + export TZ=UTC + TZ=UTC + make check make: Entering directory '/usr/src/RPM/BUILD/R-4.2.2' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE 7432,7433c7432,7433 < Fisher's Exact Test for Count Data hybrid using asym.chisq. iff < (exp=5, perc=80, Emin=1) --- > Fisher's Exact Test for Count Data hybrid using asym.chisq. iff (exp=5, > perc=80, Emin=1) 14066,14067c14066 < 4-sample test for equality of proportions without continuity < correction --- > 4-sample test for equality of proportions without continuity correction 14096,14097c14095 < 4-sample test for equality of proportions without continuity < correction --- > 4-sample test for equality of proportions without continuity correction Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests/Examples' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running strict specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'structure.R' ... OK comparing 'structure.Rout' to './structure.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running sloppy specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ... OK running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK running code in 'datetime.R' ... OK comparing 'datetime.Rout' to './datetime.Rout.save' ... OK running code in 'iec60559.R' ... OK comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK running code in 'eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' checking Sys.timezone ... make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'timezone.R' ... OK make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running regression tests ... make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in 'd-p-q-r-tst-2.R' ... OK running code in 'r-strict-tst.R' ... OK running code in 'reg-IO.R' ... OK comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK running code in 'reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK running code in 'reg-plot.R' ... OK comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK running code in 'reg-S4-examples.R' ... OK running code in 'reg-BLAS.R' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'reg-tests-3.R' ... OK comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK running code in 'reg-examples3.R' ... OK comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... FAILED running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running tests of Internet functions make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.2.2/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,145 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2/tests' make: Leaving directory '/usr/src/RPM/BUILD/R-4.2.2' + exit 0 Processing files: R-base-4.2.2-alt2 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.4733 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.2.2 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.2.2 + exit 0 warning: File listed twice: /usr/lib64/R/library/KernSmooth/html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/R.css warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde2D.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkfe.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpih.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpik.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpill.html warning: File listed twice: 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File listed twice: /usr/lib64/R/library/utils/html/memory.size.html warning: File listed twice: /usr/lib64/R/library/utils/html/menu.html warning: File listed twice: /usr/lib64/R/library/utils/html/methods.html warning: File listed twice: /usr/lib64/R/library/utils/html/mirrorAdmin.html warning: File listed twice: /usr/lib64/R/library/utils/html/modifyList.html warning: File listed twice: /usr/lib64/R/library/utils/html/news.html warning: File listed twice: /usr/lib64/R/library/utils/html/nsl.html warning: File listed twice: /usr/lib64/R/library/utils/html/object.size.html warning: File listed twice: /usr/lib64/R/library/utils/html/package.skeleton.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageDescription.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageName.html warning: File listed twice: /usr/lib64/R/library/utils/html/packageStatus.html warning: File listed twice: /usr/lib64/R/library/utils/html/page.html warning: File listed twice: /usr/lib64/R/library/utils/html/person.html warning: File listed twice: /usr/lib64/R/library/utils/html/process.events.html warning: File listed twice: /usr/lib64/R/library/utils/html/prompt.html warning: File listed twice: /usr/lib64/R/library/utils/html/promptData.html warning: File listed twice: /usr/lib64/R/library/utils/html/promptPackage.html warning: File listed twice: /usr/lib64/R/library/utils/html/rcompgen.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.DIF.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.fortran.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.fwf.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.socket.html warning: File listed twice: /usr/lib64/R/library/utils/html/read.table.html warning: File listed twice: /usr/lib64/R/library/utils/html/readRegistry.html warning: File listed twice: /usr/lib64/R/library/utils/html/recover.html warning: File listed twice: /usr/lib64/R/library/utils/html/relist.html warning: File listed twice: /usr/lib64/R/library/utils/html/remove.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/removeSource.html warning: File listed twice: /usr/lib64/R/library/utils/html/roman.html warning: File listed twice: /usr/lib64/R/library/utils/html/rtags.html warning: File listed twice: /usr/lib64/R/library/utils/html/savehistory.html warning: File listed twice: /usr/lib64/R/library/utils/html/select.list.html warning: File listed twice: /usr/lib64/R/library/utils/html/sessionInfo.html warning: File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html warning: File listed twice: /usr/lib64/R/library/utils/html/setWindowTitle.html warning: File listed twice: /usr/lib64/R/library/utils/html/shortPathName.html warning: File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html warning: File listed twice: /usr/lib64/R/library/utils/html/stack.html warning: File listed twice: /usr/lib64/R/library/utils/html/str.html warning: File listed twice: /usr/lib64/R/library/utils/html/strcapture.html warning: File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html warning: File listed twice: /usr/lib64/R/library/utils/html/tar.html warning: File listed twice: /usr/lib64/R/library/utils/html/toLatex.html warning: File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html warning: File listed twice: /usr/lib64/R/library/utils/html/type.convert.html warning: File listed twice: /usr/lib64/R/library/utils/html/untar.html warning: File listed twice: /usr/lib64/R/library/utils/html/unzip.html warning: File listed twice: /usr/lib64/R/library/utils/html/update.packages.html warning: File listed twice: /usr/lib64/R/library/utils/html/url.show.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html warning: File listed twice: /usr/lib64/R/library/utils/html/utils-package.html warning: File listed twice: /usr/lib64/R/library/utils/html/vignette.html warning: File listed twice: /usr/lib64/R/library/utils/html/warnErrList.html warning: File listed twice: /usr/lib64/R/library/utils/html/winDialog.html warning: File listed twice: /usr/lib64/R/library/utils/html/winMenus.html warning: File listed twice: /usr/lib64/R/library/utils/html/winProgressBar.html warning: File listed twice: /usr/lib64/R/library/utils/html/winextras.html warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.9zD2Ph find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1310 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2024-05-04 02:36:09.487712744 +0000 +++ filter-provides-deps 2024-05-04 02:36:09.489712748 +0000 @@ -1 +1,2 @@ libR.so()(64bit) = set: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 +libR-2.11.so()(64bit) = set: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 Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ozPebu find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5 shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable find-requires: FINDPACKAGE-COMMANDS: cat grep sh Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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 Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:jimQ7, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426DMNK4LZg18DsceiJLiUfETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQGxRy5H9jhHeHgWMWS5vZ9CCJh0Wm5, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.17)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.27)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.33)(64bit), libc.so.6(GLIBC_2.34)(64bit), libc.so.6(GLIBC_2.38)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mfatAp2k43cHoHyudZ8yZim3OyQ01LIRoFeOerN9z5dbCyoZwgA6F1OPk550Z3ZCDOhgddN5H8RLBZo0M07mx3s6um9PpkKfPP9Nv0kAHUdUab4K3OOhNY9FTE18Xne0zzA8T8iZ4ZnO5SGudBdEgBn7o7QA0ppQr8ZbSfBHsIYjmCwbO0dKIPFkZJzK7PIj, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libcurl.so.4(CURL_GNUTLS_4)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libgomp.so.1()(64bit) >= set:miW8hXcS41e0enAGr8Hj0enR52ADodkQIHD4LVrXNkg0, libgomp.so.1(GOMP_1.0)(64bit), libgomp.so.1(GOMP_4.0)(64bit), libgomp.so.1(GOMP_4.5)(64bit), libgomp.so.1(OMP_1.0)(64bit), libicui18n.so.74()(64bit) >= set:rollO3Z6ICiJ8yrpvqQZ6dzdC0, libicuuc.so.74()(64bit) >= set:pmPnt1j01x7e3KFi2, libjpeg.so.62()(64bit) >= set:kgAooYwOwOzyHw05ow6pbGGIh, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITAzwZi7uccv48L3hfJPwCDlCRTQN0du6Hxf1PiwlB1IsJfGzE7kPRWTAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, liblzma.so.5()(64bit) >= set:kgIy0DJdgZuHF5yXYppdmYIDYAa1, liblzma.so.5(XZ_5.0)(64bit), libm.so.6(GLIBC_2.2.5)(64bit), libm.so.6(GLIBC_2.23)(64bit), libm.so.6(GLIBC_2.29)(64bit), libm.so.6(GLIBC_2.35)(64bit), libm.so.6(GLIBC_2.38)(64bit), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQCfq9fPhNQgw41BExdcI9mdt, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgdZcM1, libpcre2-8.so.0()(64bit) >= set:kfq9tJAJZakapZcr8gHlRiHX2PuBva483hqVseVZw6HMZF1, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libreadline.so.8()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1sJrxkVeobEeqk3ZjtG8A4bFXX0BVWCPf4en3kY78IO0, libtiff.so.5()(64bit) >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1()(64bit) >= set:kgb6dgb5xDnazO8BhqfiJqdZd6eIL9, rtld(GNU_HASH), sh Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.HWD24M Creating R-base-debuginfo package Processing files: R-full-4.2.2-alt2 Requires: R-devel = 4.2.2-alt2, R-tcltk = 4.2.2-alt2, R-doc-html = 4.2.2-alt2, gcc-c++, gcc-fortran, liblapack-devel, make Processing files: R-devel-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.0SPKn8 find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.GSOmJX find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header 43 | # error R_ext/GraphicsEngine.h must be included first, and includes this header | ^~~~~ cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header 43 | # error R_ext/GraphicsEngine.h must be included first, and includes this header | ^~~~~ cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rmdir Provides: pkgconfig(libR) = 4.2.2 Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils Requires(pre): R-base = 4.2.2-alt2 Requires(postun): R-base = 4.2.2-alt2 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.tf2Rzt Processing files: R-tcltk-4.2.2-alt2 warning: File listed twice: /usr/lib64/R/library/tcltk/html warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.aya8Sb find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.phCM48 find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Provides: tcl(::Utility), tcl(::Utility)-1 = 1.0, tcl(::Utility::dump), tcl(::Utility::dump)-1 = 1.0, tcl(::Utility::expand), tcl(::Utility::expand)-1 = 1.0, tcl(::Utility::number), tcl(::Utility::number)-1 = 1.0, tcl(::Utility::string), tcl(::Utility::string)-1 = 1.0, tcl(::Utility::tk), tcl(::Utility::tk)-1 = 1.0, tcl(Hierarchy), tcl(Hierarchy)-2 = 2.0, tcl(PBar), tcl(PBar)-1 = 1.0, tcl(Widget), tcl(Widget)-2 = 2.0 Requires: R-base = 4.2.2-alt2, libR.so()(64bit) >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE1atzKMNmL5wj1XTzOOW0cQ6tLN8BjJrkKZnL1TEzhiItObZCaSl9pqVwPzwTv35ZmWMAXnz5WOfaBOCf02nKkV441OH5pR09Da07HhWgbjgmeagfNIHgS1oluZiX23S3, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.38)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk), tcl(Tk)-8 >= 8 Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.zyzawS Creating R-tcltk-debuginfo package Processing files: R-doc-html-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.XCpzgP find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Xc4v98 find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: R-base = 4.2.2-alt2, xdg-utils Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.kRI8Dg Processing files: R-doc-pdf-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.EbNknZ find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.MCVQwq find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: xdg-utils Conflicts: R-base > 4.2.2, R-base < 4.2.2 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.xoJjS3 Processing files: R-doc-info-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.WIiBWT find-provides: running scripts (alternatives,debuginfo,gir,lib,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.c0r6ST find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 4.2.2, R-base < 4.2.2 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.L5AkDf Processing files: R-base-debuginfo-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.xufI8S find-provides: running scripts (debuginfo) ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.sroWz9 find-requires: running scripts (debuginfo) Provides: debug64(libR.so) Requires: R-base = 4.2.2-alt2, /usr/lib/debug/lib64/ld-linux-x86-64.so.2.debug, debug64(ld-linux-x86-64.so.2), debug64(libX11.so.6), debug64(libXmu.so.6), debug64(libXt.so.6), debug64(libbz2.so.1), debug64(libc.so.6), debug64(libcairo.so.2), debug64(libcurl.so.4), debug64(libgobject-2.0.so.0), debug64(libgomp.so.1), debug64(libicui18n.so.74), debug64(libicuuc.so.74), debug64(libjpeg.so.62), debug64(liblapack.so.4), debug64(liblzma.so.5), debug64(libm.so.6), debug64(libopenblas.so.0), debug64(libpango-1.0.so.0), debug64(libpangocairo-1.0.so.0), debug64(libpcre2-8.so.0), debug64(libpng16.so.16), debug64(libreadline.so.8), debug64(libtiff.so.5), debug64(libz.so.1) Processing files: R-tcltk-debuginfo-4.2.2-alt2 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.0SEwlE find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.IuhdAm find-requires: running scripts (debuginfo) Requires: R-tcltk = 4.2.2-alt2, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so) Adding to R-devel a strict dependency on R-base Adding to R-tcltk a strict dependency on R-base Adding to R-doc-html a strict dependency on R-base Adding to R-base-debuginfo a strict dependency on R-base Adding to R-full a strict dependency on R-devel Adding to R-full a strict dependency on R-tcltk Adding to R-full a strict dependency on R-doc-html Adding to R-tcltk-debuginfo a strict dependency on R-tcltk Adding to R-devel a strict dependency on R-base Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo also prunning dir /usr/src/debug/R-4.2.2/include/R_ext also prunning dir /usr/src/debug/R-4.2.2/src/include also prunning dir /usr/src/debug/R-4.2.2/include Removing 1 extra deps from R-devel due to dependency on R-base Removing 1 extra deps from R-tcltk due to dependency on R-base Removing 1 extra deps from R-tcltk-debuginfo due to dependency on R-base-debuginfo Removing 2 extra deps from R-devel due to repentancy on R-base Removing 6 extra deps from R-tcltk due to repentancy on R-base Removing 1 extra deps from R-tcltk-debuginfo due to repentancy on R-base-debuginfo warning: Installed (but unpackaged) file(s) found: /usr/lib64/R/COPYING /usr/lib64/R/SVN-REVISION Wrote: /usr/src/RPM/RPMS/x86_64/R-base-4.2.2-alt2.x86_64.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-full-4.2.2-alt2.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-4.2.2-alt2.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-4.2.2-alt2.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-html-4.2.2-alt2.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-pdf-4.2.2-alt2.x86_64.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-doc-info-4.2.2-alt2.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-4.2.2-alt2.x86_64.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-4.2.2-alt2.x86_64.rpm (w2.lzdio) 1038.83user 142.15system 11:53.27elapsed 165%CPU (0avgtext+0avgdata 700800maxresident)k 0inputs+0outputs (0major+22093978minor)pagefaults 0swaps 11.29user 4.02system 15:11.19elapsed 1%CPU (0avgtext+0avgdata 131524maxresident)k 2048296inputs+0outputs (0major+319961minor)pagefaults 0swaps --- R-base-4.2.2-alt2.x86_64.rpm.repo 2024-02-27 06:57:06.000000000 +0000 +++ R-base-4.2.2-alt2.x86_64.rpm.hasher 2024-05-04 02:37:18.219832767 +0000 @@ -13219,2 +13219,3 @@ Requires: libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p +Requires: libcurl.so.4(CURL_GNUTLS_4)(64bit) Requires: libgobject-2.0.so.0()(64bit) >= set:ml6W90 @@ -13252,4 +13253,4 @@ File: /etc/R 40755 root:root -File: /etc/R/Makeconf 100644 root:root 1d24eee61957edd05973a3b3495e7df5 -File: /etc/R/Renviron 100644 root:root 17b1b45791913d89a08a63e4da993478 +File: /etc/R/Makeconf 100644 root:root 93f673c1f2df58c2db98c10c10eb24ba +File: /etc/R/Renviron 100644 root:root 70d303530a9575c75ba01f1557fb6654 File: /etc/R/javaconf 100644 root:root 27058ecb5021b041c370727b8b2905bb @@ -13262,3 +13263,3 @@ File: /usr/lib64/R/bin/BATCH 100755 root:root efcdc69689a5a2e3b65945b6a2c38b44 -File: /usr/lib64/R/bin/R 100755 root:root 30b9d935f7c14ca6323179cc231c847b +File: /usr/lib64/R/bin/R 100755 root:root b386a8e361ab1ff078fc38ec81bf70a3 File: /usr/lib64/R/bin/Rcmd 100755 root:root 576452b713fc03061eeefddba0d1f7a3 @@ -13267,3 +13268,3 @@ File: /usr/lib64/R/bin/Rprof 100755 root:root 3702490ff9880f9d5760aa1529e6d331 -File: /usr/lib64/R/bin/Rscript 100755 root:root d501fbd84faa63b6ea3f8062058ba83f +File: /usr/lib64/R/bin/Rscript 100755 root:root 47ade51a1b0952413414fc25c381dde5 File: /usr/lib64/R/bin/Stangle 100755 root:root 9f7c220f3bb9d851b47704e27698fd08 @@ -13271,3 +13272,3 @@ File: /usr/lib64/R/bin/exec 40755 root:root -File: /usr/lib64/R/bin/exec/R 100755 root:root 37aa3edfe5235904ee3dd0e02991a610 +File: /usr/lib64/R/bin/exec/R 100755 root:root 85d2f615cfdd5a00b862371c4ca27ccb File: /usr/lib64/R/bin/javareconf 100755 root:root fff86ef701b6105a15df2000241a207c @@ -13281,3 +13282,3 @@ File: /usr/lib64/R/library/KernSmooth 40755 root:root -File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root d0a5db4e6553e96418780f25fb1516ad +File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root a508c3d1a0ed917adf6cefb792fc8bee File: /usr/lib64/R/library/KernSmooth/INDEX 100644 root:root 56080cdf3d21fa33a8cae73825b9ef9f @@ -13289,3 +13290,3 @@ File: /usr/lib64/R/library/KernSmooth/Meta/nsInfo.rds 100644 root:root 20f6783ac60d139a29358afc803f056c -File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 6acb308a26bf73503030b643cf90ee6a +File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 211f4fe38ae25bb6563575712ad97e6f File: /usr/lib64/R/library/KernSmooth/NAMESPACE 100644 root:root a93c919c53d25488f67acbe057fff7ed @@ -13297,4 +13298,4 @@ File: /usr/lib64/R/library/KernSmooth/help/AnIndex 100644 root:root 000e790525eb6d551fc2a2f3edd1f6d1 -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root c25bf0bf8cb39a6225c1bd536c393612 -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root b863afc2413339e82eef98ee71f8e298 +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root 3949ff50f6e09d4ad38a35f5fc5e09e7 +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root f07b3afe3788da1e7ceb617e05a7bd61 File: /usr/lib64/R/library/KernSmooth/help/aliases.rds 100644 root:root a83591bbaee23e8a754571a4ef3242a5 @@ -13307,3 +13308,3 @@ File: /usr/lib64/R/library/KernSmooth/help/locpoly.html 100644 root:root 736c5e120c9f03fa45ac62c49af0ada3 -File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root 88fe41fc45d443bc71b84efdf3e44515 +File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root 274341c8ab52fae578fee9a571d53dc6 File: /usr/lib64/R/library/KernSmooth/html 40755 root:root @@ -13319,3 +13320,3 @@ File: /usr/lib64/R/library/KernSmooth/libs 40755 root:root -File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root a82bc99cb2a2c92dd6a4bd07c8d2836c +File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root b0ea857c38cdfd364ea70ca535e46cd1 File: /usr/lib64/R/library/KernSmooth/po 40755 root:root @@ -13341,3 +13342,3 @@ File: /usr/lib64/R/library/MASS/CITATION 100644 root:root b712abcbf880df8140a6ba49b039db53 -File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 9fa2ae3c405c067020e7d2f9fadda67e +File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 0d4556d16c0345f4b62f3a8bfbce2eec File: /usr/lib64/R/library/MASS/INDEX 100644 root:root 35aff05a505ecf7e81e0473767794ca9 @@ -13350,3 +13351,3 @@ File: /usr/lib64/R/library/MASS/Meta/nsInfo.rds 100644 root:root dce4118a0ee7d2545b47cfd4f653bec3 -File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root 0b4d6a747216b844f741f24cdb529c72 +File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root 3a83ae498c0e05436ae56ec55fa92eaa File: /usr/lib64/R/library/MASS/NAMESPACE 100644 root:root 3058570082fa395ff650dacb82f17442 @@ -13375,4 +13376,4 @@ File: /usr/lib64/R/library/MASS/help/MASS-internal.html 100644 root:root c3544c17c77607c46c79680c24f30866 -File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root e204385aefee21a176ef10ea98ec355e -File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root 6427dbbb1efec190f0a474f9b71beb0e +File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root 7adfe39f07e100a7658d9c434e62ebd5 +File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root e5a8b463f52038544d171c3793109c2e File: /usr/lib64/R/library/MASS/help/Math.fractions.html 100644 root:root 1b133675e498a7e925c0fae299ead78b @@ -13541,3 +13542,3 @@ File: /usr/lib64/R/library/MASS/help/parcoord.html 100644 root:root 0d24c3e9afc7e03ad13b480c38fb627e -File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root e3c72c17e3f1d043c1ee90916ff961ce +File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root cf42e73c163667374ec9689309f7bdd3 File: /usr/lib64/R/library/MASS/help/petrol.html 100644 root:root 77e890820bd7f271c90a190c2b8e01a2 @@ -13780,3 +13781,3 @@ File: /usr/lib64/R/library/MASS/libs 40755 root:root -File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root c57dbce1a93abeaf8886dfd06edaac64 +File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root bd47424249cd67fc5ab7a3b6ef729eba File: /usr/lib64/R/library/MASS/po 40755 root:root @@ -13819,3 +13820,3 @@ File: /usr/lib64/R/library/Matrix/Copyrights 100644 root:root 8734f0b040c6292983d273d4251d250a -File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root 0477d6c26819e13cde27472814d171da +File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root c87fef3940c82da06e7ac22005bca591 File: 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