<86>May 13 00:58:50 userdel[2400193]: delete user 'rooter' <86>May 13 00:58:50 userdel[2400193]: removed group 'rooter' owned by 'rooter' <86>May 13 00:58:50 userdel[2400193]: removed shadow group 'rooter' owned by 'rooter' <86>May 13 00:58:50 groupadd[2400217]: group added to /etc/group: name=rooter, GID=972 <86>May 13 00:58:50 groupadd[2400217]: group added to /etc/gshadow: name=rooter <86>May 13 00:58:50 groupadd[2400217]: new group: name=rooter, GID=972 <86>May 13 00:58:50 useradd[2400228]: new user: name=rooter, UID=972, GID=972, home=/root, shell=/bin/bash <86>May 13 00:58:50 userdel[2400254]: delete user 'builder' <86>May 13 00:58:50 userdel[2400254]: removed group 'builder' owned by 'builder' <86>May 13 00:58:50 userdel[2400254]: removed shadow group 'builder' owned by 'builder' <86>May 13 00:58:50 groupadd[2400273]: group added to /etc/group: name=builder, GID=973 <86>May 13 00:58:50 groupadd[2400273]: group added to /etc/gshadow: name=builder <86>May 13 00:58:50 groupadd[2400273]: new group: name=builder, GID=973 <86>May 13 00:58:50 useradd[2400288]: new user: name=builder, UID=973, GID=973, home=/usr/src, shell=/bin/bash warning: Macro %add_tcl_lib_path not found <13>May 13 00:58:58 rpmi: xorg-proto-devel-2022.1-alt1 sisyphus+299488.100.1.1 1651731532 installed <13>May 13 00:58:58 rpmi: libpng16-1.6.37-alt1 sisyphus+275734.100.2.1 1624788826 installed <13>May 13 00:58:58 rpmi: libexpat-2.4.7-alt1 sisyphus+296417.100.1.1 1646812525 installed <13>May 13 00:58:58 rpmi: libjpeg-2:2.1.2-alt1 sisyphus+294623.100.2.1 1643889731 installed <13>May 13 00:58:58 rpmi: perl-HTTP-Date-6.05-alt1 sisyphus+258981.100.1.1 1601542386 installed <13>May 13 00:58:58 rpmi: libglvnd-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:58:58 rpmi: libwayland-client-1.20.0-alt1.1 sisyphus+296452.100.1.1 1646839576 installed <13>May 13 00:58:58 rpmi: tex-common-0.2-alt4 sisyphus+276869.100.1.1 1625246366 installed <13>May 13 00:58:58 rpmi: perl-Unicode-Normalize-1:5.34.0-alt1 sisyphus+279621.700.1.1 1626629811 installed <13>May 13 00:58:58 rpmi: liblcms2-2.13.1-alt1 sisyphus+296040.100.1.1 1646123109 installed <13>May 13 00:58:58 rpmi: perl-Term-ANSIColor-5.01-alt1 sisyphus+244783.100.1.2 1579747505 installed <13>May 13 00:58:58 rpmi: perl-XML-NamespaceSupport-1.12-alt1 1491296348 installed <13>May 13 00:58:58 rpmi: less-590-alt2 sisyphus+299300.100.1.1 1651318217 installed <13>May 13 00:58:58 rpmi: libICE-1.0.10-alt1 sisyphus+278827.100.1.1 1626220279 installed <13>May 13 00:58:58 rpmi: libidn2-2.3.2-alt1 sisyphus+281238.100.1.2 1627476321 installed <13>May 13 00:58:58 rpmi: libicu71-1:7.1.1-alt1 sisyphus+289194.300.3.1 1650228448 installed <13>May 13 00:58:58 rpmi: libgraphite2-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed <13>May 13 00:58:58 rpmi: libSM-1.2.3-alt1 sisyphus+278820.100.1.1 1626219264 installed <13>May 13 00:58:58 rpmi: perl-Tie-RefHash-1.40-alt1 sisyphus+260329.100.1.1 1603548550 installed <13>May 13 00:58:58 rpmi: perl-IO-Stringy-2.113-alt1 sisyphus+289915.300.2.1 1637124493 installed <13>May 13 00:58:58 rpmi: rpm-macros-info-install-6.7-alt1 sisyphus+278099.4400.1.1 1626031435 installed <13>May 13 00:58:58 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed <13>May 13 00:58:58 rpmi: libtcl-8.6.12-alt1 sisyphus+289207.100.1.1 1636393871 installed <13>May 13 00:58:58 rpmi: tcl-8.6.12-alt1 sisyphus+289207.100.1.1 1636393871 installed <13>May 13 00:58:58 rpmi: libopenblas-0.3.19-alt1.1 sisyphus+293828.100.1.1 1642694459 installed <13>May 13 00:58:58 rpmi: zlib-devel-1.2.12-alt1 sisyphus+298590.100.1.1 1650147041 installed <13>May 13 00:58:58 rpmi: liblksctp-1.0.19-alt1 sisyphus+286802.100.2.1 1633967462 installed <13>May 13 00:58:58 rpmi: javapackages-filesystem-1:5.3.0-alt1_15jpp11 sisyphus+278038.500.1.3 1625987751 installed <13>May 13 00:58:58 rpmi: javapackages-tools-1:5.3.0-alt1_15jpp11 sisyphus+278038.500.1.3 1625987751 installed <13>May 13 00:58:58 rpmi: perl-IO-Socket-IP-0.41-alt1 sisyphus+259012.100.1.2 1601553446 installed <13>May 13 00:58:58 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed <13>May 13 00:58:58 rpmi: perl-Compress-Raw-Zlib-2.103-alt1 sisyphus+298003.100.1.1 1649324304 installed <13>May 13 00:58:58 rpmi: perl-libnet-1:3.13-alt1 sisyphus+266120.100.1.1 1612961310 installed <13>May 13 00:58:58 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed <13>May 13 00:58:58 rpmi: perl-XML-SAX-Base-1.09-alt1 1494364363 installed <13>May 13 00:58:58 rpmi: libfribidi-1.0.12-alt1 sisyphus+298746.100.1.1 1650435949 installed <13>May 13 00:58:58 rpmi: libepoxy-1.5.10-alt1 sisyphus+296853.200.2.1 1647631866 installed <13>May 13 00:58:58 rpmi: libpixman-3:0.40.0-alt2 sisyphus+281167.100.1.1 1627444504 installed <13>May 13 00:58:58 rpmi: libwayland-server-1.20.0-alt1.1 sisyphus+296452.100.1.1 1646839576 installed <13>May 13 00:58:58 rpmi: libwebp7-1.2.2-alt1 sisyphus+293797.100.1.1 1642668641 installed <13>May 13 00:58:58 rpmi: libpaper-1.1.28-alt1 sisyphus+278439.100.1.1 1626100422 installed <13>May 13 00:58:58 rpmi: libnettle8-3.7.3-alt1 sisyphus+276723.100.1.2 1625211788 installed <13>May 13 00:58:58 rpmi: libquadmath0-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:58:58 rpmi: libgfortran5-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:58:58 rpmi: libbrotlicommon-1.0.9-alt2 sisyphus+278430.100.1.2 1626213212 installed <13>May 13 00:58:58 rpmi: libbrotlidec-1.0.9-alt2 sisyphus+278430.100.1.2 1626213212 installed <13>May 13 00:58:59 rpmi: libharfbuzz-4.2.1-alt1 sisyphus+299180.100.1.1 1651137935 installed <13>May 13 00:58:59 rpmi: libfreetype-2.12.1-alt1 sisyphus+299380.100.1.1 1651508331 installed <13>May 13 00:58:59 rpmi: libbrotlienc-1.0.9-alt2 sisyphus+278430.100.1.2 1626213212 installed <13>May 13 00:58:59 rpmi: libgdbm-1.8.3-alt10 sisyphus+278100.1600.1.1 1626058413 installed <13>May 13 00:58:59 rpmi: xml-utils-1:2.9.14-alt1 sisyphus+299383.100.1.1 1651519547 installed <13>May 13 00:58:59 rpmi: fontconfig-2.13.1-alt3 sisyphus+297937.100.1.1 1649228296 installed Updating fonts cache: <29>May 13 00:59:00 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>May 13 00:59:00 rpmi: libp11-kit-0.24.1-alt1 sisyphus+293720.100.1.1 1642535264 installed <13>May 13 00:59:00 rpmi: libtasn1-4.18.0-alt1 sisyphus+294217.100.3.1 1643755522 installed <13>May 13 00:59:00 rpmi: libXau-1.0.9-alt1 sisyphus+278247.100.1.1 1626080736 installed <13>May 13 00:59:00 rpmi: libXau-devel-1.0.9-alt1 sisyphus+278247.100.1.1 1626080736 installed <13>May 13 00:59:00 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed <13>May 13 00:59:00 rpmi: fonts-type1-xorg-7.0.0-alt4 sisyphus+276845.100.1.1 1625243059 installed <13>May 13 00:59:00 rpmi: rpm-build-gir-0.7.3-alt3 sisyphus+242150.100.1.1 1575312005 installed <13>May 13 00:59:00 rpmi: libwoff2-1.0.2-alt2.1 sisyphus+277277.100.1.2 1625464643 installed <13>May 13 00:59:00 rpmi: libharfbuzz-icu-4.2.1-alt1 sisyphus+299180.100.1.1 1651137935 installed <13>May 13 00:59:00 rpmi: libharfbuzz-gobject-4.2.1-alt1 sisyphus+299180.100.1.1 1651137935 installed <13>May 13 00:59:00 rpmi: libquadmath11-devel-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:00 rpmi: libhogweed6-3.7.3-alt1 sisyphus+276723.100.1.2 1625211788 installed <13>May 13 00:59:00 rpmi: libgnutls30-3.6.16-alt1 sisyphus+273086.100.1.1 1622478144 installed <13>May 13 00:59:00 rpmi: java-common-1.6.0-alt1 sisyphus+234020.100.1.1 1562437039 installed <13>May 13 00:59:00 rpmi: lksctp-tools-1.0.19-alt1 sisyphus+286802.100.2.1 1633967462 installed <13>May 13 00:59:00 rpmi: libpng-devel-1.6.37-alt1 sisyphus+275734.100.2.1 1624788826 installed <13>May 13 00:59:00 rpmi: libopenblas-devel-0.3.19-alt1.1 sisyphus+293828.100.1.1 1642694459 installed <13>May 13 00:59:00 rpmi: perl-OLE-Storage_Lite-0.20-alt1 sisyphus+243912.100.1.1 1578493389 installed <13>May 13 00:59:00 rpmi: perl-autodie-2.34-alt1 sisyphus+265208.100.1.1 1611567479 installed <13>May 13 00:59:00 rpmi: libgraphite2-devel-1.3.14-alt2.1 sisyphus+279571.100.1.2 1626605111 installed <13>May 13 00:59:00 rpmi: icu-utils-1:7.1.1-alt1 sisyphus+289194.300.3.1 1650228448 installed <13>May 13 00:59:00 rpmi: libicu-devel-1:7.1.1-alt1 sisyphus+289194.300.3.1 1650228448 installed <13>May 13 00:59:00 rpmi: libICE-devel-1.0.10-alt1 sisyphus+278827.100.1.1 1626220279 installed <13>May 13 00:59:00 rpmi: libSM-devel-1.2.3-alt1 sisyphus+278820.100.1.1 1626219264 installed <13>May 13 00:59:00 rpmi: perl-Data-Dump-1.25-alt1 sisyphus+276551.100.1.1 1625126880 installed <13>May 13 00:59:00 rpmi: perl-unicore-1:5.34.0-alt1 sisyphus+279621.700.1.1 1626629811 installed <13>May 13 00:59:00 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+279723.3100.1.1 1626649600 installed <13>May 13 00:59:00 rpmi: libwayland-cursor-1.20.0-alt1.1 sisyphus+296452.100.1.1 1646839576 installed <13>May 13 00:59:00 rpmi: libwayland-egl-4:18.1.0-alt1.1 sisyphus+296452.100.1.1 1646839576 installed <13>May 13 00:59:00 rpmi: libGLES-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:00 rpmi: libOpenGL-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:00 rpmi: perl-File-Listing-6.15-alt1 sisyphus+298606.100.1.1 1650203737 installed <13>May 13 00:59:00 rpmi: groff-base-1.22.3-alt2 sisyphus+275306.100.2.1 1624538375 installed <13>May 13 00:59:00 rpmi: zziplib-0.13.72-alt1 sisyphus+278032.100.1.2 1625982008 installed <13>May 13 00:59:00 rpmi: t1utils-1.42-alt1 sisyphus+278458.100.1.1 1626102085 installed <13>May 13 00:59:00 rpmi: ttf2pt1-3.4.4-alt1.qa1 sisyphus+275192.100.2.1 1624905844 installed <13>May 13 00:59:00 rpmi: rpm-build-tcl-0.6.2-alt1 sisyphus+299320.100.1.1 1651401392 installed <13>May 13 00:59:00 rpmi: tcl-devel-8.6.12-alt1 sisyphus+289207.100.1.1 1636393871 installed <13>May 13 00:59:00 rpmi: rpm-macros-java-1:5.3.0-alt1_15jpp11 sisyphus+278038.500.1.3 1625987751 installed <13>May 13 00:59:00 rpmi: perl-X11-Protocol-0.56-alt1.1 1290621401 installed <13>May 13 00:59:00 rpmi: perl-TimeDate-2.33-alt1 sisyphus+252901.100.1.1 1591387378 installed <13>May 13 00:59:00 rpmi: perl-Unicode-Map-0.112-alt8 sisyphus+279723.3600.1.1 1626649989 installed <13>May 13 00:59:00 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed <13>May 13 00:59:00 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed <13>May 13 00:59:00 rpmi: perl-IPC-System-Simple-1.30-alt1 sisyphus+248544.100.1.1 1585154078 installed <13>May 13 00:59:00 rpmi: perl-IPC-Run3-0.048-alt1 1410690027 installed <13>May 13 00:59:00 rpmi: psutils-2:2.07-alt1 sisyphus+299224.700.1.1 1651226336 installed <13>May 13 00:59:00 rpmi: perl-File-Which-1.27-alt1 sisyphus+271986.100.1.1 1621196035 installed <13>May 13 00:59:00 rpmi: perl-File-Copy-Recursive-0.45-alt1 sisyphus+235291.100.1.1 1564606222 installed <13>May 13 00:59:00 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+279723.3400.1.1 1626649913 installed <13>May 13 00:59:00 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed <13>May 13 00:59:00 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed <13>May 13 00:59:00 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>May 13 00:59:00 rpmi: perl-IO-String-1.08-alt2 1321677915 installed <13>May 13 00:59:00 rpmi: perl-Algorithm-Diff-1:1.201-alt1 sisyphus+263447.100.1.1 1607956595 installed <13>May 13 00:59:00 rpmi: perl-Unicode-EastAsianWidth-12.0-alt1 sisyphus+237401.100.1.1 1568197363 installed <13>May 13 00:59:00 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>May 13 00:59:00 rpmi: lua5.3-5.3.6-alt2 sisyphus+286316.100.2.1 1634197699 installed <13>May 13 00:59:00 rpmi: libxxhash-0.8.0-alt2 sisyphus+277476.100.2.1 1625621312 installed <13>May 13 00:59:00 rpmi: libxslt-1.1.35-alt2 sisyphus+296567.100.1.1 1647097777 installed <13>May 13 00:59:00 rpmi: libtre5-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed <13>May 13 00:59:00 rpmi: libtexlua5-2021-alt2_3 sisyphus+298655.100.1.1 1650294737 installed <13>May 13 00:59:00 rpmi: libteckit-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed <13>May 13 00:59:00 rpmi: libteckit-utils-2.5.1-alt2.1 sisyphus+275250.100.2.1 1624906328 installed <13>May 13 00:59:00 rpmi: libsynctex2-2021-alt2_3 sisyphus+298655.100.1.1 1650294737 installed <13>May 13 00:59:00 rpmi: libqqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed <13>May 13 00:59:00 rpmi: qqwing-1.3.4-alt2 sisyphus+275255.100.2.1 1624562960 installed <13>May 13 00:59:00 rpmi: libpotrace-1.16-alt1 sisyphus+275746.100.1.1 1624752901 installed <13>May 13 00:59:00 rpmi: libpipeline-1.5.6-alt1_1 sisyphus+299648.100.1.1 1651919602 installed <13>May 13 00:59:00 rpmi: man-db-2.9.4-alt1 sisyphus+299224.500.1.1 1651226286 installed <13>May 13 00:59:00 rpmi: libxblas-1.0.248-alt2 sisyphus+285045.40.2.1 1631388330 installed <13>May 13 00:59:01 rpmi: liblapack-1:3.8.0-alt7 sisyphus+293726.100.1.1 1642544497 installed <13>May 13 00:59:01 rpmi: libkpathsea6-2021-alt2_3 sisyphus+298655.100.1.1 1650294737 installed <13>May 13 00:59:01 rpmi: libptexenc1-2021-alt2_3 sisyphus+298655.100.1.1 1650294737 installed <13>May 13 00:59:01 rpmi: libgomp1-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:01 rpmi: libgomp11-devel-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:01 rpmi: libnuma-2.0.14-alt2 sisyphus+278485.100.1.1 1626104244 installed <13>May 13 00:59:01 rpmi: libx265-199-3.5-alt1.1 sisyphus+277560.100.1.1 1625697230 installed <13>May 13 00:59:01 rpmi: libde265-1.0.7-alt1 sisyphus+275350.100.1.2 1624489754 installed <13>May 13 00:59:01 rpmi: libaom3-3.3.0-alt1 sisyphus+295999.100.1.1 1646050399 installed <13>May 13 00:59:01 rpmi: libpcsclite-1.9.5-alt1 sisyphus+294120.100.1.1 1643185199 installed <13>May 13 00:59:01 rpmi: javazi-2021a-alt1.1 sisyphus+284432.100.1.1 1630593048 installed <13>May 13 00:59:01 rpmi: libgif-4.1.6-alt3 sisyphus+276911.100.1.3 1625273979 installed <13>May 13 00:59:01 rpmi: hd2u-1.0.3-alt2 sisyphus+275312.100.2.1 1624906676 installed <13>May 13 00:59:01 rpmi: libxkbcommon-1.4.0-alt1 sisyphus+296072.100.1.1 1646200355 installed <13>May 13 00:59:01 rpmi: libsqlite3-3.38.5-alt1 sisyphus+299670.100.1.1 1651925944 installed <13>May 13 00:59:01 rpmi: libusb-1.0.26-alt1 sisyphus+298877.100.1.1 1650636948 installed <13>May 13 00:59:01 rpmi: libgudev-1:237-alt1 sisyphus+282754.100.1.1 1629006690 installed <13>May 13 00:59:01 rpmi: perl-Try-Tiny-0.31-alt1 sisyphus+290597.100.1.1 1637915507 installed <13>May 13 00:59:01 rpmi: perl-Compress-Raw-Bzip2-2.103-alt1 sisyphus+298002.100.1.1 1649324299 installed <13>May 13 00:59:01 rpmi: perl-Filter-1.60-alt1 sisyphus+279723.100.1.1 1626648797 installed <13>May 13 00:59:01 rpmi: perl-Encode-3.17-alt1 sisyphus+298022.100.1.1 1649332148 installed <13>May 13 00:59:01 rpmi: perl-URI-5.10-alt1 sisyphus+288175.100.1.1 1635236817 installed <13>May 13 00:59:01 rpmi: perl-IO-Compress-2.106-alt1 sisyphus+298415.100.1.1 1649922773 installed <13>May 13 00:59:01 rpmi: perl-HTML-Parser-3.78-alt1 sisyphus+298007.100.1.3 1649326318 installed <13>May 13 00:59:01 rpmi: perl-Net-HTTP-6.22-alt1 sisyphus+294185.100.1.1 1643275428 installed <13>May 13 00:59:01 rpmi: perl-Pod-Simple-3.43-alt1 sisyphus+276561.100.1.1 1625127752 installed <13>May 13 00:59:01 rpmi: perl-Pod-Usage-2.01-alt1 sisyphus+277175.100.1.1 1625408247 installed <13>May 13 00:59:01 rpmi: perl-podlators-4.14-alt1 sisyphus+277178.100.1.2 1625426264 installed <13>May 13 00:59:01 rpmi: perl-IO-Zlib-1.11-alt1 sisyphus+258984.100.1.1 1601542681 installed <13>May 13 00:59:01 rpmi: perl-Archive-Tar-2.40-alt1 sisyphus+281653.100.1.1 1627900756 installed <13>May 13 00:59:01 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>May 13 00:59:01 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>May 13 00:59:01 rpmi: perl-IO-HTML-1.004-alt1 sisyphus+258983.100.1.1 1601542619 installed <13>May 13 00:59:01 rpmi: perl-HTTP-Message-6.36-alt1 sisyphus+293128.100.1.1 1641619603 installed <13>May 13 00:59:01 rpmi: perl-HTTP-Cookies-6.10-alt1 sisyphus+264349.100.1.1 1609891183 installed <13>May 13 00:59:01 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>May 13 00:59:01 rpmi: perl-libwww-6.65-alt1 sisyphus+299785.100.1.1 1652264729 installed <13>May 13 00:59:01 rpmi: perl-HTML-Tree-5.07-alt1 sisyphus+277105.100.1.1 1625402682 installed <13>May 13 00:59:01 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed <13>May 13 00:59:01 rpmi: perl-XML-Parser-2.46-alt1 sisyphus+279723.1300.1.1 1626649131 installed <13>May 13 00:59:01 rpmi: perl-XML-LibXML-2.0207-alt5 sisyphus+299385.100.1.1 1651522441 installed <13>May 13 00:59:01 rpmi: perl-XML-SAX-1.02-alt1 sisyphus+232322.100.1.1 1560758406 installed <13>May 13 00:59:01 rpmi: perl-XML-Simple-2.25-alt2 sisyphus+257498.100.1.1 1599324034 installed <13>May 13 00:59:01 rpmi: icon-naming-utils-0.8.90-alt1 sisyphus+276851.100.1.1 1625243947 installed <13>May 13 00:59:01 rpmi: icon-theme-adwaita-42.0-alt1 sisyphus+296812.4140.4.2 1647966473 installed <13>May 13 00:59:01 rpmi: perl-XML-Twig-3.52-alt1 sisyphus+277116.100.1.2 1625410693 installed <13>May 13 00:59:01 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed <13>May 13 00:59:01 rpmi: perl-HTML-Form-6.07-alt1 sisyphus+246847.100.1.1 1582555741 installed <13>May 13 00:59:01 rpmi: perl-WWW-Mechanize-2.07-alt1 sisyphus+299332.100.1.1 1651412227 installed <13>May 13 00:59:01 rpmi: perl-libintl-1.32-alt1 sisyphus+279723.5100.1.1 1626650309 installed <13>May 13 00:59:01 rpmi: perl-Text-CSV_XS-1.47-alt1 sisyphus+292763.100.1.1 1640743923 installed <13>May 13 00:59:01 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed <13>May 13 00:59:01 rpmi: libdatrie-0.2.13-alt1_2 sisyphus+285649.100.1.1 1632260802 installed <13>May 13 00:59:01 rpmi: libthai-0.1.29-alt1_1 sisyphus+292947.100.1.1 1641111915 installed <13>May 13 00:59:01 rpmi: libgdk-pixbuf-locales-2.42.8-alt1 sisyphus+296847.100.1.1 1647616018 installed <13>May 13 00:59:01 rpmi: libxshmfence-1.3-alt1 sisyphus+278248.100.1.1 1626080762 installed <13>May 13 00:59:01 rpmi: libpciaccess-1:0.16-alt1 sisyphus+278288.100.1.1 1626084210 installed <13>May 13 00:59:01 rpmi: libdrm-1:2.4.109-alt1 sisyphus+291482.100.1.1 1638787694 installed <13>May 13 00:59:01 rpmi: libgbm-4:22.0.3-alt1 sisyphus+299513.100.1.1 1651761350 installed <13>May 13 00:59:01 rpmi: gtk+3-themes-incompatible-3.20-alt3 1461944560 installed <13>May 13 00:59:01 rpmi: publicsuffix-list-dafsa-20220406-alt1 sisyphus+297986.100.1.1 1649274774 installed <13>May 13 00:59:01 rpmi: libpsl-0.21.1-alt2 sisyphus+279461.100.1.1 1626547547 installed <13>May 13 00:59:01 rpmi: libnghttp2-1.47.0-alt1 sisyphus+297351.100.1.1 1648403625 installed <13>May 13 00:59:01 rpmi: openldap-common-2.4.59-alt1 sisyphus+282933.100.1.1 1629124747 installed <13>May 13 00:59:01 rpmi: rsync-3.1.3-alt2 sisyphus+278100.6000.1.1 1626060142 installed <13>May 13 00:59:01 rpmi: libverto-0.3.2-alt1_1 sisyphus+279289.100.1.3 1626493868 installed <13>May 13 00:59:01 rpmi: liblmdb-0.9.23-alt1 sisyphus+275369.100.1.2 1624493869 installed <13>May 13 00:59:01 rpmi: libkeyutils-1.6.3-alt1 sisyphus+266061.100.1.1 1612919566 installed <13>May 13 00:59:01 rpmi: libcom_err-1.46.4.0.5.4cda-alt1 sisyphus+283826.100.1.1 1629975345 installed <13>May 13 00:59:01 rpmi: libedit3-3.1.20191231-alt1 sisyphus+278505.100.1.1 1626106374 installed <13>May 13 00:59:01 rpmi: libjbig-2.1-alt1 sisyphus+276068.100.1.1 1624815400 installed <13>May 13 00:59:01 rpmi: libdeflate-1.10-alt1 sisyphus+297316.100.1.1 1648316820 installed <13>May 13 00:59:01 rpmi: libtiff5-4.3.0-alt2 sisyphus+290923.300.4.1 1638162792 installed <13>May 13 00:59:01 rpmi: libopenjpeg2.0-2.4.0-alt2 sisyphus+270166.100.1.1 1618663536 installed <13>May 13 00:59:01 rpmi: gcc-fortran-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed <13>May 13 00:59:01 rpmi: libgfortran11-devel-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:02 rpmi: gcc11-fortran-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:02 rpmi: gcc-c++-common-1.4.27-alt1 sisyphus+278099.1300.1.1 1626028636 installed <13>May 13 00:59:02 rpmi: libstdc++11-devel-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:03 rpmi: gcc11-c++-11.2.1-alt2 sisyphus+291192.100.1.1 1638461683 installed <13>May 13 00:59:03 rpmi: mpdecimal-2.5.1-alt1 sisyphus+291245.40.54.1 1643293433 installed <13>May 13 00:59:03 rpmi: ed-1:0.2-alt10 sisyphus+278100.1100.1.1 1626056843 installed <13>May 13 00:59:03 rpmi: libdevmapper-1.02.179-alt2 sisyphus+287340.100.1.1 1634383919 installed <13>May 13 00:59:03 rpmi: mount-2.37.3-alt2 sisyphus+294073.100.1.1 1643117174 installed <13>May 13 00:59:03 rpmi: losetup-2.37.3-alt2 sisyphus+294073.100.1.1 1643117174 installed <13>May 13 00:59:03 rpmi: lsblk-2.37.3-alt2 sisyphus+294073.100.1.1 1643117174 installed <13>May 13 00:59:03 rpmi: diffstat-1.64-alt1 sisyphus+278100.700.1.1 1626056683 installed <13>May 13 00:59:03 rpmi: libdialog-1.3.20171209-alt2 sisyphus+284461.40.2.1 1630655674 installed <13>May 13 00:59:03 rpmi: dialog-1.3.20171209-alt2 sisyphus+284461.40.2.1 1630655674 installed <13>May 13 00:59:03 rpmi: bc-1:1.07.1-alt1 sisyphus+278100.400.1.1 1626056612 installed <13>May 13 00:59:03 rpmi: libatk-locales-2.38.0-alt1 sisyphus+297117.100.1.1 1648128465 installed <13>May 13 00:59:03 rpmi: libatk-2.38.0-alt1 sisyphus+297117.100.1.1 1648128465 installed <13>May 13 00:59:03 rpmi: desktop-file-utils-0.26-alt3 sisyphus+297027.100.1.1 1648023315 installed <13>May 13 00:59:03 rpmi: shared-mime-info-2.2-alt1 sisyphus+297388.100.1.1 1648466615 installed <13>May 13 00:59:03 rpmi: gsettings-desktop-schemas-data-42.0-alt1 sisyphus+296812.200.4.2 1647962578 installed <13>May 13 00:59:03 rpmi: libgio-2.72.1-alt1 sisyphus+298438.100.1.1 1649945703 installed <13>May 13 00:59:03 rpmi: gsettings-desktop-schemas-42.0-alt1 sisyphus+296812.200.4.2 1647962578 installed <13>May 13 00:59:03 rpmi: libgdk-pixbuf-2.42.8-alt1 sisyphus+296847.100.1.1 1647616018 installed <13>May 13 00:59:03 rpmi: libgusb-0.3.10-alt1 sisyphus+293257.100.1.1 1641836015 installed <13>May 13 00:59:03 rpmi: libcolord-1.4.6-alt1 sisyphus+296000.100.1.1 1646050421 installed <13>May 13 00:59:03 rpmi: gtk4-update-icon-cache-4.6.3-alt1 sisyphus+298962.400.2.2 1650888024 installed <13>May 13 00:59:03 rpmi: libheif-1.11.0-alt1 sisyphus+279399.100.1.2 1626532543 installed <13>May 13 00:59:03 rpmi: libdconf-0.40.0-alt1 sisyphus+279299.100.1.2 1626495967 installed <13>May 13 00:59:03 rpmi: liblz4-1:1.9.3-alt1 sisyphus+278100.4000.1.1 1626059441 installed <13>May 13 00:59:03 rpmi: libsystemd-1:249.12-alt2 sisyphus+299531.100.2.1 1652296661 installed <13>May 13 00:59:03 rpmi: libdbus-1.12.22-alt1 sisyphus+298998.100.1.1 1650885222 installed <13>May 13 00:59:03 rpmi: dbus-tools-1.12.22-alt1 sisyphus+298998.100.1.1 1650885222 installed <86>May 13 00:59:03 groupadd[2443207]: group added to /etc/group: name=messagebus, GID=499 <86>May 13 00:59:03 groupadd[2443207]: group added to /etc/gshadow: name=messagebus <86>May 13 00:59:03 groupadd[2443207]: new group: name=messagebus, GID=499 <86>May 13 00:59:03 useradd[2443220]: new user: name=messagebus, UID=499, GID=499, home=/run/dbus, shell=/dev/null <13>May 13 00:59:03 rpmi: dbus-1.12.22-alt1 sisyphus+298998.100.1.1 1650885222 installed <13>May 13 00:59:03 rpmi: dconf-0.40.0-alt1 sisyphus+279299.100.1.2 1626495967 installed <13>May 13 00:59:03 rpmi: libgtk+3-schemas-3.24.33-alt1 sisyphus+297378.300.3.1 1648630792 installed <13>May 13 00:59:03 rpmi: libavahi-0.8-alt2 sisyphus+279391.100.1.2 1626530679 installed <13>May 13 00:59:03 rpmi: libcups-2.3.3-alt7.op2 sisyphus+289457.100.2.1 1636771520 installed <13>May 13 00:59:04 rpmi: libgs-9.54.0-alt3 sisyphus+285041.100.1.1 1631376584 installed <13>May 13 00:59:04 rpmi: ghostscript-common-9.54.0-alt3 sisyphus+285041.100.1.1 1631376584 installed <13>May 13 00:59:04 rpmi: ghostscript-classic-9.54.0-alt3 sisyphus+285041.100.1.1 1631376584 installed <13>May 13 00:59:04 rpmi: ghostscript-9.54.0-alt3 sisyphus+285041.100.1.1 1631376584 installed <13>May 13 00:59:04 rpmi: perl-Net-DBus-1.2.0-alt1 sisyphus+279723.2700.1.1 1626649518 installed <13>May 13 00:59:04 rpmi: libpolkit-0.120-alt1.qa2 sisyphus+296007.100.1.1 1646053422 installed <13>May 13 00:59:04 rpmi: libX11-locales-3:1.8-alt1 sisyphus+299436.100.1.1 1651655356 installed <13>May 13 00:59:04 rpmi: libXdmcp-1.1.3-alt1 sisyphus+278816.100.1.1 1626219231 installed <13>May 13 00:59:04 rpmi: libxcb-1.15-alt1 sisyphus+299436.300.1.1 1651655472 installed <13>May 13 00:59:04 rpmi: libX11-3:1.8-alt1 sisyphus+299436.100.1.1 1651655356 installed <13>May 13 00:59:04 rpmi: libXext-1.3.4-alt1 sisyphus+278817.100.1.3 1626262596 installed <13>May 13 00:59:04 rpmi: libXrender-0.9.10-alt1 sisyphus+278480.100.1.2 1626227740 installed <13>May 13 00:59:04 rpmi: libXt-1.2.1-alt1 sisyphus+265202.200.1.1 1611565457 installed <13>May 13 00:59:04 rpmi: libXmu-1.1.3-alt1 sisyphus+278818.100.1.3 1626263295 installed <13>May 13 00:59:04 rpmi: libXft-2.3.4-alt1 sisyphus+284644.500.1.1 1630910476 installed <13>May 13 00:59:04 rpmi: libXi-1.8-alt1 sisyphus+285490.200.1.1 1632124174 installed <13>May 13 00:59:04 rpmi: libXfixes-6.0.0-alt1 sisyphus+284644.300.1.1 1630910331 installed <13>May 13 00:59:04 rpmi: libat-spi2-core-2.44.1-alt1 sisyphus+298837.100.1.1 1650578259 installed <13>May 13 00:59:04 rpmi: libXpm-3.5.13-alt1 sisyphus+278339.100.1.2 1626171698 installed <13>May 13 00:59:04 rpmi: libXtst-1.2.3-alt1 sisyphus+278848.100.1.2 1626298055 installed <13>May 13 00:59:04 rpmi: xprop-1.2.5-alt1 sisyphus+279025.100.1.1 1626354198 installed <13>May 13 00:59:04 rpmi: libXcomposite-0.4.5-alt1 sisyphus+275323.100.2.2 1624573269 installed <13>May 13 00:59:06 rpmi: libxcb-devel-1.15-alt1 sisyphus+299436.300.1.1 1651655472 installed <13>May 13 00:59:06 rpmi: libX11-devel-3:1.8-alt1 sisyphus+299436.100.1.1 1651655356 installed <13>May 13 00:59:06 rpmi: libXrender-devel-0.9.10-alt1 sisyphus+278480.100.1.2 1626227740 installed <13>May 13 00:59:06 rpmi: libXext-devel-1.3.4-alt1 sisyphus+278817.100.1.3 1626262596 installed <13>May 13 00:59:06 rpmi: libXt-devel-1.2.1-alt1 sisyphus+265202.200.1.1 1611565457 installed <13>May 13 00:59:06 rpmi: libXaw-1.0.14-alt1 sisyphus+284644.100.1.1 1630910247 installed <13>May 13 00:59:06 rpmi: libgd3-2.3.3-alt1 sisyphus+286379.100.1.1 1633353307 installed <13>May 13 00:59:06 rpmi: libXcursor-1.2.1-alt1 sisyphus+297765.200.1.1 1649053926 installed <13>May 13 00:59:06 rpmi: libtk-8.6.12-alt1 sisyphus+289207.200.1.1 1636394135 installed <13>May 13 00:59:06 rpmi: tk-8.6.12-alt1 sisyphus+289207.200.1.1 1636394135 installed <13>May 13 00:59:06 rpmi: perl-Tk-804.036-alt1 sisyphus+279723.3300.1.1 1626649879 installed <13>May 13 00:59:06 rpmi: xset-1.2.4-alt1 sisyphus+275497.100.2.2 1624918317 installed <13>May 13 00:59:06 rpmi: xdg-utils-1.1.3-alt8 sisyphus+273592.100.1.1 1622810329 installed <13>May 13 00:59:06 rpmi: ghostscript-module-X-9.54.0-alt3 sisyphus+285041.100.1.1 1631376584 installed <13>May 13 00:59:06 rpmi: libXrandr-1.5.2-alt1 sisyphus+275330.100.2.2 1624575558 installed <13>May 13 00:59:06 rpmi: libXxf86vm-1.1.4-alt2 sisyphus+275334.100.2.2 1624577011 installed <13>May 13 00:59:06 rpmi: libGLX-mesa-4:22.0.3-alt1 sisyphus+299513.100.1.1 1651761350 installed <13>May 13 00:59:06 rpmi: libEGL-mesa-4:22.0.3-alt1 sisyphus+299513.100.1.1 1651761350 installed <13>May 13 00:59:06 rpmi: libEGL-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:06 rpmi: libGLX-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:06 rpmi: libGL-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:06 rpmi: libcairo-1:1.16.0-alt1 sisyphus+275343.100.2.3 1624578007 installed <13>May 13 00:59:06 rpmi: libpango-1.50.7-alt1 sisyphus+298455.100.1.1 1649965703 installed <13>May 13 00:59:06 rpmi: libcairo-gobject-1:1.16.0-alt1 sisyphus+275343.100.2.3 1624578007 installed <13>May 13 00:59:06 rpmi: libglvnd-devel-7:1.4.0-alt1 sisyphus+292743.100.1.1 1640688162 installed <13>May 13 00:59:06 rpmi: libXinerama-1.1.4-alt1 sisyphus+275328.100.2.2 1624575558 installed <13>May 13 00:59:06 rpmi: dbus-tools-gui-1.12.22-alt1 sisyphus+298998.100.1.1 1650885222 installed <13>May 13 00:59:06 rpmi: at-spi2-core-2.44.1-alt1 sisyphus+298837.100.1.1 1650578259 installed <13>May 13 00:59:06 rpmi: at-spi2-atk-2.38.0-alt1 sisyphus+277983.100.1.2 1625960719 installed <13>May 13 00:59:06 rpmi: libXdamage-1.1.5-alt1 sisyphus+275324.100.2.2 1624573269 installed <13>May 13 00:59:06 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+278157.100.2.1 1626055790 installed <13>May 13 00:59:06 rpmi: alternatives-0.5.1-alt1 sisyphus+278157.100.2.1 1626055790 installed <13>May 13 00:59:06 rpmi: ca-certificates-2022.04.01-alt1 sisyphus+297635.100.1.1 1648830809 installed <13>May 13 00:59:06 rpmi: ca-trust-0.1.3-alt1 sisyphus+299449.100.1.1 1651660001 installed <13>May 13 00:59:06 rpmi: p11-kit-trust-0.24.1-alt1 sisyphus+293720.100.1.1 1642535264 installed <13>May 13 00:59:06 rpmi: libcrypto1.1-1.1.1n-alt2 sisyphus+297394.100.2.1 1648745095 installed <13>May 13 00:59:06 rpmi: libssl1.1-1.1.1n-alt2 sisyphus+297394.100.2.1 1648745095 installed <13>May 13 00:59:06 rpmi: python3-3.10.4-alt1 sisyphus+297487.100.1.1 1648620051 installed <13>May 13 00:59:07 rpmi: python3-base-3.10.4-alt1 sisyphus+297487.100.1.1 1648620051 installed <13>May 13 00:59:07 rpmi: python3-module-six-1.16.0-alt1 sisyphus+283489.100.2.1 1629527308 installed <86>May 13 00:59:07 groupadd[2458685]: group added to /etc/group: name=_keytab, GID=498 <86>May 13 00:59:07 groupadd[2458685]: group added to /etc/gshadow: name=_keytab <86>May 13 00:59:07 groupadd[2458685]: new group: name=_keytab, GID=498 <13>May 13 00:59:07 rpmi: libkrb5-1.19.3-alt1 sisyphus+296671.100.1.1 1647339827 installed <13>May 13 00:59:07 rpmi: glib2-devel-2.72.1-alt1 sisyphus+298438.100.1.1 1649945703 installed <13>May 13 00:59:07 rpmi: libfreetype-devel-2.12.1-alt1 sisyphus+299380.100.1.1 1651508331 installed <13>May 13 00:59:07 rpmi: libharfbuzz-devel-4.2.1-alt1 sisyphus+299180.100.1.1 1651137935 installed <13>May 13 00:59:07 rpmi: fontconfig-devel-2.13.1-alt3 sisyphus+297937.100.1.1 1649228296 installed <13>May 13 00:59:07 rpmi: libkmod-29-alt1 sisyphus+288763.100.1.1 1635886490 installed <13>May 13 00:59:07 rpmi: kmod-29-alt1 sisyphus+288763.100.1.1 1635886490 installed <13>May 13 00:59:07 rpmi: dmsetup-1.02.179-alt2 sisyphus+287340.100.1.1 1634383919 installed <86>May 13 00:59:07 groupadd[2459336]: group added to /etc/group: name=tape, GID=497 <86>May 13 00:59:07 groupadd[2459336]: group added to /etc/gshadow: name=tape <86>May 13 00:59:07 groupadd[2459336]: new group: name=tape, GID=497 <86>May 13 00:59:07 groupadd[2459347]: group added to /etc/group: name=dialout, GID=496 <86>May 13 00:59:07 groupadd[2459347]: group added to /etc/gshadow: name=dialout <86>May 13 00:59:07 groupadd[2459347]: new group: name=dialout, GID=496 <86>May 13 00:59:07 groupadd[2459356]: group added to /etc/group: name=input, GID=495 <86>May 13 00:59:07 groupadd[2459356]: group added to /etc/gshadow: name=input <86>May 13 00:59:07 groupadd[2459356]: new group: name=input, GID=495 <86>May 13 00:59:07 groupadd[2459367]: group added to /etc/group: name=video, GID=494 <86>May 13 00:59:07 groupadd[2459367]: group added to /etc/gshadow: name=video <86>May 13 00:59:07 groupadd[2459367]: new group: name=video, GID=494 <86>May 13 00:59:07 groupadd[2459377]: group added to /etc/group: name=render, GID=493 <86>May 13 00:59:07 groupadd[2459377]: group added to /etc/gshadow: name=render <86>May 13 00:59:07 groupadd[2459377]: new group: name=render, GID=493 <13>May 13 00:59:07 rpmi: udev-1:249.12-alt2 sisyphus+299531.100.2.1 1652296661 installed <86>May 13 00:59:07 groupadd[2461038]: group added to /etc/group: name=colord, GID=492 <86>May 13 00:59:07 groupadd[2461038]: group added to /etc/gshadow: name=colord <86>May 13 00:59:07 groupadd[2461038]: new group: name=colord, GID=492 <86>May 13 00:59:07 useradd[2461053]: new user: name=colord, UID=498, GID=492, home=/var/colord, shell=/dev/null <13>May 13 00:59:07 rpmi: colord-1.4.6-alt1 sisyphus+296000.100.1.1 1646050421 installed <13>May 13 00:59:08 rpmi: libgtk+3-3.24.33-alt1 sisyphus+297378.300.3.1 1648630792 installed <13>May 13 00:59:08 rpmi: gtk3-demo-3.24.33-alt1 sisyphus+297378.300.3.1 1648630792 installed <13>May 13 00:59:08 rpmi: libgail3-3.24.33-alt1 sisyphus+297378.300.3.1 1648630792 installed <13>May 13 00:59:08 rpmi: libXft-devel-2.3.4-alt1 sisyphus+284644.500.1.1 1630910476 installed <13>May 13 00:59:08 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+275343.100.2.3 1624578007 installed <86>May 13 00:59:08 groupadd[2462241]: group added to /etc/group: name=sasl, GID=491 <86>May 13 00:59:08 groupadd[2462241]: group added to /etc/gshadow: name=sasl <86>May 13 00:59:08 groupadd[2462241]: new group: name=sasl, GID=491 <13>May 13 00:59:08 rpmi: libsasl2-3-2.1.27-alt2.2 sisyphus+282040.40.2.1 1628929840 installed <13>May 13 00:59:08 rpmi: libldap-2.4.59-alt1 sisyphus+282933.100.1.1 1629124747 installed <13>May 13 00:59:08 rpmi: libcurl-7.83.1-alt1 sisyphus+299767.100.1.1 1652258369 installed <13>May 13 00:59:08 rpmi: python3-module-genshi-0.7.7-alt1 sisyphus+299111.100.1.1 1651061009 installed <13>May 13 00:59:08 rpmi: python3-module-webencodings-0.5.1-alt2 sisyphus+276020.100.1.1 1624812421 installed <13>May 13 00:59:08 rpmi: python3-module-html5lib-1:1.1-alt1 sisyphus+278096.120.5.1 1626086978 installed <13>May 13 00:59:08 rpmi: python3-module-lxml-4.8.0-alt1 sisyphus+296797.100.1.1 1647522217 installed <13>May 13 00:59:08 rpmi: python3-module-cssselect-0.9.1-alt3 sisyphus+270533.2600.6.1 1619684675 installed <13>May 13 00:59:08 rpmi: python3-module-javapackages-1:5.3.0-alt1_15jpp11 sisyphus+278038.500.1.3 1625987751 installed <13>May 13 00:59:08 rpmi: rpm-build-java-1:5.3.0-alt1_15jpp11 sisyphus+278038.500.1.3 1625987751 installed <13>May 13 00:59:08 rpmi: perl-Net-SSLeay-1.92-alt1 sisyphus+293775.100.1.1 1642613337 installed <13>May 13 00:59:08 rpmi: perl-IO-Socket-SSL-2.074-alt1 sisyphus+293129.100.1.1 1641619608 installed <13>May 13 00:59:08 rpmi: perl-Net-HTTPS-6.22-alt1 sisyphus+294185.100.1.1 1643275428 installed <13>May 13 00:59:08 rpmi: perl-LWP-Protocol-https-6.10-alt1 sisyphus+263916.100.1.3 1608937434 installed <13>May 13 00:59:08 rpmi: openssh-common-8.6p1-alt3 sisyphus+294457.100.2.1 1643759038 installed <86>May 13 00:59:08 groupadd[2463036]: group added to /etc/group: name=sshagent, GID=490 <86>May 13 00:59:08 groupadd[2463036]: group added to /etc/gshadow: name=sshagent <86>May 13 00:59:08 groupadd[2463036]: new group: name=sshagent, GID=490 <13>May 13 00:59:08 rpmi: openssh-clients-8.6p1-alt3 sisyphus+294457.100.2.1 1643759038 installed <13>May 13 00:59:08 rpmi: git-core-2.33.3-alt1 sisyphus+299018.100.1.1 1650919481 installed <13>May 13 00:59:08 rpmi: ca-trust-java-0.1.3-alt1 sisyphus+299449.100.1.1 1651660001 installed <13>May 13 00:59:08 rpmi: foomatic-db-engine-4.0.12-alt1 sisyphus+278189.100.1.1 1626076171 installed <13>May 13 00:59:09 rpmi: texlive-2021-alt2_3 sisyphus+298655.100.1.1 1650294737 installed <13>May 13 00:59:18 rpmi: texlive-collection-basic-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed <13>May 13 00:59:20 rpmi: texlive-fonts-sources-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed <13>May 13 00:59:20 rpmi: texlive-texmf-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed <13>May 13 00:59:56 rpmi: texlive-dist-2021-alt1_4 sisyphus+285425.100.1.1 1631913341 installed <13>May 13 00:59:56 rpmi: java-stub-javadoc-0.1-alt1 sisyphus+276859.100.1.1 1625245070 installed <13>May 13 00:59:56 rpmi: alsa-ucm-conf-1.2.6.3-alt2 sisyphus+298070.100.2.1 1649686435 installed <13>May 13 00:59:56 rpmi: alsa-topology-conf-1.2.5.1-alt1 sisyphus+274777.100.1.1 1624089141 installed <13>May 13 00:59:56 rpmi: libalsa-1:1.2.6.1-alt1 sisyphus+291831.100.1.1 1639213772 installed <13>May 13 00:59:59 rpmi: java-11-openjdk-headless-0:11.0.14.1.1-alt2_1jpp11 sisyphus+298664.100.1.1 1650296285 installed <13>May 13 00:59:59 rpmi: java-11-openjdk-0:11.0.14.1.1-alt2_1jpp11 sisyphus+298664.100.1.1 1650296285 installed <13>May 13 00:59:59 rpmi: java-11-openjdk-devel-0:11.0.14.1.1-alt2_1jpp11 sisyphus+298664.100.1.1 1650296285 installed <13>May 13 00:59:59 rpmi: java-devel-default-9-alt1 sisyphus+285101.100.1.1 1631518060 installed <13>May 13 00:59:59 rpmi: libcurl-devel-7.83.1-alt1 sisyphus+299767.100.1.1 1652258369 installed <13>May 13 00:59:59 rpmi: libpango-devel-1.50.7-alt1 sisyphus+298455.100.1.1 1649965703 installed <13>May 13 00:59:59 rpmi: tk-devel-8.6.12-alt1 sisyphus+289207.200.1.1 1636394135 installed <13>May 13 00:59:59 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+278818.100.1.3 1626263295 installed <13>May 13 00:59:59 rpmi: gcc-c++-11-alt1 sisyphus+285602.400.1.1 1632238564 installed <13>May 13 00:59:59 rpmi: gcc-fortran-11-alt1 sisyphus+285602.400.1.1 1632238564 installed <13>May 13 00:59:59 rpmi: libtiff-devel-4.3.0-alt2 sisyphus+290923.300.4.1 1638162792 installed <13>May 13 00:59:59 rpmi: makeinfo-6.7-alt1 sisyphus+278099.4400.1.1 1626031435 installed <13>May 13 00:59:59 rpmi: libgomp-devel-11-alt1 sisyphus+285602.400.1.1 1632238564 installed <13>May 13 00:59:59 rpmi: liblapack-devel-1:3.8.0-alt7 sisyphus+293726.100.1.1 1642544497 installed <13>May 13 00:59:59 rpmi: libtre-devel-0.8.0-alt2.2 sisyphus+278356.100.1.1 1626091408 installed <13>May 13 00:59:59 rpmi: texi2dvi-6.7-alt1 sisyphus+278099.4400.1.1 1626031435 installed <13>May 13 00:59:59 rpmi: libjpeg-devel-2:2.1.2-alt1 sisyphus+294623.100.2.1 1643889731 installed <13>May 13 01:00:00 rpmi: libreadline-devel-7.0.3-alt4 sisyphus+283725.100.1.2 1629849376 installed <13>May 13 01:00:00 rpmi: libpcre2-devel-10.40-alt1 sisyphus+298584.100.1.1 1650130405 installed <13>May 13 01:00:00 rpmi: liblzma-devel-5.2.5-alt3.1 sisyphus+291400.100.1.1 1638634809 installed <13>May 13 01:00:00 rpmi: bzlib-devel-1:1.0.8-alt2 sisyphus+283723.100.1.1 1629847653 installed egrep: warning: egrep is obsolescent; using grep -E egrep: warning: egrep is obsolescent; using grep -E 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-4.1.3-alt1.nosrc.rpm (w1.gzdio) Installing R-base-4.1.3-alt1.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.88825 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-4.1.3 + echo 'Source #0 (R-4.1.3.tar):' Source #0 (R-4.1.3.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-4.1.3.tar + cd R-4.1.3 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-4.1.3-alt1.patch):' Patch #0 (R-4.1.3-alt1.patch): + /usr/bin/patch -p1 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/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 + 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.88825 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.1.3 + 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 --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 --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-4.1' 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... /bin/pwd checking whether builddir is srcdir... yes checking whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /bin/install -c checking for sed... /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... /bin/gzip checking for bzip2... /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... /bin/grep checking for egrep... /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) /bin/sed checking for fgrep... /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... /bin/dd checking how to truncate binary pipes... /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... 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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 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(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 -j16 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-4.1.3/src/scripts' creating src/scripts/R.fe make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/scripts' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/scripts' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/include' mkdir -p -- ../../include make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/include' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/include/R_ext' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' making xdr_float.d from xdr_float.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' making xdr_mem.d from xdr_mem.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' making xdr.d from xdr.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' making xdr_stdio.d from xdr_stdio.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making regerror.d from regerror.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making regcomp.d from regcomp.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-ast.d from tre-ast.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making regexec.d from regexec.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-compile.d from tre-compile.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-stack.d from tre-stack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-match-parallel.d from tre-match-parallel.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-match-approx.d from tre-match-approx.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-match-backtrack.d from tre-match-backtrack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making xmalloc.d from xmalloc.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-parse.d from tre-parse.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' making tre-mem.d from tre-mem.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/extra/tre' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making interv.d from interv.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making integrate.d from integrate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making maxcol.d from maxcol.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making pretty.d from pretty.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making uncmin.d from uncmin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' making optim.d from optim.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/appl' #@make install-Linpack make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making mlutils.d from mlutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making d1mach.d from d1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making fmax2.d from fmax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making fmin2.d from fmin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making fprec.d from fprec.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making i1mach.d from i1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making fsign.d from fsign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making sign.d from sign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making fround.d from fround.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making ftrunc.d from ftrunc.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making imax2.d from imax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making imin2.d from imin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making chebyshev.d from chebyshev.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making log1p.d from log1p.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making lgammacor.d from lgammacor.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making gammalims.d from gammalims.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making stirlerr.d from stirlerr.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making bd0.d from bd0.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making gamma.d from gamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making lgamma.d from lgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making gamma_cody.d from gamma_cody.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making beta.d from beta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making lbeta.d from lbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making cospi.d from cospi.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making bessel_i.d from bessel_i.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making polygamma.d from polygamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making bessel_j.d from bessel_j.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making bessel_k.d from bessel_k.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making choose.d from choose.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making bessel_y.d from bessel_y.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making snorm.d from snorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making sexp.d from sexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dgamma.d from dgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qgamma.d from qgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pgamma.d from pgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rgamma.d from rgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dbeta.d from dbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pbeta.d from pbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qbeta.d from qbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rbeta.d from rbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dunif.d from dunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making punif.d from punif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qunif.d from qunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making runif.d from runif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnorm.d from pnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnorm.d from dnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnorm.d from qnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rnorm.d from rnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making plnorm.d from plnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dlnorm.d from dlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qlnorm.d from qlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rlnorm.d from rlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making df.d from df.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pf.d from pf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qf.d from qf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rf.d from rf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnf.d from dnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dt.d from dt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pt.d from pt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rt.d from rt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qt.d from qt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnt.d from dnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dchisq.d from dchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pchisq.d from pchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qchisq.d from qchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rchisq.d from rchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rnchisq.d from rnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dbinom.d from dbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pbinom.d from pbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qbinom.d from qbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dcauchy.d from dcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pcauchy.d from pcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qcauchy.d from qcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rbinom.d from rbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rmultinom.d from rmultinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rcauchy.d from rcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dexp.d from dexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pexp.d from pexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qexp.d from qexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rexp.d from rexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pgeom.d from pgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dgeom.d from dgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qgeom.d from qgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dhyper.d from dhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rgeom.d from rgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making phyper.d from phyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qhyper.d from qhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnbinom.d from dnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rhyper.d from rhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnbinom.d from pnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnbinom.d from qnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dpois.d from dpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnbinom_mu.d from qnbinom_mu.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rnbinom.d from rnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making ppois.d from ppois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rpois.d from rpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pweibull.d from pweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qpois.d from qpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dweibull.d from dweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qweibull.d from qweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rweibull.d from rweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making plogis.d from plogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dlogis.d from dlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making rlogis.d from rlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qlogis.d from qlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnchisq.d from pnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnchisq.d from dnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnchisq.d from qnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making dnbeta.d from dnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnbeta.d from pnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnbeta.d from qnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnf.d from pnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making pnt.d from pnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnf.d from qnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qtukey.d from qtukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making qnt.d from qnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making ptukey.d from ptukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making toms708.d from toms708.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making signrank.d from signrank.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' making wilcox.d from wilcox.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making Rembedded.d from Rembedded.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making dynload.d from dynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making sys-unix.d from sys-unix.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making system.d from system.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making sys-std.d from sys-std.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' making X11.d from X11.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making CommandLineArgs.d from CommandLineArgs.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making Renviron.d from Renviron.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making RNG.d from RNG.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making Rdynload.d from Rdynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making agrep.d from agrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making altrep.d from altrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making arithmetic.d from arithmetic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making altclasses.d from altclasses.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making array.d from array.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making apply.d from apply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making character.d from character.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making attrib.d from attrib.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making bind.d from bind.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making builtin.d from builtin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making coerce.d from coerce.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making colors.d from colors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making complex.d from complex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making connections.d from connections.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making context.d from context.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making dcf.d from dcf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making cum.d from cum.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making datetime.d from datetime.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making debug.d from debug.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making deparse.d from deparse.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making devices.d from devices.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making dotcode.d from dotcode.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making dounzip.d from dounzip.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making dstruct.d from dstruct.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making duplicate.d from duplicate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making edit.d from edit.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making engine.d from engine.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making errors.d from errors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making envir.d from envir.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making eval.d from eval.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making gram-ex.d from gram-ex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making gevents.d from gevents.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making format.d from format.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making grep.d from grep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making identical.d from identical.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making inlined.d from inlined.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making gram.d from gram.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making graphics.d from graphics.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making inspect.d from inspect.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making internet.d from internet.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making iosupport.d from iosupport.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making lapack.d from lapack.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making list.d from list.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making localecharset.d from localecharset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making mapply.d from mapply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making logic.d from logic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making main.d from main.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making match.d from match.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making memory.d from memory.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making names.d from names.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making patterns.d from patterns.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making options.d from options.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making objects.d from objects.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making paste.d from paste.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making plot.d from plot.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making printarray.d from printarray.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making print.d from print.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making plotmath.d from plotmath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making plot3d.d from plot3d.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making platform.d from platform.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making printvector.d from printvector.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making printutils.d from printutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making random.d from random.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making qsort.d from qsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making raw.d from raw.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making rlocale.d from rlocale.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making radixsort.d from radixsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making registration.d from registration.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making relop.d from relop.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making saveload.d from saveload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making seq.d from seq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making scan.d from scan.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making serialize.d from serialize.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making sort.d from sort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making split.d from split.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making sprintf.d from sprintf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making source.d from source.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making startup.d from startup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making subassign.d from subassign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making subscript.d from subscript.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making summary.d from summary.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making subset.d from subset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making sysutils.d from sysutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making times.d from times.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making version.d from version.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making g_cntrlify.d from g_cntrlify.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making Rmain.d from Rmain.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making unique.d from unique.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making g_alab_her.d from g_alab_her.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making g_fontdb.d from g_fontdb.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making g_her_glyph.d from g_her_glyph.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making alloca.d from alloca.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making util.d from util.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making strdup.d from strdup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making strncasecmp.d from strncasecmp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' making mkdtemp.d from mkdtemp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 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 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-4.1.3/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.1.3/bin/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.1.3/lib make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making Rhttpd.d from Rhttpd.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making Rsock.d from Rsock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/lapack' making Lapack.d from Lapack.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/lapack' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making libcurl.d from libcurl.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making nanoftp.d from nanoftp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' making rbitmap.d from rbitmap.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making nanohttp.d from nanohttp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' making rotated.d from rotated.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making sock.d from sock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making internet.d from internet.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' making sockconn.d from sockconn.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' making devX11.d from devX11.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 nanohttp.c -o nanohttp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -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-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -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-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 nanoftp.c -o nanoftp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -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-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/libpng16 -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-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/lapack' mkdir -p -- /usr/src/RPM/BUILD/R-4.1.3/modules make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/modules/internet' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library' mkdir -p -- ../../library make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/profile' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/translations' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' building package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making text.d from text.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making md5.d from md5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making Rmd5.d from Rmd5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making install.d from install.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making getfmts.d from getfmts.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making signals.d from signals.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making http.d from http.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making gramLatex.d from gramLatex.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making gramRd.d from gramRd.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' making pdscan.d from pdscan.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/tools/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/compiler' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' mkdir -p -- ../../../library/utils/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making io.d from io.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making size.d from size.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making sock.d from sock.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/utils' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making chull.d from chull.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making axis_scales.d from axis_scales.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making devices.d from devices.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making clippath.d from clippath.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making colors.d from colors.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making mask.d from mask.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making patterns.d from patterns.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making devCairo.d from devCairo.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making devPicTeX.d from devPicTeX.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making devQuartz.d from devQuartz.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' making devPS.d from devPS.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src' make[7]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[7]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices/src/cairo' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grDevices' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making par.d from par.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making plot.d from plot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making base.d from base.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making plot3d.d from plot3d.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making graphics.d from graphics.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' making stem.d from stem.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/graphics/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/graphics' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making kmeans.d from kmeans.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making ansari.d from ansari.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making d2x2xk.d from d2x2xk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making bandwidths.d from bandwidths.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making chisqsim.d from chisqsim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making fexact.d from fexact.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making kendall.d from kendall.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making line.d from line.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making ks.d from ks.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making smooth.d from smooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making prho.d from prho.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making swilk.d from swilk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making loessc.d from loessc.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making isoreg.d from isoreg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making Srunmed.d from Srunmed.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making monoSpl.d from monoSpl.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making dblcen.d from dblcen.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making distance.d from distance.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making hclust-utils.d from hclust-utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making ksmooth.d from ksmooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making nls.d from nls.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making rWishart.d from rWishart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making HoltWinters.d from HoltWinters.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making PPsum.d from PPsum.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making filter.d from filter.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making mAR.d from mAR.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making pacf.d from pacf.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making arima.d from arima.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making family.d from family.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making starma.d from starma.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making burg.d from burg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making port.d from port.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making sbart.d from sbart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making approx.d from approx.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making loglin.d from loglin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making massdist.d from massdist.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making lowess.d from lowess.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making lm.d from lm.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making complete_cases.d from complete_cases.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making deriv.d from deriv.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making fft.d from fft.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making cov.d from cov.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making fourier.d from fourier.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making model.d from model.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making optim.d from optim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making random.d from random.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making optimize.d from optimize.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making integrate.d from integrate.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making distn.d from distn.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making zeroin.d from zeroin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making rcont.d from rcont.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' making influence.d from influence.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 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'/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe 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-DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -flto=auto -fno-strict-aliasing -c optimize.c -o optimize.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 random.c -o random.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 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-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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/stats/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/stats' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making slot.d from slot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making class_support.d from class_support.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making tests.d from tests.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making methods_list_dispatch.d from methods_list_dispatch.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/methods/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/methods' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making gpar.d from gpar.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making clippath.d from clippath.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making grid.d from grid.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making just.d from just.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making layout.d from layout.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making mask.d from mask.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making matrix.d from matrix.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making register.d from register.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making unit.d from unit.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making viewport.d from viewport.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making state.d from state.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' making util.d from util.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/grid' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/splines/src' make[5]: Entering directory 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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 browseURL html browseVignettes html bug.report html capture.output html changedFiles html charClass html choose.dir html choose.files html chooseBioCmirror html chooseCRANmirror html citEntry html citation html cite html clipboard html close.socket html combn html compareVersion html contrib.url html count.fields html create.post html data html dataentry html debugcall html debugger html demo html download.file html download.packages html edit html edit.data.frame html example html file.edit html filetest html findLineNum html fix html flush.console html format html getAnywhere html getFromNamespace html getParseData html getS3method html getWindowsHandle html getWindowsHandles html glob2rx html globalVariables html hasName html head html help html help.request html help.search html help.start html hsearch-utils html install.packages html installed.packages html isS3method html isS3stdGen html localeToCharset html ls_str html maintainer html make.packages.html html make.socket html memory.size html menu html methods html mirrorAdmin html modifyList html news html nsl html object.size html package.skeleton html packageDescription html packageName html packageStatus html page html person html process.events html prompt html promptData html promptPackage html rcompgen html read.DIF html read.fortran html read.fwf html read.socket html read.table html readRegistry html recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories html setWindowTitle html shortPathName html sourceutils html stack html str html strcapture html summaryRprof html tar html toLatex html txtProgressBar html type.convert html untar html unzip html update.packages html url.show html utils-defunct html utils-deprecated html utils-package html vignette html warnErrList html winDialog html winMenus html winProgressBar html winextras html write.table html zip html 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 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 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.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.text html grid.xaxis html grid.xspline html grid.yaxis 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 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-4.1.3/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package lattice make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package MASS make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package codetools make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package foreign make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package KernSmooth make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package rpart make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package nnet make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package spatial make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' make[3]: Entering directory '/usr/src/tmp/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' make[3]: Entering directory '/usr/src/tmp/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' make[3]: Entering directory '/usr/src/tmp/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmphu6oCC/R.INSTALL2d47a940b9324e/spatial/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpzHI12b/R.INSTALL2d477d12ea061e/nnet/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpzHI12b/R.INSTALL2d477d12ea061e/nnet/src' make[3]: Entering directory '/usr/src/tmp/RtmpzHI12b/R.INSTALL2d477d12ea061e/nnet/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpzHI12b/R.INSTALL2d477d12ea061e/nnet/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/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/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmptZaFyH/R.INSTALL2d477764cb0018/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpIHdRjT/R.INSTALL2d47527d760ae/foreign/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpIGyw0S/R.INSTALL2d47a61e6d8d33/rpart/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpiF55TB/R.INSTALL2d46f95cb4ecce/MASS/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package cluster make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package class make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpH8Doku/R.INSTALL2d4f761a8d60cc/class/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpH8Doku/R.INSTALL2d4f761a8d60cc/class/src' make[3]: Entering directory '/usr/src/tmp/RtmpH8Doku/R.INSTALL2d4f761a8d60cc/class/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpH8Doku/R.INSTALL2d4f761a8d60cc/class/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpJEk9uQ/R.INSTALL2d46fd7eb1cbcb/lattice/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package Matrix make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package nlme make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpPQjKrH/R.INSTALL2d4f63288835c2/cluster/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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 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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmptLEDc2/R.INSTALL2d51ca24aa617/nlme/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' ( cd Lib ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 make[3]: Leaving directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' ( cd Source ; make clean ) ( cd Source ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-4.1.3/etc/Makeconf" -f Makefile ) make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 */ | ~~~~~~~^~~~~~~~ In file included from ../Core/cholmod_add.c:27: ../Include/cholmod_core.h:1583:5: note: previously declared as 'double *' 1583 | double *, int, int, cholmod_common *) ; | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 */ | ~~~~~~~^~~~~~ In file included from ../Modify/cholmod_rowadd.c:24: ../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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 */ | ~~~~~~~^~~~~~ In file included from ../Modify/cholmod_rowdel.c:25: ../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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 */ | ~~~~~~~^~~~~~~~ In file included from ../MatrixOps/cholmod_sdmult.c:36: ../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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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' */ | ~~~~~~~^~~~~~~~ In file included from ../Cholesky/cholmod_rowfac.c:103: ../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' */ | ~~~~~~~^~~~~~~~ In file included from ../Cholesky/cholmod_rowfac.c:103: ../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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/CHOLMOD/Lib' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.1.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/COLAMD/Source' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.1.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/AMD/Source' make[4]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/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/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src/SuiteSparse_config' make[3]: Entering directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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 CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpVaS126/R.INSTALL2d51b710b55a79/Matrix/src' installing to /usr/src/RPM/BUILD/R-4.1.3/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading 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 'diag' from package 'base' in package 'Matrix' 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' 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' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" 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.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': 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.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': 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 '"matrix.csc","Matrix"': no definition for class "matrix.csc" 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' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" 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' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" 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' ** 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 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 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 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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package survival make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package mgcv make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpkcOd70/R.INSTALL2db1e135580786/survival/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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 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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' begin installing recommended package boot make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 make[3]: Leaving directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.1.3/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 mat.c: In function 'Rlanczos': mat.c:3623:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 3623 | for (i=0;i< *n+1;i++) if (q[i]) FREE(q[i]);FREE(q); | ^~~ In file included from mat.c:58: mgcv.h:62:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 62 | #define FREE R_chk_free | ^~~~~~~~~~ mat.c:3623:46: note: in expansion of macro 'FREE' 3623 | for (i=0;i< *n+1;i++) if (q[i]) FREE(q[i]);FREE(q); | ^~~~ make[3]: Leaving directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.1.3/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 qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/usr/src/RPM/BUILD/R-4.1.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpSyzk3B/R.INSTALL2db1df389edf5d/mgcv/src' installing to /usr/src/RPM/BUILD/R-4.1.3/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 blas.thread.test html bug.reports.mgcv html cSplineDes html chol.down html choose.k html columb html concurvity html coxph html coxpht html dDeta html exclude.too.far html extract.lme.cov html family.mgcv html fix.family.link html fixDependence html formXtViX html formula.gam html fs.test html full.score html gam html gam.check html gam.control html gam.convergence html gam.fit html gam.fit3 html gam.fit5.post.proc html gam.mh html gam.models html gam.outer html gam.reparam html gam.scale html gam.selection html gam.side html gam.vcomp html gam2objective html gamObject html gamSim html gamlss.etamu html gamlss.gH html gamm html gammals html gaulss html get.var html gevlss html ginla html gumbls html identifiability html in.out html inSide html influence.gam html initial.sp html interpret.gam html jagam html k.check html ldTweedie html ldetS html linear.functional.terms html logLik.gam html ls.size html magic html magic.post.proc html mgcv-FAQ html mgcv-package html mgcv-parallel html mini.roots html missing.data html model.matrix.gam html mono.con html mroot html multinom html mvn html negbin html new.name html notExp html notExp2 html null.space.dimension html ocat html one.se.rule html pcls html pdIdnot html pdTens html pen.edf html place.knots html plot.gam html polys.plot html predict.bam html predict.gam html print.gam html psum.chisq html qq.gam html rTweedie html random.effects html residuals.gam html rig html rmvn html s html scat html sdiag html shash html single.index html slanczos html smooth.construct html smooth.construct.ad.smooth.spec html smooth.construct.bs.smooth.spec html smooth.construct.cr.smooth.spec html smooth.construct.ds.smooth.spec html smooth.construct.fs.smooth.spec html smooth.construct.gp.smooth.spec html smooth.construct.mrf.smooth.spec html smooth.construct.ps.smooth.spec html smooth.construct.re.smooth.spec html smooth.construct.so.smooth.spec html smooth.construct.sos.smooth.spec html smooth.construct.t2.smooth.spec html smooth.construct.tensor.smooth.spec html smooth.construct.tp.smooth.spec html smooth.info html smooth.terms html smooth2random html smoothCon html sp.vcov html spasm.construct html step.gam html summary.gam html t2 html te html tensor.prod.model.matrix html totalPenaltySpace html trichol html trind.generator html twlss html uniquecombs html vcov.gam html vis.gam html ziP html ziplss html ** building package indices ** testing if installed package can be loaded * DONE (mgcv) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src/library/Recommended' + make -j16 pdf info make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' creating doc/manual/version.tex make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' collecting LaTeX docs for package 'stats4' ... 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R-exts.texi make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-data.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/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, 265842 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-data.vrs [29]) (Concept index) [30] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.cps) [31] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 305725 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-data.vrs [29]) (Concept index) [30] (/usr/src/RPM/BUILD/R-4.1.3/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. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' collecting LaTeX docs for package 'nlme' ... Converting parsed Rd's to LaTeX ............................ make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' collecting LaTeX docs for package 'mgcv' ... Converting parsed Rd's to LaTeX ............... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-FAQ.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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 290--312 @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 639--642 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 639--642 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 639--642 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 666--671 @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 1534--1537 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1534--1537 @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 3137--3151 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3288--3296 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 356692 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 290--312 @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 639--642 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 639--642 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 639--642 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 666--671 @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 1534--1537 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1534--1537 @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 3137--3151 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3288--3296 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 373148 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] Underfull \hbox (badness 10000) in paragraph at lines 290--312 @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 639--642 []@textrm Robert Gen-tle-man (2008), ``R Pro-gram-ming for Bioin-for-mat-ics'' . Underfull \hbox (badness 7379) in paragraph at lines 639--642 @textrm Chap-man & Hall/CRC, Boca Ra-ton, FL, ISBN 978-1-420-06367-7, Underfull \hbox (badness 10000) in paragraph at lines 639--642 [][]@texttt https:// master. bioconductor. org/ help/ publications/ book s/ [7] Underfull \hbox (badness 10000) in paragraph at lines 666--671 @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 1534--1537 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1534--1537 @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 3137--3151 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3288--3296 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 373142 bytes). Transcript written on R-FAQ.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-admin.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/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 1500--1504 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make Chapter 4 [17] [18] [19] Chapter 5 [20] Chapter 6 [21] [22] [23] Overfull \hbox (16.31242pt too wide) in paragraph at lines 2106--2106 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] Overfull \hbox (56.55324pt too wide) in paragraph at lines 2319--2319 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34] [35] Appendix A [36] [37] [38] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3289--3289 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [39] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] [59] Overfull \hbox (112.72658pt too wide) in paragraph at lines 5042--5042 []@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 5044--5044 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] [60] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5128--5128 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] Overfull \hbox (17.16873pt too wide) in paragraph at lines 5178--5179 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [61] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5244--5244 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5350--5350 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [63] [64] [65] [66] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5667--5667 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5669--5675 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5702--5702 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [67] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5810--5810 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [68] [69] Overfull \hbox (119.7888pt too wide) in paragraph at lines 6030--6030 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [70] [71] (Function and variable index) [72] No file R-admin.vrs. (Concept index) [73] No file R-admin.cps. (Environment variable index) [74] No file R-admin.ens. [75] ) (see the transcript file for additional information) Output written on R-admin.pdf (78 pages, 478494 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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 1500--1504 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make Chapter 4 [17] [18] [19] Chapter 5 [20] Chapter 6 [21] [22] [23] Overfull \hbox (16.31242pt too wide) in paragraph at lines 2106--2106 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] Overfull \hbox (56.55324pt too wide) in paragraph at lines 2319--2319 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34] [35] Appendix A [36] [37] [38] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3289--3289 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [39] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] [59] Overfull \hbox (112.72658pt too wide) in paragraph at lines 5042--5042 []@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 5044--5044 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5128--5128 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [60] Overfull \hbox (17.16873pt too wide) in paragraph at lines 5178--5179 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [61] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5244--5244 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5350--5350 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [63] [64] [65] [66] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5667--5667 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5669--5675 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5702--5702 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [67] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5810--5810 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [68] [69] Overfull \hbox (119.7888pt too wide) in paragraph at lines 6030--6030 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [70] [71] (Function and variable index) [72] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.vrs) (Concept index) [73] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.cps) (Environment variable index) [74] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.ens) [75] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (80 pages, 523506 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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 1500--1504 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make Chapter 4 [17] [18] [19] Chapter 5 [20] Chapter 6 [21] [22] [23] Overfull \hbox (16.31242pt too wide) in paragraph at lines 2106--2106 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] Overfull \hbox (56.55324pt too wide) in paragraph at lines 2319--2319 []@texttt ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm 64" CXXFLAGS=-O2[] [26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34] [35] Appendix A [36] [37] [38] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3289--3289 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [39] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] [59] Overfull \hbox (112.72658pt too wide) in paragraph at lines 5042--5042 []@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 5044--5044 []@texttt curl -OL https://mac.r-project.org/bin/darwin17/x86_64/xz-5.2.5-darw in.17-x86_64.tar.xz[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5128--5128 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [60] Overfull \hbox (17.16873pt too wide) in paragraph at lines 5178--5179 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][][]@smallrm .| [61] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5244--5244 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [62] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5350--5350 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [63] [64] [65] [66] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5667--5667 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5669--5675 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5669--5675 @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 5702--5702 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [67] Overfull \hbox (51.1502pt too wide) in paragraph at lines 5810--5810 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][][]| [68] [69] Overfull \hbox (119.7888pt too wide) in paragraph at lines 6030--6030 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [70] [71] (Function and variable index) [72] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.vrs) (Concept index) [73] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.cps) (Environment variable index) [74] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-admin.ens) [75] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (80 pages, 523508 bytes). Transcript written on R-admin.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' collecting LaTeX docs for package 'base' ... Converting parsed Rd's to LaTeX ........................................... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-ints.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1468--1468 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1469--1469 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1470--1470 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1471--1471 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [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] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3654--3663 @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 3654--3663 @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 3654--3663 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] Underfull \hbox (badness 10000) in paragraph at lines 3841--3845 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [46] Underfull \hbox (badness 10000) in paragraph at lines 3875--3880 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10 [58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index) [62] No file R-ints.vrs. (Concept index) [63] No file R-ints.cps. [64] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on R-ints.pdf (67 pages, 404328 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1468--1468 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1469--1469 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1470--1470 [] @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 1471--1471 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [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] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3654--3663 @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 3654--3663 @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 3654--3663 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] Underfull \hbox (badness 10000) in paragraph at lines 3841--3845 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [46] Underfull \hbox (badness 10000) in paragraph at lines 3875--3880 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10 [58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index) [62] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.vrs [63]) (Concept index) [64] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.cps) [65] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 455371 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1468--1468 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1469--1469 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1470--1470 [] @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 1471--1471 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [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] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3654--3663 @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 3654--3663 @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 3654--3663 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] Underfull \hbox (badness 10000) in paragraph at lines 3841--3845 []@textrm If true, make use of the [][]@textbf codetools @textrm (@texttt http s:// CRAN. R-project. org/ [46] Underfull \hbox (badness 10000) in paragraph at lines 3875--3880 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10 [58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index) [62] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.vrs [63]) (Concept index) [64] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-ints.cps) [65] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 455367 bytes). Transcript written on R-ints.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-exts.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/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 494--497 []@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 1522--1522 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1523--1523 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1622--1632 @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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2561--2561 []@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 2563--2563 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 2804--2807 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [32] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2876--2876 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2899--2905 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4549--4549 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4568--4568 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [52] [53] [54] [55] [56] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5002--5002 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5004--5004 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5005--5005 [] @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 5020--5020 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [57] Underfull \hbox (badness 7558) in paragraph at lines 5079--5083 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [58] [59] [60] [61] [62] Underfull \hbox (badness 10000) in paragraph at lines 5533--5536 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [63] [64] [65] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5754--5754 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Underfull \hbox (badness 10000) in paragraph at lines 5845--5846 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 10000) in paragraph at lines 6302--6312 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 7354--7361 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [85] Underfull \hbox (badness 10000) in paragraph at lines 7533--7539 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [86] [87] [88] [89] Chapter 3 [90] [91] [92] [93] [94] [95] [96] [97] Chapter 4 [98] [99] [100] [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 8828--8837 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 9093--9105 @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 9109--9110 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [106] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9247--9247 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [107] Underfull \hbox (badness 10000) in paragraph at lines 9280--9282 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [108] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9426--9426 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [109] [110] [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 9793--9795 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [114] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9850--9850 []@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 9869--9869 []@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 9880--9880 []@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 9910--9910 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10757--10757 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [125] [126] [127] [128] [129] [130] [131] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11334--11334 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [132] [133] [134] [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12228--12230 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13275--13275 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [154] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13373--13373 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [155] Chapter 6 [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 [][]@texttt https:// software. intel. com/ content/ www/ us/ en/ develo p/ documentation/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [164] [165] [166] [167] [168] [169] [170] [171] [172] Warning: unbalanced parentheses in @def... [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15379--15385 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ [178] Chapter 7 [179] [180] Chapter 8 [181] [182] [183] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15790--15790 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [184] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15848--15848 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 16351--16358 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [191] Underfull \hbox (badness 10000) in paragraph at lines 16474--16478 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or [192] (Function and variable index) [193] No file R-exts.vrs. (Concept index) [194] No file R-exts.cps. [195] ) (see the transcript file for additional information) Output written on R-exts.pdf (198 pages, 936230 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.1.3/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 494--497 []@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 1522--1522 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1523--1523 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1622--1632 @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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2561--2561 []@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 2563--2563 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 2804--2807 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [32] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2876--2876 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2899--2905 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4549--4549 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4568--4568 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [52] [53] [54] [55] [56] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5002--5002 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5004--5004 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5005--5005 [] @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 5020--5020 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [57] Underfull \hbox (badness 7558) in paragraph at lines 5079--5083 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [58] [59] [60] [61] [62] Underfull \hbox (badness 10000) in paragraph at lines 5533--5536 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [63] [64] [65] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5754--5754 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Underfull \hbox (badness 10000) in paragraph at lines 5845--5846 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 10000) in paragraph at lines 6302--6312 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 7354--7361 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [85] Underfull \hbox (badness 10000) in paragraph at lines 7533--7539 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [86] [87] [88] [89] Chapter 3 [90] [91] [92] [93] [94] [95] [96] [97] Chapter 4 [98] [99] [100] [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 8828--8837 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 9093--9105 @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 9109--9110 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [106] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9247--9247 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [107] Underfull \hbox (badness 10000) in paragraph at lines 9280--9282 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [108] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9426--9426 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [109] [110] [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 9793--9795 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [114] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9850--9850 []@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 9869--9869 []@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 9880--9880 []@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 9910--9910 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10757--10757 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [125] [126] [127] [128] [129] [130] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11334--11334 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12228--12230 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13275--13275 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [154] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13373--13373 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [155] Chapter 6 [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 [][]@texttt https:// software. intel. com/ content/ www/ us/ en/ develo p/ documentation/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [164] [165] [166] [167] [168] [169] [170] [171] [172] Warning: unbalanced parentheses in @def... [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15379--15385 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ [178] Chapter 7 [179] [180] Chapter 8 [181] [182] [183] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15790--15790 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [184] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15848--15848 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 16351--16358 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [191] Underfull \hbox (badness 10000) in paragraph at lines 16474--16478 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or [192] (Function and variable index) [193] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.vrs [194] [195] [196]) (Concept index) [197] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.cps [198]) [199] ) (see the transcript file for additional information) Output written on R-exts.pdf (205 pages, 1000932 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.1.3/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 494--497 []@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 1522--1522 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 1523--1523 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] [18] Underfull \hbox (badness 10000) in paragraph at lines 1622--1632 @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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2561--2561 []@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 2563--2563 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 2804--2807 [][][]@smallrm Some changes are linked from [][]@smalltt https:// isocpp. org / std/ standing-documents/ [32] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2876--2876 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] Underfull \hbox (badness 10000) in paragraph at lines 2899--2905 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][][] @smallrm or [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4549--4549 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4568--4568 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [52] [53] [54] [55] [56] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5002--5002 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 5004--5004 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 5005--5005 [] @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 5020--5020 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [57] Underfull \hbox (badness 7558) in paragraph at lines 5079--5083 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [58] [59] [60] [61] [62] Underfull \hbox (badness 10000) in paragraph at lines 5533--5536 @texttt gcc/ C-Extensions. html[][][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [63] [64] [65] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5754--5754 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] Underfull \hbox (badness 10000) in paragraph at lines 5845--5846 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [66] [67] [68] [69] [70] [71] Underfull \hbox (badness 10000) in paragraph at lines 6302--6312 []@textrm R-Forge ([][]R-Forge.r-project.org (@texttt https:// R-Forge. r-pro ject. org[]@textrm )[][]) and RForge Chapter 2 [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 7354--7361 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [85] Underfull \hbox (badness 10000) in paragraph at lines 7533--7539 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [86] [87] [88] [89] Chapter 3 [90] [91] [92] [93] [94] [95] [96] [97] Chapter 4 [98] [99] [100] [101] [102] Underfull \hbox (badness 10000) in paragraph at lines 8828--8837 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [103] [104] [105] Underfull \hbox (badness 10000) in paragraph at lines 9093--9105 @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 9109--9110 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [106] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9247--9247 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [107] Underfull \hbox (badness 10000) in paragraph at lines 9280--9282 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [108] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9426--9426 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [109] [110] [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 9793--9795 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][][]@smallrm : [114] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9850--9850 []@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 9869--9869 []@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 9880--9880 []@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 9910--9910 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10757--10757 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [125] [126] [127] [128] [129] [130] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11334--11334 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 10000) in paragraph at lines 12228--12230 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] Overfull \hbox (22.06111pt too wide) in paragraph at lines 13275--13275 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [154] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13373--13373 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [155] Chapter 6 [156] [157] [158] [159] [160] [161] [162] [163] Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 []@textrm Passing a variable-length string from C to For-tran is trick-ier, but Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 [][]@texttt https:// software. intel. com/ content/ www/ us/ en/ develo p/ documentation/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt fortran-compiler-oneapi-dev-guide-and-reference/ top/ compiler-refere nce/ Underfull \hbox (badness 10000) in paragraph at lines 14128--14133 @texttt mixed-language-programming/ standard-tools-for-interoperability/ bind . html[][][] [164] [165] [166] [167] [168] [169] [170] [171] [172] Warning: unbalanced parentheses in @def... [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15379--15385 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ [178] Chapter 7 [179] [180] Chapter 8 [181] [182] [183] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15790--15790 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [184] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15848--15848 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [185] [186] [187] [188] [189] [190] Underfull \hbox (badness 10000) in paragraph at lines 16351--16358 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [191] Underfull \hbox (badness 10000) in paragraph at lines 16474--16478 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or [192] (Function and variable index) [193] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.vrs [194] [195] [196]) (Concept index) [197] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-exts.cps [198]) [199] ) (see the transcript file for additional information) Output written on R-exts.pdf (205 pages, 1000930 bytes). Transcript written on R-exts.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-lang.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/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, 326937 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-lang.vrs [52]) (Concept Index) [53] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 375623 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-lang.vrs [52]) (Concept Index) [53] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-lang.cps) Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 375612 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi egrep: warning: egrep is obsolescent; using grep -E @setfilename R-intro.info This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/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] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6648--6653 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6648--6653 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] No file R-intro.vrs. Appendix E [94] No file R-intro.cps. Appendix F [95] [96] ) (see the transcript file for additional information) Output written on R-intro.pdf (99 pages, 571522 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-4.1.3/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] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6648--6653 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6648--6653 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.vrs [94] [95]) Appendix E [96] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.cps [97]) Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 628203 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2021-02-20.11]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-4.1.3/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] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6648--6653 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6648--6653 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.vrs [94] [95]) Appendix E [96] (/usr/src/RPM/BUILD/R-4.1.3/doc/manual/R-intro.cps [97]) Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 628213 bytes). Transcript written on R-intro.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' collecting LaTeX docs for package 'stats' ... Converting parsed Rd's to LaTeX ............................... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' PDF/LaTeX documentation: full reference index ... 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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] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.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 5050) 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 \T1/pt m/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/pcr/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 1668) in paragraph at lines 154--161 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] Underfull \hbox (badness 3009) in paragraph at lines 226--238 \T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1 0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou sly to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 369--372 [][][]\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-lar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 567--573 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 635--635 []\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 636--636 []\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 912--912 []\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 933--933 []\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 962--962 []\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 1578--1584 Underfull \hbox (badness 10000) in paragraph at lines 1591--1593 []\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 1770--1770 [] \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 1799--1802 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1919--1921 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2056--2056 []\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 2094--2096 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e 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 2366--2366 []\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 2408--2408 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] Underfull \hbox (badness 10000) in paragraph at lines 2503--2505 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2506--2511 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [39] Underfull \hbox (badness 1107) in paragraph at lines 2574--2576 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] [42] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2741--2741 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3410--3410 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [52] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3441--3441 []\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 3442--3442 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; 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See the help on [][]Com-par -i-son[][][] and [69] [70] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4717--4717 []\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 4748--4754 []\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 4759--4762 []\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 4935--4935 []\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 5191--5193 []\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 10000) in paragraph at lines 5614--5622 []\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 [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6183--6191 []\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 6380--6380 []\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 6382--6382 []\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 6383--6383 []\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 6585--6588 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6589--6592 []\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 6632--6640 []\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 6796--6796 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6848--6851 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC onnection\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 7031--7034 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 7031--7034 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [104] [105] [106] Underfull \hbox (badness 1406) in paragraph at lines 7213--7219 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 7233--7235 []\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 7275--7282 []\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio n = "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 7275--7282 \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 7275--7282 \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] [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7479--7479 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] Underfull \hbox (badness 1231) in paragraph at lines 7604--7610 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7816--7818 []\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 7975--7975 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8208--8208 []\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 8327--8337 []\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 8327--8337 [][]\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] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8359--8364 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8501--8501 [] \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 1629) in paragraph at lines 8850--8862 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8850--8862 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9299--9303 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9390--9390 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9392--9392 []\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 9418--9418 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9419--9419 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] Underfull \hbox (badness 1924) in paragraph at lines 9480--9485 []\T1/ptm/m/n/10 Attributes named \T1/pcr/m/n/10 dim\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 dimnames\T1/ptm/m/n/10 , \T1/pcr/m/n/10 levels\T1/ptm/m/n/10 , \T1/pcr/m/n /10 names \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 are de-parsed to \T1/pcr/m/n/10 .Dim\T1/ptm/m/n/10 , [139] Underfull \hbox (badness 5403) in paragraph at lines 9550--9552 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9569--9571 []\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 9800--9803 []\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 10415--10420 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \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 10470--10470 []\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 10471--10471 []\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 10573--10578 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10613--10619 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10675--10675 []\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 10677--10677 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10797--10802 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10797--10802 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10797--10802 \T1/pcr/m/n/10 754-[]2019$[][]\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 10828--10828 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10902--10902 []\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 11049--11049 []\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 11247--11255 []\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 11256--11258 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11473--11476 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11928--11928 []\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/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12259--12261 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] Underfull \hbox (badness 4569) in paragraph at lines 12396--12400 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 12396--12400 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] Underfull \vbox (badness 10000) has occurred while \output is active [193] [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2221) in paragraph at lines 13820--13829 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13820--13829 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14081--14083 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14201--14203 []\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 14360--14362 []\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 14477--14481 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\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 14488--14491 [][][]$\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 14509--14509 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [210] [211] Underfull \hbox (badness 10000) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\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 14641--14641 []\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 14707--14710 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14724--14724 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14753--14753 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [213] Underfull \hbox (badness 1472) in paragraph at lines 14777--14784 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14777--14784 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14785--14789 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14949--14949 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14950--14950 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15184--15184 []\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 15187--15187 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [220] Underfull \hbox (badness 1168) in paragraph at lines 15271--15275 []\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 15271--15275 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [221] Underfull \hbox (badness 6944) in paragraph at lines 15369--15372 [][][]\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/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15394--15394 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [223] [224] Underfull \hbox (badness 10000) in paragraph at lines 15532--15534 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15552--15552 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15558--15558 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [225] Underfull \hbox (badness 2790) in paragraph at lines 15565--15568 []\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 Underfull \hbox (badness 1024) in paragraph at lines 15596--15603 []\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 [226] Underfull \hbox (badness 10000) in paragraph at lines 15671--15673 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15671--15673 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15693--15698 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15699--15701 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [227] Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15710--15718 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15818--15818 []\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 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [229] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15840--15840 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16669--16669 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] Underfull \hbox (badness 2418) in paragraph at lines 16778--16782 \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/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16785--16788 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [243] Underfull \hbox (badness 2326) in paragraph at lines 16820--16827 [][][]\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[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [244] [245] [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17077--17077 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [247] Underfull \hbox (badness 1867) in paragraph at lines 17105--17112 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17406--17406 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Underfull \vbox (badness 10000) has occurred while \output is active [252] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17435--17435 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [253] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17491--17491 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [254] [255] [256] [257] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17864--17864 []\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))) [258] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17929--17929 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [259] [260] [261] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [262] [263] [264] [265] Underfull \hbox (badness 2285) in paragraph at lines 18461--18463 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / [266] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18469--18469 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18499--18499 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [267] [268] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18632--18632 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18638--18638 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18641--18641 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18647--18647 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [269] [270] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18774--18774 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18782--18782 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 18987--18989 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [274] [275] [276] [277] [278] Underfull \hbox (badness 10000) in paragraph at lines 19325--19331 Underfull \hbox (badness 10000) in paragraph at lines 19338--19340 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [279] [280] [281] Underfull \hbox (badness 4699) in paragraph at lines 19570--19573 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\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 , [282] [283] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19698--19698 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [284] [285] [286] Underfull \hbox (badness 4739) in paragraph at lines 19833--19835 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [287] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19882--19882 []\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 19883--19883 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1975) in paragraph at lines 20494--20497 []\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 [296] [297] [298] [299] [300] [301] [302] Underfull \hbox (badness 1077) in paragraph at lines 20892--20897 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20906--20913 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [303] Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec- Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 \T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr /m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o r [304] [305] Underfull \hbox (badness 10000) in paragraph at lines 21135--21139 []\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 21135--21139 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll 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 21140--21147 []\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- [306] [307] Underfull \hbox (badness 10000) in paragraph at lines 21271--21278 [][][]\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 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21392--21396 []\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 [310] Underfull \hbox (badness 5161) in paragraph at lines 21462--21467 []\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 21462--21467 \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 21462--21467 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21462--21467 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [311] [312] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21629--21629 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21633--21633 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [313] Underfull \hbox (badness 3343) in paragraph at lines 21694--21698 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [314] [315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21835--21835 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 21846--21846 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [316] [317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21957--21957 []\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 21960--21960 []\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 22005--22010 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [318] [319] Underfull \hbox (badness 2564) in paragraph at lines 22096--22099 []\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 22133--22133 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [320] [321] Underfull \hbox (badness 1400) in paragraph at lines 22301--22305 [][][]\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 do uble[][][] \T1/ptm/m/n/10 (class [322] [323] [324] Underfull \hbox (badness 1824) in paragraph at lines 22471--22479 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. In nu-meric and Underfull \hbox (badness 6758) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1 0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/ m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23137--23137 []\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 23138--23138 [] \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 23141--23141 []\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)[] [335] [336] Underfull \hbox (badness 1655) in paragraph at lines 23270--23274 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [337] [338] [339] Underfull \hbox (badness 2277) in paragraph at lines 23519--23522 []\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 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [340] [341] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0. 0, [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1484) in paragraph at lines 24107--24115 []\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 24107--24115 \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 / [349] [350] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24185--24185 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [351] [352] [353] [354] [355] [356] [357] Underfull \hbox (badness 1448) in paragraph at lines 24699--24707 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [358] [359] Underfull \hbox (badness 3849) in paragraph at lines 24814--24819 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [360] Underfull \hbox (badness 7308) in paragraph at lines 24891--24897 []\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-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24891--24897 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24891--24897 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [361] [362] Underfull \hbox (badness 10000) in paragraph at lines 25054--25056 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [363] [364] [365] Underfull \hbox (badness 6188) in paragraph at lines 25281--25284 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [366] [367] [368] Underfull \hbox (badness 1521) in paragraph at lines 25466--25480 \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- [369] [370] [371] [372] [373] Underfull \hbox (badness 2197) in paragraph at lines 25780--25784 []\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 25780--25784 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 25794--25798 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 25794--25798 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 25836--25836 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [374] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25840--25840 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [375] Underfull \hbox (badness 10000) in paragraph at lines 25888--25894 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25888--25894 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25901--25903 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [376] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25968--25968 [] \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:[] [377] [378] Underfull \hbox (badness 8189) in paragraph at lines 26163--26169 []\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 [][][] [379] [380] [381] Underfull \hbox (badness 1694) in paragraph at lines 26388--26391 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [382] [383] [384] [385] Underfull \hbox (badness 1603) in paragraph at lines 26635--26637 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [386] [387] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26762--26770 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [388] [389] Underfull \hbox (badness 3271) in paragraph at lines 26981--26984 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [390] [391] [392] Underfull \hbox (badness 3138) in paragraph at lines 27287--27293 []\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 27287--27293 \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 27287--27293 \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 [393] Underfull \hbox (badness 1194) in paragraph at lines 27300--27303 []\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/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27326--27328 []\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 27346--27352 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27361--27366 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 27379--27382 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [394] Underfull \hbox (badness 10000) in paragraph at lines 27395--27398 []\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 27403--27409 []\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 27403--27409 \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 27403--27409 \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 27403--27409 \T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina ry.universal" \T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27418--27425 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27418--27425 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27418--27425 \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 27418--27425 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [395] [396] [397] [398] Underfull \vbox (badness 10000) has occurred while \output is active [399] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27765--27765 []\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 27778--27782 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 27778--27782 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27925--27928 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27925--27928 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 28207--28213 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 28207--28213 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and Overfull \hbox (42.18039pt too wide) in paragraph at lines 28229--28229 []\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 28241--28241 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28254--28254 []\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 28258--28258 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [406] [407] [408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28433--28433 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28442--28442 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [409] Underfull \hbox (badness 1360) in paragraph at lines 28497--28501 []\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 = [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 2005) in paragraph at lines 28892--28896 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc r/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 = [416] Underfull \hbox (badness 1796) in paragraph at lines 28960--28963 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [417] [418] [419] [420] Underfull \hbox (badness 10000) in paragraph at lines 29164--29167 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29859--29859 [] \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))[] [431] [432] [433] [434] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30150--30150 []\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 30161--30161 []\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 30167--30167 []\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 30173--30173 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [435] [436] Underfull \hbox (badness 7415) in paragraph at lines 30256--30260 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 30277--30277 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [437] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30323--30323 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [438] Underfull \hbox (badness 3713) in paragraph at lines 30468--30479 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [439] [440] Underfull \hbox (badness 1248) in paragraph at lines 30620--30627 \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 30620--30627 \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 / [441] [442] Underfull \hbox (badness 1533) in paragraph at lines 30738--30741 []\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 [443] [444] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30883--30883 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30901--30912 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [445] [446] [447] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31045--31045 []\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 31047--31047 []\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 31048--31048 []\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 31049--31049 []\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 31050--31050 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31057--31057 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [448] [449] [450] [451] [452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31365--31365 []\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 31367--31367 []\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 31377--31377 []\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 31378--31378 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [453] Underfull \hbox (badness 4048) in paragraph at lines 31473--31478 []\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 31473--31478 \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 31473--31478 \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 , [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 2080) in paragraph at lines 32011--32021 []\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), [462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [463] [464] [465] [466] [467] [468] [469] Underfull \hbox (badness 7558) in paragraph at lines 32564--32568 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32574--32576 []\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 Underfull \hbox (badness 10000) in paragraph at lines 32585--32587 []\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 32588--32592 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht tps : / / www . [470] [471] [472] [473] [474] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32959--32959 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [475] Underfull \hbox (badness 10000) in paragraph at lines 33030--33034 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [476] [477] [478] [479] Underfull \hbox (badness 2302) in paragraph at lines 33256--33261 []\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me nt to the spec-i-fied num-ber of sig-nif-i-cant Underfull \hbox (badness 3769) in paragraph at lines 33256--33261 \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 [480] [481] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33389--33389 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33392--33392 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [482] [483] [484] [485] [486] [487] [488] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33833--33833 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [489] [490] [491] [492] [493] [494] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34270--34270 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [495] Underfull \hbox (badness 1158) in paragraph at lines 34374--34379 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [496] Underfull \hbox (badness 10000) in paragraph at lines 34401--34407 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 34401--34407 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [497] [498] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34559--34559 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [499] [500] [501] Underfull \hbox (badness 8151) in paragraph at lines 34819--34822 []\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 . [502] [503] [504] Underfull \hbox (badness 10000) in paragraph at lines 35034--35039 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by = [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36023--36023 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [520] [521] [522] [523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36277--36277 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36279--36279 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 36322--36328 [][][]\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[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36322--36328 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [524] [525] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36433--36433 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [526] [527] [528] [529] [530] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36774--36774 []\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 36789--36789 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [531] [532] [533] Underfull \hbox (badness 10000) in paragraph at lines 37014--37016 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [534] [535] [536] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37241--37241 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37242--37242 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [537] [538] [539] [540] Overfull \hbox (63.78036pt too wide) in paragraph at lines 37509--37509 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [541] Underfull \hbox (badness 6110) in paragraph at lines 37600--37610 []\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-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 37600--37610 \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 37600--37610 \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 37600--37610 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n 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 37600--37610 \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 [542] Underfull \hbox (badness 10000) in paragraph at lines 37646--37652 []\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 37646--37652 \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 37646--37652 \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 37661--37668 []\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 37661--37668 \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 37661--37668 \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 [543] [544] [545] Underfull \hbox (badness 1484) in paragraph at lines 37893--37897 []\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/ m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [546] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37955--37955 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [547] [548] [549] [550] [551] [552] [553] [554] [555] Overfull \hbox (0.78088pt too wide) in paragraph at lines 38535--38535 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [556] [557] [558] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38785--38785 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [559] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38829--38829 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [560] [561] [562] [563] [564] [565] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39263--39263 []\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 39266--39266 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [566] Underfull \hbox (badness 10000) in paragraph at lines 39317--39324 []\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 39317--39324 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39370--39370 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [568] [569] [570] [571] [572] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39681--39681 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [573] [574] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39846--39846 []\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. [575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39884--39884 []\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 39914--39920 []\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 39914--39920 \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 39933--39938 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 39933--39938 \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 [576] [577] [578] [579] Underfull \hbox (badness 10000) in paragraph at lines 40221--40225 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \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 [580] Underfull \hbox (badness 1584) in paragraph at lines 40236--40239 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \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 [581] [582] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40374--40374 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [583] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40451--40451 []\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 [584] [585] Underfull \hbox (badness 1082) in paragraph at lines 40595--40598 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [586] [587] [588] Underfull \hbox (badness 1038) in paragraph at lines 40786--40789 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [589] [590] [591] [592] [593] Underfull \hbox (badness 1442) in paragraph at lines 41150--41154 \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 = [594] [595] [596] [597] Underfull \hbox (badness 4096) in paragraph at lines 41400--41403 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [598] Underfull \hbox (badness 7888) in paragraph at lines 41514--41518 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10 length(bin) > [599] [600] [601] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41668--41668 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (35.4281pt too wide) in paragraph at lines 41670--41670 [] \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 41672--41672 [] \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 41685--41687 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [602] Underfull \hbox (badness 10000) in paragraph at lines 41765--41768 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [603] [604] Underfull \hbox (badness 3872) in paragraph at lines 41883--41886 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [605] Underfull \hbox (badness 5475) in paragraph at lines 41949--41953 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [606] [607] [608] [609] [610] [611] Underfull \hbox (badness 10000) in paragraph at lines 42373--42380 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 42429--42438 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42429--42438 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [612] Underfull \hbox (badness 1082) in paragraph at lines 42439--42451 \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' in that di-rec-tory states the ver-sion. That op-tion is Underfull \hbox (badness 1337) in paragraph at lines 42512--42520 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or [613] Underfull \hbox (badness 10000) in paragraph at lines 42521--42524 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 42575--42578 [][][]$\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 42579--42581 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 42588--42588 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 42809--42811 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [617] [618] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42931--42931 []\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 42933--42933 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [619] [620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43034--43034 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43036--43036 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [621] [622] [623] Underfull \hbox (badness 6542) in paragraph at lines 43310--43312 []\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 , and [624] [625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43429--43429 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [626] Underfull \hbox (badness 1708) in paragraph at lines 43497--43505 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 43497--43505 \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 [627] Underfull \hbox (badness 4859) in paragraph at lines 43527--43532 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [628] Underfull \hbox (badness 3895) in paragraph at lines 43589--43601 []\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 43589--43601 \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 , [629] [630] [631] [632] [633] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43912--43912 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [634] [635] [636] [637] [638] [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44381--44381 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [640] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44390--44390 []\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 44456--44462 [][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[ ][][]\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 , [641] Underfull \hbox (badness 3861) in paragraph at lines 44465--44470 [][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex ists[][][]\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 , [642] Overfull \hbox (36.7804pt too wide) in paragraph at lines 44558--44558 []\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[] [643] Underfull \hbox (badness 1803) in paragraph at lines 44611--44614 []\T1/ptm/m/n/10 The atomic modes are \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/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 44615--44622 []\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 [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 44830--44832 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44936--44936 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [648] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45011--45011 []\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[] [649] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45019--45019 []\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 ...[] [650] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45113--45113 []\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 45117--45117 []\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 45118--45118 [] \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 45125--45125 []\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 45128--45128 []\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[] [651] Underfull \hbox (badness 6220) in paragraph at lines 45167--45172 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 45167--45172 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 10000) in paragraph at lines 45188--45193 []\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 4229) in paragraph at lines 45188--45193 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [652] Underfull \hbox (badness 2818) in paragraph at lines 45284--45290 []\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 a nd \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 [653] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45319--45319 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 2846) in paragraph at lines 45778--45782 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas Overfull \hbox (4.38043pt too wide) in paragraph at lines 45818--45818 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] [661] Underfull \hbox (badness 3209) in paragraph at lines 45839--45843 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [662]) (./compiler-pkg.tex Chapter 2. [663] 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 be us ed 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 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] 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,[] [672] 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)[] Underfull \vbox (badness 1472) has occurred while \output is active [673] [674] [675] [676] 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)[] [677] Overfull \hbox (48.81013pt too wide) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [678] [679] Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [680] [681] [682] 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. [683] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [684] [685] [686] [687] [688] 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)")[] [689] [690] 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 frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\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-tained from the a bove [691] [692] [693] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [694] 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)[] [695] [696] 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]]))))[] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] [702] [703] Overfull \vbox (4.29591pt too high) has occurred while \output is active [704] [705] [706] [707] [708] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [709] Overfull \vbox (13.87083pt too high) has occurred while \output is active [710] Underfull \vbox (badness 2376) has occurred while \output is active [711] [712] [713] [714] [715] 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 = ".")[] [716] [717] [718] [719] [720] [721] [722] [723] 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:[] [724] [725] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [726] Overfull \vbox (10.49593pt too high) has occurred while \output is active [727] Overfull \vbox (15.49593pt too high) has occurred while \output is active [728] 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 / [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742]) (./grDevices-pkg.tex Chapter 4. [743] [744] [745] [746] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to 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/ptm/m/n/1 0 in [747] [748] Underfull \hbox (badness 10000) in paragraph at lines 382--390 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 382--390 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [749] [750] 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",[] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] 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 [761] [762] [763] 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))[] Underfull \hbox (badness 1173) in paragraph at lines 1405--1408 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [764] [765] [766] [767] [768] [769] [770] [771] Underfull \hbox (badness 1565) in paragraph at lines 1893--1898 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1893--1898 \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 [772] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1976--1976 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2017--2027 []\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 2017--2027 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 2129--2131 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [775] [776] Underfull \hbox (badness 6758) in paragraph at lines 2308--2311 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [777] [778] Underfull \hbox (badness 2326) in paragraph at lines 2426--2436 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2426--2436 \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 2426--2436 \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 2426--2436 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [779] [780] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2529--2529 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2645--2645 []\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 2646--2646 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 2919--2920 Underfull \vbox (badness 10000) has occurred while \output is active [787] [788] [789] [790] [791] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3252--3252 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [792] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3336--3336 []\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 3337--3337 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 3493--3498 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3493--3498 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [795] [796] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3567--3567 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [797] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3651--3651 []\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 3671--3671 []\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 3678--3678 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [798] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3734--3734 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [799] Underfull \hbox (badness 8170) in paragraph at lines 3763--3766 []\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 , [800] Underfull \hbox (badness 2189) in paragraph at lines 3824--3829 []\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we ll for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3862--3866 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [801] Underfull \vbox (badness 10000) has occurred while \output is active [802] Underfull \hbox (badness 5260) in paragraph at lines 3992--3995 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [803] [804] [805] [806] [807] Underfull \hbox (badness 5939) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [808] [809] [810] [811] [812] [813] Underfull \hbox (badness 10000) in paragraph at lines 4732--4737 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [814] [815] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4847--4847 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [816] [817] Underfull \hbox (badness 1348) in paragraph at lines 5052--5055 []\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 [818] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5076--5076 []\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 5117--5123 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [819] Underfull \hbox (badness 1112) in paragraph at lines 5150--5154 []\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" [820] Underfull \hbox (badness 1755) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [821] [822] [823] Underfull \hbox (badness 7344) in paragraph at lines 5472--5474 []\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 5483--5487 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [824] [825] Underfull \hbox (badness 1552) in paragraph at lines 5610--5619 \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 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \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/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5620--5622 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5652--5658 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [826] Underfull \hbox (badness 5388) in paragraph at lines 5678--5680 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [827] [828] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5779--5779 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [829] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5891--5891 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 5977--5979 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [832] [833] [834] [835] [836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6344--6344 []\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 6358--6361 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [837] [838] [839] [840] [841] [842] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6693--6693 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6700--6700 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [843] [844] [845] [846] Underfull \hbox (badness 10000) in paragraph at lines 6963--6968 []\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 6963--6968 \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 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6963--6968 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7069--7069 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [848] Underfull \hbox (badness 3590) in paragraph at lines 7108--7111 []\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 7108--7111 \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 7119--7119 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [849] Underfull \hbox (badness 1189) in paragraph at lines 7184--7186 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [850] Underfull \hbox (badness 10000) in paragraph at lines 7289--7291 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [851] Underfull \hbox (badness 10000) in paragraph at lines 7335--7342 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7335--7342 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [852] Underfull \hbox (badness 5607) in paragraph at lines 7419--7423 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [853] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7471--7471 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [854] [855] Underfull \hbox (badness 5637) in paragraph at lines 7603--7609 \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 7636--7639 []\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 / [856] [857] [858] Underfull \hbox (badness 1231) in paragraph at lines 7805--7807 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [859] [860]) (./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 = [861] [862] [863] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [864] [865] [866] [867] 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 [868] [869] 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[] [870] 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 \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [871] [872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \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 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [873] [874] [875] Underfull \hbox (badness 10000) in paragraph at lines 964--968 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able. Overfull \hbox (133.98029pt too wide) in paragraph at lines 981--981 [] \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 983--983 []\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 985--985 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [876] [877] [878] [879] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [880] [881] [882] Underfull \hbox (badness 2503) in paragraph at lines 1431--1440 \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 1466--1468 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [883] [884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1540--1540 []\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 1541--1541 []\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 1547--1547 []\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 1548--1548 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [885] [886] [887] [888] [889] Underfull \hbox (badness 10000) in paragraph at lines 1851--1857 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.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 1871--1871 []\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 1883--1883 []\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 1899--1899 []\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 1908--1908 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [890] [891] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1993--1993 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [892] [893] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2122--2122 []\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 2127--2127 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [894] [895] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2301--2301 []\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 2302--2302 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [896] Underfull \hbox (badness 1430) in paragraph at lines 2333--2335 []\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 [897] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2414--2414 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2426--2433 \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 [898] Underfull \hbox (badness 7273) in paragraph at lines 2508--2512 [][][]\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[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and [899] [900] [901] [902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2756--2756 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [903] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2793--2793 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [904] [905] Underfull \hbox (badness 1226) in paragraph at lines 2918--2922 \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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 2971--2971 []\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 :[] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2975--2975 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] Underfull \hbox (badness 10000) in paragraph at lines 3027--3030 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [907] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3232--3232 []\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 3237--3237 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 [][]\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 3379--3384 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [912] [913] [914] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3565--3565 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3584--3584 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [915] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [916] [917] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3765--3765 [] \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 3766--3766 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [918] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3805--3805 [] \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 [919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3865--3865 []\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 3867--3867 []\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 3875--3875 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [920] Underfull \hbox (badness 10000) in paragraph at lines 3938--3942 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [921] [922] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4050--4050 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [923] [924] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4204--4204 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [925] Underfull \hbox (badness 3930) in paragraph at lines 4283--4285 []\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 [926] [927] [928] [929] [930] Underfull \hbox (badness 1286) in paragraph at lines 4594--4597 \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 4602--4607 []\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 [931] [932] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4699--4699 []\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 4704--4704 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [933] Underfull \hbox (badness 1264) in paragraph at lines 4895--4908 \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/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 5032--5038 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 5163--5166 [938 ] Underfull \hbox (badness 10000) in paragraph at lines 5224--5226 [939 ] [940] Underfull \hbox (badness 10000) in paragraph at lines 5414--5416 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [941] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5470--5470 []\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 5471--5471 [] \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 [942] [943] [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5836--5836 []\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 5837--5837 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5896 \aliasA{plot}{plot.default}{plot} [949] [950] [951] [952] [953] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6234--6234 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 6664--6666 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [960] [961] Underfull \hbox (badness 1028) in paragraph at lines 6758--6760 []\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 6801--6802 [][] [962 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6895--6895 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [963] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6926--6926 [] \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 [964] [965] Underfull \hbox (badness 10000) in paragraph at lines 7048--7050 []\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 7075--7075 [] \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 7081--7081 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [966] Underfull \hbox (badness 2600) in paragraph at lines 7138--7140 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7370--7370 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [971] [972] [973] [974] [975] [976] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7757--7757 []\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 7761--7761 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [977] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [978] [979] [980] [981] [982] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8122--8122 []\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 8125--8125 []\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 8129--8129 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [983] [984] [985] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\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 8301--8301 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [986] [987] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8405--8405 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8416--8421 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [988] Underfull \hbox (badness 1112) in paragraph at lines 8464--8468 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [989] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8524--8524 []\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 8539--8539 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [990] [991] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8676--8676 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [992] [993] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8861--8861 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [994] Underfull \hbox (badness 10000) in paragraph at lines 8889--8891 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8891--8893 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8923--8929 []\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 are \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 [995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8971 \HeaderA{units}{Graphical Units}{units} [996] Underfull \hbox (badness 1205) in paragraph at lines 9036--9038 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [997] [998] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9155--9155 []\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)[] [999]) (./grid-pkg.tex [1000] Chapter 6. [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 10000) in paragraph at lines 479--485 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 479--485 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [1009] Underfull \hbox (badness 4859) in paragraph at lines 565--568 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1010] [1011] [1012] [1013] [1014] [1015] Overfull \hbox (31.3804pt too wide) in paragraph at lines 959--959 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1016] [1017] [1018] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1164--1164 [] \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 1165--1165 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1166--1166 [] \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 1167--1167 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1168--1168 [] \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 1169--1169 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1019] Underfull \hbox (badness 1430) in paragraph at lines 1214--1219 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1020] [1021] [1022] Underfull \hbox (badness 3219) in paragraph at lines 1428--1431 []\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 [1023] [1024] [1025] [1026] [1027] [1028] [1029] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1816--1816 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1030] [1031] [1032] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2030--2030 []\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 2031--2031 []\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 2032--2032 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1033] Underfull \hbox (badness 2961) in paragraph at lines 2067--2072 []\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 , [1034] Underfull \hbox (badness 1430) in paragraph at lines 2126--2131 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2155--2158 []\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 [1035] [1036] [1037] Underfull \hbox (badness 2894) in paragraph at lines 2362--2369 []\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 [1038] [1039] [1040] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2518--2518 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2530--2535 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1041] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1042] [1043] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2741--2741 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1044] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2773--2773 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1045] [1046] [1047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3015--3015 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1048] [1049] [1050] [1051] [1052] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3330--3330 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1053] [1054] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3426--3426 []\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 3460--3466 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1055] [1056] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3552--3552 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3559--3559 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1057] [1058] [1059] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3760--3760 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1060] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3796--3796 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Underfull \hbox (badness 1067) in paragraph at lines 4537--4540 []\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 [1073] Underfull \hbox (badness 1430) in paragraph at lines 4583--4588 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1074] [1075] [1076] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] Underfull \hbox (badness 7256) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 5419--5421 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 6859) in paragraph at lines 6206--6212 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1099] [1100] [1101] [1102] [1103] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6484--6484 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1104] Underfull \hbox (badness 1867) in paragraph at lines 6584--6586 []\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 [1105] Underfull \hbox (badness 10000) in paragraph at lines 6621--6627 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1106] [1107] Underfull \hbox (badness 1371) in paragraph at lines 6753--6756 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1108] Underfull \vbox (badness 10000) has occurred while \output is active [1109] [1110] [1111] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1112]) (./methods-pkg.tex Chapter 7. [1113] [1114] 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 c o-erce meth-ods work. Use [1115] [1116] [1117] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1118] [1119] 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[] [1120] 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 [1121] 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 [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] 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[] [1137] [1138] 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 c an be an ob-ject of class [1139] [1140] [1141] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\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 = [1142] [1143] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\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 [1144] [1145] [1146] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\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 [1147] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1148] [1149] [1150] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1151] [1152] [1153] [1154] [1155] [1156] [1157] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1160] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1163] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\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 [1164] [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1167] [1168] [1169] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1171] [1172] [1173] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\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 , [1174] [1175] [1176] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\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 [1177] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1181] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\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 5237--5237 []\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 [1182] [1183] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1184] [1185] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1186] [1187] [1188] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1189] [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1195] [1196] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \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 [1197] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1198] [1199] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\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 6647--6656 [][]\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 [1200] Underfull \vbox (badness 10000) has occurred while \output is active [1201] [1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1204] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1205] [1206] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\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 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1208] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/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 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/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 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1209] [1210] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\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 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1211] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7517--7517 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1212] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1225] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1230] [1231] [1232] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1233] [1234] [1235] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1236] [1237] [1238] [1239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1240] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\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 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1251] [1252] [1253]) (./parallel-pkg.tex [1254] 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/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1255] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1256] [1257] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\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 [1258] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 444--446 []\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 [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 1917) in paragraph at lines 778--787 []\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 778--787 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1266] [1267] Overfull \hbox (60.78088pt too wide) in paragraph at lines 871--871 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1268] [1269] [1270] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1062--1062 []\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 1066--1066 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1271] Underfull \hbox (badness 5388) in paragraph at lines 1181--1186 []\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 [1272] Underfull \hbox (badness 10000) in paragraph at lines 1205--1213 []\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 1242--1242 []\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)[] [1273] [1274] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1358--1358 [] \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 1372--1372 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1275] Underfull \hbox (badness 1577) in paragraph at lines 1401--1404 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1448--1450 []\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 [1276] [1277]) (./splines-pkg.tex [1278] 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 [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] 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))[] [1287] Underfull \hbox (badness 1424) 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(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1288] [1289] 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)))[] [1290] [1291] [1292]) (./stats-pkg.tex Chapter 10. [1293] 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 o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/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[] [1294] [1295] [1296] [1297] [1298] 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[] [1299] 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) [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 1024) in paragraph at lines 888--890 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1316] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1626--1626 [] \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 1629--1629 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1317] [1318] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1776--1776 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1319] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1788--1788 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[ ] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2806--2806 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1334] [1335] [1336] [1337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3046--3046 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1338] [1339] [1340] Underfull \hbox (badness 10000) in paragraph at lines 3257--3259 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3306--3306 []\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 3307--3307 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1342] [1343] [1344] [1345] [1346] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1347] [1348] [1349] [1350] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3980--3980 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1351] [1352] [1353] [1354] [1355] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4269--4269 []\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 4270--4270 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1356] [1357] [1358] [1359] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4510--4510 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1360] [1361] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4685--4685 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1362] [1363] Underfull \hbox (badness 3989) in paragraph at lines 4779--4786 []\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 = [1364] [1365] [1366] [1367] [1368] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5164--5164 []\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 5166--5166 []\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))[] [1369] [1370] [1371] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5387--5387 []\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 5405--5405 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1372] Underfull \hbox (badness 2680) in paragraph at lines 5432--5434 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1373] [1374] [1375] Underfull \hbox (badness 1436) in paragraph at lines 5615--5620 []\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 5615--5620 \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 5615--5620 \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 , [1376] [1377] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1378] [1379] [1380] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5985--5985 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1381] [1382] [1383] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6170--6170 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1384] [1385] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6278--6278 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1386] Underfull \hbox (badness 10000) in paragraph at lines 6345--6350 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1387] [1388] [1389] Underfull \hbox (badness 5954) in paragraph at lines 6541--6543 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1390] Underfull \hbox (badness 2503) in paragraph at lines 6623--6626 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can 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 6627--6629 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \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 6630--6635 \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, [1391] Underfull \hbox (badness 7238) in paragraph at lines 6666--6669 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6678--6678 []\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 6701--6701 []\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 6716--6716 []\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):[] [1392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6731--6731 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1393] [1394] [1395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6976--6976 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1396] [1397] [1398] Underfull \vbox (badness 10000) has occurred while \output is active [1399] [1400] [1401] [1402] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 \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 "binary" \T1/ptm/ m/n/10 or [1403] Underfull \hbox (badness 6493) in paragraph at lines 7474--7477 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1404] [1405] Underfull \hbox (badness 10000) in paragraph at lines 7611--7614 []\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 = [1406] [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 10000) in paragraph at lines 8023--8028 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1412] [1413] [1414] [1415] [1416] [1417] Underfull \hbox (badness 1210) in paragraph at lines 8378--8380 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1418] [1419] [1420] [1421] [1422] [1423] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8841--8841 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1424] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8886--8886 []\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 8889--8889 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1425] [1426] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9027--9027 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1427] [1428] [1429] [1430] [1431] [1432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9454--9454 [] \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 9455--9455 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1433] [1434] [1435] Underfull \hbox (badness 7291) in paragraph at lines 9634--9636 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1436] [1437] [1438] [1439] [1440] [1441] [1442] Underfull \hbox (badness 6944) in paragraph at lines 10122--10128 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1443] [1444] [1445] Underfull \hbox (badness 3758) in paragraph at lines 10336--10339 []\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 [1446] [1447] [1448] [1449] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10580--10580 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10606--10611 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1450] Underfull \hbox (badness 4132) in paragraph at lines 10645--10649 []\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 10699--10705 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1451] Underfull \hbox (badness 10000) in paragraph at lines 10750--10753 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\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 [1452] [1453] [1454] Underfull \hbox (badness 2142) in paragraph at lines 10967--10970 []\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 ^^@ [1455] Underfull \hbox (badness 1708) in paragraph at lines 11048--11052 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1456] Underfull \hbox (badness 10000) in paragraph at lines 11090--11096 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11128--11133 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1457] [1458] Underfull \hbox (badness 2635) in paragraph at lines 11261--11264 \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/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1459] [1460] [1461] Underfull \hbox (badness 1694) in paragraph at lines 11444--11447 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1462] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11545--11545 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1463] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11578--11578 [] \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 11591--11595 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1464] [1465] [1466] [1467] [1468] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11913--11913 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11928 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11988--11988 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1470] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12000--12000 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12053--12058 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12070--12072 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1471] [1472] [1473] [1474] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12324--12324 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12325--12325 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1475] [1476] [1477] [1478] [1479] [1480] Underfull \hbox (badness 10000) in paragraph at lines 12669--12671 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12692--12694 []\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 [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 6910) in paragraph at lines 12999--13001 []\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 13005--13009 []\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 13005--13009 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13611--13611 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1495] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13712--13712 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13760--13765 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] Underfull \hbox (badness 1275) in paragraph at lines 13869--13871 []\T1/pcr/m/n/10 lm \T1/ptm/m/n/10 re-turns an ob-ject of [][]\T1/pcr/m/n/10 cl ass[][][] "lm" \T1/ptm/m/n/10 or for mul-ti-vari-ate (`mul-ti-ple') re-sponses of class [1498] [1499] Underfull \hbox (badness 10000) in paragraph at lines 13967--13971 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 1163) in paragraph at lines 14301--14309 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1505] [1506] Underfull \hbox (badness 4518) in paragraph at lines 14421--14426 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1507] [1508] [1509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14609--14609 []\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 14610--14610 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1510] [1511] [1512] [1513] [1514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14953--14953 []\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 14954--14954 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1515] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15047--15047 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 2726) in paragraph at lines 15456--15459 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/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 , [1523] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15550--15550 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16178--16178 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1534] [1535] Underfull \hbox (badness 1490) in paragraph at lines 16325--16330 \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 [1536] Underfull \hbox (badness 1648) in paragraph at lines 16391--16393 []\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 2591) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1537] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16476--16476 []\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 16477--16477 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17034--17034 []\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[] [1547] [1548] [1549] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17266--17266 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \vbox (badness 10000) has occurred while \output is active [1560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 17988--17988 []\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 [1561] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18006--18006 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc urate numerical[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18007--18007 []\T1/pcr/m/n/9 ## differentiation; the first fit gives Error: "step factor .. reduced below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/ m/n/9 .."[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18010--18010 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central diff. typically work:[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 18011--18011 [] \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral =TRUE, warnOnly=TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18013--18013 []\T1/pcr/m/n/9 ## 2nd fit still fails on some (less accurate) platforms => us ing warnOnly[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18043--18043 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1562] [1563] [1564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18219--18219 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1565] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18266--18266 []\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 18313--18313 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1566] [1567] [1568] [1569] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18519--18519 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1248) in paragraph at lines 18834--18837 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18847--18851 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 18855--18859 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$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 [1575] Underfull \hbox (badness 2042) in paragraph at lines 18913--18915 []\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 [1576] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19019--19019 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1577] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19062--19062 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19080--19080 []\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 19083--19083 []\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 19103--19103 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1578] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19141--19152 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19141--19152 \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 [1579] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19204--19204 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1580] [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19431--19431 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1583] [1584] Underfull \hbox (badness 1337) in paragraph at lines 19542--19545 []\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 [1585] [1586] [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19861--19861 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1590] [1591] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19949--19949 [] \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 19951--19951 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19953--19953 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1592] Underfull \hbox (badness 10000) in paragraph at lines 19999--20005 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 3049) in paragraph at lines 20040--20044 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1593] [1594] [1595] [1596] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20293--20293 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20303--20306 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1597] Underfull \hbox (badness 1107) in paragraph at lines 20361--20363 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1598] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20416--20416 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20423--20423 []\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)[] [1600] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20517--20517 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1601] [1602] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20646--20646 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1603] Underfull \hbox (badness 7740) in paragraph at lines 20709--20711 []\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 [1604] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20757--20757 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1605] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20849--20849 [] \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 20854--20854 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21709--21709 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1619] Underfull \hbox (badness 6859) in paragraph at lines 21776--21783 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21787--21793 []\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/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22533--22533 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22817--22817 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22818--22818 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1337) in paragraph at lines 23144--23150 []\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 [1642] [1643] [1644] [1645] [1646] [1647] [1648] Underfull \hbox (badness 2913) in paragraph at lines 23569--23572 []\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th e pre-ci-sion to use when for-mat- Underfull \hbox (badness 1152) in paragraph at lines 23569--23572 \T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s ions up to 4.0.x, this had been set to [1649] Underfull \hbox (badness 10000) in paragraph at lines 23703--23705 []\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 23703--23705 \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 23710--23711 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1650] [1651] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23821--23821 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1652] Underfull \hbox (badness 1028) in paragraph at lines 23879--23882 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1653] [1654] Underfull \hbox (badness 10000) in paragraph at lines 23994--23997 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7944) in paragraph at lines 24049--24051 []\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,levels = [1655] Underfull \hbox (badness 7944) in paragraph at lines 24111--24113 []\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,levels = [1656] [1657] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24213--24213 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1658] [1659] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24330--24330 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24331--24331 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24332--24332 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24333--24333 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 24493--24498 [][][]\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 re-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 24493--24498 [][]\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 24504--24504 []\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 24505--24505 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] [1662] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24524--24524 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1663] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24628--24628 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1664] Underfull \hbox (badness 1033) in paragraph at lines 24671--24677 \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 24692--24695 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1665] Underfull \hbox (badness 2134) in paragraph at lines 24761--24765 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24774--24774 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24803--24803 []\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 24815--24815 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1667] [1668] [1669] [1670] [1671] [1672] [1673] Underfull \hbox (badness 6268) in paragraph at lines 25273--25278 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/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 , [1674] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25301--25301 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1675] [1676] [1677] Underfull \hbox (badness 1867) in paragraph at lines 25478--25480 []\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 25493--25497 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25493--25497 \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 25529--25529 []\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 25536--25536 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1678] [1679] [1680] Underfull \hbox (badness 2495) in paragraph at lines 25719--25728 []\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 . [1681] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25801--25801 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1682] Underfull \hbox (badness 1412) in paragraph at lines 25808--25810 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1683] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25895--25895 []\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 25920--25920 []\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 25923--25923 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1684] [1685] [1686] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26147--26147 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26151--26157 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26197--26197 []\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 26218--26218 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1688] Underfull \hbox (badness 1019) in paragraph at lines 26280--26285 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1689] [1690] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26410--26410 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1691] [1692] [1693] [1694] [1695] [1696] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1697] [1698] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26971--26971 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1699] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26977--26977 []\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 26986--26986 []\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 26987--26987 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1700] Underfull \hbox (badness 2922) in paragraph at lines 27056--27061 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27093--27093 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1701] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27096--27096 [] \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 27105--27105 [] \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 27106--27106 [] \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 27110--27110 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1702] Underfull \hbox (badness 3240) in paragraph at lines 27164--27167 [][][]\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 grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 27185--27185 [] \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 27188--27188 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1703] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27271--27271 [] \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 27275--27275 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1704] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27285--27285 [] \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 27290--27290 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27326--27332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27364--27364 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27380--27380 [] \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 27383--27383 []\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 27385--27385 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1706] [1707] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27497--27497 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1708] Underfull \hbox (badness 2922) in paragraph at lines 27559--27564 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1709] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27597--27597 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 27646--27651 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27677--27677 []\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 27711--27716 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27736--27736 []\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 27740--27740 []\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 27760--27760 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1712] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27770--27770 [] \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[] Underfull \hbox (badness 2922) in paragraph at lines 27805--27810 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27827--27827 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1713] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27845--27845 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1714] Underfull \hbox (badness 6493) in paragraph at lines 27897--27902 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27925--27925 []\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 27928--27928 []\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 27931--27931 []\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 27934--27934 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] Underfull \hbox (badness 3396) in paragraph at lines 28817--28819 []\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 [1729] [1730] Underfull \hbox (badness 2237) in paragraph at lines 28994--28996 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1731] [1732] [1733] Underfull \hbox (badness 2591) in paragraph at lines 29158--29160 []\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 [1734] Underfull \hbox (badness 2237) in paragraph at lines 29204--29207 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1735] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1736] Underfull \hbox (badness 3407) in paragraph at lines 29386--29390 []\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) [1737] [1738] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29456--29456 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1739] Underfull \hbox (badness 1337) in paragraph at lines 29519--29523 []\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 [1740] [1741] [1742] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29777--29777 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1743] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29805--29805 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 29831--29834 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1744] [1745] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29910--29910 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29988--29988 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1747] Underfull \hbox (badness 2205) in paragraph at lines 30077--30082 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30676--30676 []\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 30677--30677 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1757] [1758] [1759] [1760] [1761] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30977--30977 [] \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 30978--30978 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1762] [1763] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31104--31104 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\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 [1764] [1765] [1766] Underfull \hbox (badness 1337) in paragraph at lines 31330--31334 []\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 [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 1337) in paragraph at lines 31859--31863 []\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 Underfull \hbox (badness 5878) in paragraph at lines 31873--31875 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i -tive nu-meric tol-er-ance, used in [1776] [1777] [1778] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32066--32066 []\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 32068--32068 []\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)[] [1779] [1780] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32227--32227 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32312--32312 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1782] Underfull \hbox (badness 6775) in paragraph at lines 32369--32374 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1783] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32445--32445 []\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 "")[] [1784] [1785]) (./stats4-pkg.tex [1786] Chapter 11. [1787] [1788] [1789] 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 [1790] 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[] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797]) (./tcltk-pkg.tex [1798] Chapter 12. [1799] [1800] [1801] [1802] 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[] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] 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-ing any Tk or Tcl com-mand by sim-ply run-ning [1807] [1808] [1809] [1810] [1811] [1812] 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"))))[] [1813] [1814] [1815] [1816] [1817] 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-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1818]) (./tools-pkg.tex Chapter 13. [1819] 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.[] [1820] Underfull \hbox (badness 10000) in paragraph at lines 141--143 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via 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 b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1821] 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)[] [1822] 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/1 0 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/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1823] 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-gine to use. Over-rides any [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1831] [1832] 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")[] [1833] [1834] [1835] 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, ...)[] [1836] 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/p tm/m/n/10 and [1837] 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-he r-it-ing from class [1838] [1839] 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/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and [1840] [1841] [1842] [1843] [1844] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1700--1700 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1707--1715 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1707--1715 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 1707--1715 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1845] [1846] [1847]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1919 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig nored \relax l.1920 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1848] [1849] [1850] [1851] Underfull \hbox (badness 1142) in paragraph at lines 2188--2194 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2222--2222 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1852] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2223--2223 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2250--2257 []\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 2250--2257 \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 2250--2257 \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 [1853] Underfull \hbox (badness 1342) in paragraph at lines 2302--2308 \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 [1854] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2391--2399 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2391--2399 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 2391--2399 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1855] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2427--2427 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2460--2460 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1856] [1857] [1858] [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2744--2744 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1860] Underfull \hbox (badness 2486) in paragraph at lines 2789--2797 []\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 [1861] [1862] [1863] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3001--3001 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3005--3005 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1864] [1865] [1866] Underfull \hbox (badness 1072) in paragraph at lines 3177--3179 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1867] [1868] [1869] [1870] [1871] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1872] [1873] [1874] [1875] Underfull \hbox (badness 4108) in paragraph at lines 3758--3765 []\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 [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3858--3858 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] [1877] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3861--3861 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3878--3880 []\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 3895--3901 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1878] [1879] Underfull \hbox (badness 7832) in paragraph at lines 4017--4020 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1880] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4093--4093 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] Underfull \hbox (badness 1137) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1881] [1882] [1883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4304--4304 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1884] [1885] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) [1886] Underfull \hbox (badness 10000) in paragraph at lines 4477--4480 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4493--4498 []\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/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4501--4507 []\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 4501--4507 \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 [1887] [1888] [1889] [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4758--4758 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4759--4759 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4772--4775 []\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 4776--4786 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4814--4820 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4814--4820 \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 ', [1891] Underfull \hbox (badness 1571) in paragraph at lines 4842--4846 []\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 4868--4873 \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 [1892] [1893] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5008--5008 []\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 '[] [1894]) (./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 `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1895] [1896] [1897] [1898] 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[] [1899] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1900] 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 [1901] 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"))),[] [1902] [1903] [1904] Overfull \hbox (0.78088pt too wide) in paragraph at lines 677--677 []\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 683--683 []\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 684--684 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 685--685 []\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 686--686 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 720--726 []\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 720--726 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1905] [1906] Underfull \hbox (badness 4505) in paragraph at lines 857--863 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1907] [1908] [1909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1043--1043 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1910] Underfull \hbox (badness 1748) in paragraph at lines 1108--1116 []\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 1108--1116 \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 1661) in paragraph at lines 1108--1116 \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 1108--1116 \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 1120--1122 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1911] Underfull \hbox (badness 10000) in paragraph at lines 1228--1231 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1912] [1913] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1311--1311 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1914] [1915] [1916] [1917] [1918] [1919] [1920] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1813--1813 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1921] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1848--1848 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1922] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1994--1994 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1923] Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 []\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm /m/n/10 4.1.0. A less di-rect way to ex-am-ine char- Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 \T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use some-thing like [1924] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2096--2096 []\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 2098--2098 []\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 2106--2106 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2254--2254 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1928] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2306--2306 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1929] [1930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2475--2475 [] \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")[] [1931] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1933] Underfull \hbox (badness 1082) in paragraph at lines 2692--2696 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2697 ... the Clipboard in MS Windows}{clipboard} [1934] Underfull \hbox (badness 1163) in paragraph at lines 2728--2730 []\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 . [1935] Underfull \hbox (badness 10000) in paragraph at lines 2816--2818 []\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 [1936] [1937] [1938] [1939] Underfull \hbox (badness 10000) in paragraph at lines 3034--3036 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1940] [1941] [1942] [1943] Underfull \hbox (badness 1762) in paragraph at lines 3327--3330 []\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 = [1944] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3419--3419 []\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 3420--3420 []\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 '[] [1945] Underfull \hbox (badness 2452) in paragraph at lines 3496--3499 []\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 [1946] [1947] [1948] [1949] [1950] [1951] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 4062--4070 []\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 [1954] Underfull \hbox (badness 1231) in paragraph at lines 4139--4151 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 4152--4157 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1955] [1956] Underfull \hbox (badness 4660) in paragraph at lines 4272--4275 \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 Underfull \hbox (badness 10000) in paragraph at lines 4296--4298 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1957] [1958] [1959] Underfull \hbox (badness 1565) in paragraph at lines 4481--4485 []\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 [1960] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4564--4564 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1961] Underfull \hbox (badness 1931) in paragraph at lines 4599--4606 []\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) [1962] [1963] [1964] [1965] [1966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4923--4923 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1967]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} [1968] [1969] [1970] [1971] [1972] [1973] [1974] [1975] Underfull \hbox (badness 1622) in paragraph at lines 5513--5517 []\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 [1976] [1977] [1978] [1979] [1980] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5835--5835 []\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 5847--5847 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1981] [1982] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5980--5980 [] \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 5981--5981 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1983] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6191--6191 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1986] Underfull \hbox (badness 10000) in paragraph at lines 6275--6277 []\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 [1987] Underfull \hbox (badness 1502) in paragraph at lines 6324--6329 []\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 6324--6329 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 6497--6506 []\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 6497--6506 \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 [1990] Underfull \hbox (badness 2150) in paragraph at lines 6561--6564 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6577--6580 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1991] [1992] Underfull \hbox (badness 3118) in paragraph at lines 6700--6702 []\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 [1993] [1994] Underfull \hbox (badness 5091) in paragraph at lines 6875--6877 []\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 [1995] Underfull \hbox (badness 5331) in paragraph at lines 6891--6897 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6891--6897 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6891--6897 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6905--6912 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") Underfull \hbox (badness 1270) in paragraph at lines 6920--6930 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If [1996] Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., Underfull \hbox (badness 1424) in paragraph at lines 6971--6974 []\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 [1997] Underfull \hbox (badness 2376) in paragraph at lines 7042--7049 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7042--7049 \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 7042--7049 \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 7050--7053 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1998] Underfull \hbox (badness 1314) in paragraph at lines 7129--7136 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 7176--7179 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac kages(filters = Underfull \hbox (badness 1314) in paragraph at lines 7176--7179 \T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/ 10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n /10 ver-sion (for Underfull \hbox (badness 10000) in paragraph at lines 7209--7214 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , [1999] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7232--7232 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7268--7272 []\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 7282--7285 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2000] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7329--7329 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2001] [2002] Underfull \hbox (badness 4132) in paragraph at lines 7453--7455 []\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 [2003] [2004] [2005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7620--7620 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2006] [2007] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7763--7763 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2008] Underfull \hbox (badness 10000) in paragraph at lines 7803--7805 []\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 [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 7991--7993 []\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 7996--7998 []\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 [2011] [2012] [2013] [2014] Underfull \hbox (badness 1859) in paragraph at lines 8224--8227 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [2015] Underfull \hbox (badness 1655) in paragraph at lines 8318--8321 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \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 8329--8329 []\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 8337--8337 []\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):[] [2016] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8345--8345 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2017] Underfull \hbox (badness 1917) in paragraph at lines 8432--8434 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [2018] [2019] [2020] [2021] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8704--8704 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8705--8705 [] \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 8706--8706 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2022] Underfull \hbox (badness 10000) in paragraph at lines 8734--8736 []\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 8748--8750 []\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 8756--8761 []\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, [2023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8802--8802 [] \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 8803--8803 [] \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[] [2024] [2025] Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8932--8937 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8939--8942 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [2026] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9055--9055 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9056--9056 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2027] [2028] [2029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9229--9229 [] \T1/pcr/m/n/9 "S original, "),[] [2030] Underfull \hbox (badness 1789) in paragraph at lines 9362--9364 []\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 [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 5203) in paragraph at lines 9935--9938 []\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 [2040] [2041] Underfull \hbox (badness 1394) in paragraph at lines 10161--10168 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [2042] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10185--10185 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2043] [2044] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10346--10346 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2045] [2046] [2047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10527--10527 []\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[] [2048] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10613--10613 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10616--10616 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10621--10621 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2049] Underfull \hbox (badness 2027) in paragraph at lines 10693--10696 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2050] [2051] [2052] [2053] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10972--10972 []\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 10973--10973 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10980--10985 []\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 10980--10985 \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 10980--10985 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2054] [2055] [2056] [2057] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11213--11213 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11474--11478 \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 11492--11492 []\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 11497--11497 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2062] [2063] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11630--11630 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11631--11631 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2064] [2065] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2066] Underfull \hbox (badness 1917) in paragraph at lines 11890--11893 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11890--11893 \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 [2067] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11913--11913 []\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 '[] [2068] Underfull \hbox (badness 10000) in paragraph at lines 11976--11978 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [2069] Underfull \hbox (badness 6725) in paragraph at lines 12026--12035 \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 6428) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 12026--12035 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2070] Underfull \hbox (badness 1377) in paragraph at lines 12126--12129 []\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 [2071] Underfull \hbox (badness 3646) in paragraph at lines 12161--12163 [][][]$\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 12199--12199 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 12380--12384 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12411--12417 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2075] [2076] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12587--12587 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2077] Underfull \hbox (badness 1009) in paragraph at lines 12605--12617 []\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 12645--12647 []\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 [2078] Underfull \hbox (badness 1043) in paragraph at lines 12688--12693 []\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 [2079] [2080] [2081] [2082] Underfull \hbox (badness 1888) in paragraph at lines 12981--12984 []\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 12998--13001 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2083] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13044--13044 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2084] Underfull \hbox (badness 2158) in paragraph at lines 13099--13102 []\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 13147--13147 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2085] [2086] [2087] Underfull \hbox (badness 2302) in paragraph at lines 13304--13306 []\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 [2088] Underfull \hbox (badness 3333) in paragraph at lines 13411--13413 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2089] [2090] [2091] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13578--13578 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13602--13607 []\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 have Underfull \hbox (badness 5970) in paragraph at lines 13611--13614 []\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 13611--13614 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2092] Underfull \hbox (badness 1442) in paragraph at lines 13638--13642 []\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 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 13684--13684 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2093] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13715--13715 []\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 13722--13722 []\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 13724--13724 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] Underfull \vbox (badness 10000) has occurred while \output is active [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 13892--13894 []\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 [2097] [2098] Underfull \hbox (badness 6300) in paragraph at lines 14049--14056 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14049--14056 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14049--14056 \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 [2099] [2100] Underfull \hbox (badness 2020) in paragraph at lines 14218--14234 \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 pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 14218--14234 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2101] [2102] Underfull \hbox (badness 5022) in paragraph at lines 14357--14361 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 14364--14367 [][][]$\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 14364--14367 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14528--14528 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2106] [2107] [2108] [2109] [2110] [2111] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14969--14969 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14975--14975 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14996--14998 []\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 15011--15015 \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 Underfull \hbox (badness 1694) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 \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 15031--15036 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15037--15039 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2112] Underfull \hbox (badness 10000) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault 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 15088--15093 []\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 Underfull \hbox (badness 10000) in paragraph at lines 15096--15099 [][][]\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.packages[] [][]\T1/ptm/m/n/10 , [2113] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15150--15150 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2114] [2115] [2116] Underfull \hbox (badness 10000) in paragraph at lines 15357--15360 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 15357--15360 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2117] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15373--15373 []\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:[] [2118] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15440--15440 [] \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 15462--15462 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2119] [2120] Underfull \hbox (badness 1297) in paragraph at lines 15593--15595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2121] Underfull \hbox (badness 4036) in paragraph at lines 15640--15642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2122] [2123] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2124] Underfull \hbox (badness 1715) in paragraph at lines 15829--15832 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/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 15874--15876 []\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 = [2125] [2126] [2127]) [2128] [2129] [2130] (./KernSmooth-pkg.tex Chapter 15. [2131] 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) [2132] [2133] [2134] [2135] [2136] 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, [2137] [2138] [2139] [2140]) (./MASS-pkg.tex Chapter 16. [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2419--2419 []\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 2423--2423 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2175] [2176] [2177] [2178] Underfull \hbox (badness 6559) in paragraph at lines 2703--2706 []\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 [2179] [2180] [2181] Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 , [2182] [2183] Underfull \hbox (badness 4686) in paragraph at lines 3041--3043 []\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 [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3236--3236 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2187] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3366--3366 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1845) in paragraph at lines 4154--4156 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2200] [2201] [2202] [2203] [2204] [2205] [2206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4650--4650 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2207] [2208] [2209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4872--4872 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2224] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5985--5985 []\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") [2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} [2227] [2228] Underfull \hbox (badness 1783) in paragraph at lines 6266--6270 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2229] [2230] [2231] [2232] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6566--6566 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6654--6654 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2234] [2235] [2236] [2237] [2238] [2239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7093--7093 []\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 7110--7110 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2240] Underfull \hbox (badness 10000) in paragraph at lines 7133--7135 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7188--7194 []\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 ) = [2241] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7258--7258 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2242] [2243] Underfull \hbox (badness 5091) in paragraph at lines 7367--7370 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2244] [2245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2246] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7562--7562 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 4686) in paragraph at lines 8000--8002 []\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 [2253] [2254] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8119--8119 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8143--8147 []\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 [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] [2274] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9527--9527 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2275] Underfull \hbox (badness 2035) in paragraph at lines 9639--9641 []\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 9654--9657 []\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-larly), [2276] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9736--9736 []\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 9738--9738 []\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 9741--9741 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289]) (./Matrix-pkg.tex [2290] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\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 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2291] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\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 [2292] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\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 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2293] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\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 [2294] [2295] Overfull \hbox (15.18042pt too wide) in paragraph at lines 471--471 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2296] Underfull \hbox (badness 5147) in paragraph at lines 501--504 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in Underfull \hbox (badness 5119) in paragraph at lines 514--518 []\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 518--523 [][][]\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/pcr/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 548--548 []\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 550--550 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 559--559 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2297] [2298] Overfull \hbox (52.98038pt too wide) in paragraph at lines 673--673 []\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 674--674 []\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 675--675 []\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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 688--688 [] \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 689--689 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 763--767 \T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc r/m/n/10 https : / / www . netlib . org / lapack / double / [2300] [2301] Underfull \hbox (badness 3536) in paragraph at lines 882--887 []\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c at-ing if the re-sult should be sparse, i.e., for- Underfull \hbox (badness 7777) in paragraph at lines 882--887 \T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]" \T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de- Underfull \hbox (badness 6188) in paragraph at lines 882--887 \T1/ptm/m/n/10 cides from the ``spar-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 [2302] Underfull \hbox (badness 10000) in paragraph at lines 925--930 []\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 meth-ods: [2303] Overfull \hbox (72.78088pt too wide) in paragraph at lines 986--986 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2304] [2305]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} [2306] Underfull \hbox (badness 2285) in paragraph at lines 1259--1264 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2307] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1305--1305 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2308] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1400--1400 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1428--1431 []\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 [2309] Underfull \hbox (badness 1609) in paragraph at lines 1475--1479 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra Overfull \hbox (4.38043pt too wide) in paragraph at lines 1502--1502 []\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 1516--1516 []\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[] [2310] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1524--1524 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Underfull \hbox (badness 10000) in paragraph at lines 1571--1578 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1571--1578 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or [2311] Underfull \hbox (badness 1783) in paragraph at lines 1606--1610 []\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 Underfull \hbox (badness 1221) in paragraph at lines 1622--1628 \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 . Hen ce, 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.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1664 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1685 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1696 \aliasA{rowSums}{colSums}{rowSums} [2312] 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 from 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/10 , since [2313] [2314] [2315] 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 [2316] [2317] [2318] [2319] Underfull \hbox (badness 1484) in paragraph at lines 2277--2279 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2320] Underfull \hbox (badness 7379) in paragraph at lines 2373--2375 []\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 [2321] [2322] [2323] Underfull \hbox (badness 4846) in paragraph at lines 2649--2653 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2654--2658 []\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 2661--2664 []\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 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2708--2708 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2717--2719 []\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 2721--2726 []\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 2721--2726 [][]\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 [2325] Underfull \hbox (badness 1097) in paragraph at lines 2744--2747 []\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 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2757--2762 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2326] Underfull \hbox (badness 3646) in paragraph at lines 2996--2999 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 3028--3030 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 3031--3035 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 3040--3046 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2327] Underfull \hbox (badness 10000) in paragraph at lines 3047--3051 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3057--3061 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 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 [2328] [2329] Underfull \hbox (badness 10000) in paragraph at lines 3241--3243 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3288--3290 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2330] Underfull \hbox (badness 2469) in paragraph at lines 3408--3411 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3573--3577 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3573--3577 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2333] Underfull \hbox (badness 2285) in paragraph at lines 3623--3626 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2334] [2335] Underfull \hbox (badness 10000) in paragraph at lines 3770--3775 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3770--3775 \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 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3782--3785 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2336] Underfull \hbox (badness 10000) in paragraph at lines 3858--3860 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3945--3945 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2338] [2339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4078--4078 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2340] Underfull \hbox (badness 3635) in paragraph at lines 4146--4150 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4155--4158 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4155--4158 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4160--4164 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2341] [2342] Underfull \hbox (badness 3158) in paragraph at lines 4343--4347 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2343] [2344] [2345] [2346] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4593--4593 []\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 4600--4600 [] \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 4604--4604 []\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 4607--4607 []\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 4617--4617 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2347] [2348] [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 4919--4924 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2351] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5000--5000 []\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 5002--5002 [] \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 5006--5006 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2352] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5013--5013 [] \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 '[] [2353] [2354] Underfull \hbox (badness 4120) in paragraph at lines 5157--5160 []\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 (15.18042pt too wide) in paragraph at lines 5194--5194 []\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 5200--5200 [] \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 5201--5201 [] \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 5205--5205 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5207--5207 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2355] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5214--5214 []\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 5217--5217 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2356] Underfull \hbox (badness 1817) in paragraph at lines 5306--5315 []\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 within the Underfull \hbox (badness 10000) in paragraph at lines 5348--5350 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5350--5353 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5363--5366 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2357] Underfull \hbox (badness 4765) in paragraph at lines 5381--5384 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2358] [2359] [2360] [2361] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2362] Underfull \hbox (badness 10000) in paragraph at lines 5782--5785 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5793--5793 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2363] Underfull \hbox (badness 1622) in paragraph at lines 5830--5835 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5830--5835 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2364] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5891--5891 []\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 5892--5892 [] \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 5899--5899 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2365] [2366] Underfull \hbox (badness 1062) in paragraph at lines 6028--6031 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 6057--6060 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2367] Underfull \hbox (badness 2635) in paragraph at lines 6169--6174 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6169--6174 \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 "Matrix"\T1/ptm/ m/n/10 , by class [2368] Underfull \hbox (badness 10000) in paragraph at lines 6177--6180 []\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 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6287--6297 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6287--6297 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2369] Underfull \hbox (badness 3179) in paragraph at lines 6369--6372 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2370] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\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., [2371] Underfull \hbox (badness 10000) in paragraph at lines 6542--6545 []\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., [2372] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6558--6558 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6597--6603 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6597--6603 [][]\T1/pcr/m/n/10 stop[][][]\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, Underfull \hbox (badness 1675) in paragraph at lines 6618--6621 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2373] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6688--6688 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2374] [2375] Underfull \hbox (badness 10000) in paragraph at lines 6829--6832 []\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 [2376] Underfull \hbox (badness 1490) in paragraph at lines 6851--6853 []\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[][][] \T 1/ptm/m/n/10 and (one case of) [2377] Underfull \hbox (badness 5036) in paragraph at lines 6931--6935 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6931--6935 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2378]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.7030 \aliasA{det}{Matrix-class}{det} [2379] Underfull \hbox (badness 10000) in paragraph at lines 7133--7136 Underfull \hbox (badness 10000) in paragraph at lines 7143--7145 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2380]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7206 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7314 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7413 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7510--7516 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2381] Underfull \hbox (badness 10000) in paragraph at lines 7583--7586 []\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 1199) in paragraph at lines 7583--7586 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7586--7591 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7586--7591 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7591--7595 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7591--7595 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7601--7602 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2382] [2383] Underfull \hbox (badness 1009) in paragraph at lines 7737--7739 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see [2384] Underfull \hbox (badness 1062) in paragraph at lines 7782--7785 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 7816--7819 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2385] Underfull \hbox (badness 10000) in paragraph at lines 7872--7874 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7974--7974 [] \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 8014--8014 []\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 [2388] Underfull \hbox (badness 2635) in paragraph at lines 8079--8084 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8079--8084 \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 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8087--8090 []\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 ); us e, e.g., [2389] Underfull \hbox (badness 3482) in paragraph at lines 8161--8167 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2390] Underfull \hbox (badness 1867) in paragraph at lines 8281--8283 []\T1/ptm/m/n/10 fast sim- [2391]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} [2392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8408--8408 []\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 8409--8409 []\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 8410--8410 []\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 8523--8533 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2393] Underfull \hbox (badness 3179) in paragraph at lines 8594--8597 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 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 8684--8687 []\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 8760--8763 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8776--8776 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2397] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8888--8891 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8894--8901 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2398] [2399] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8987--8987 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8990--8990 []\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 8992--8992 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8996--8996 []\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 8997--8997 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 9022--9032 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9022--9032 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2400] [2401]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9123 \aliasA{qr}{qr-methods}{qr} [2402] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9196--9196 []\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 9207--9207 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9227--9227 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9235--9235 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2403] Underfull \hbox (badness 10000) in paragraph at lines 9292--9298 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9309--9312 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2404] [2405] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9408--9408 []\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 9424--9424 []\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 9430--9430 []\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 9431--9431 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9449 ... the Reciprocal Condition Number}{rcond} [2406] [2407] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9562--9562 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2408] [2409] [2410] Underfull \hbox (badness 2351) in paragraph at lines 9753--9761 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9753--9761 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2411] [2412] Underfull \hbox (badness 1558) in paragraph at lines 9900--9903 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2413] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9962--9962 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9966--9966 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2414]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.10028 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10125--10125 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10132--10132 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2415] Underfull \hbox (badness 1616) in paragraph at lines 10167--10179 []\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 10184--10187 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 10193--10200 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10206--10216 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10206--10216 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10233--10237 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's [2416] Underfull \hbox (badness 10000) in paragraph at lines 10240--10242 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10263--10264 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10269--10271 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10273--10274 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10281--10284 [][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10299--10299 []\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 10303--10303 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2417] Underfull \hbox (badness 10000) in paragraph at lines 10324--10327 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10352--10354 []\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 10360--10363 []\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 10360--10363 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10371--10375 []\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 10371--10375 \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 [2418] Underfull \hbox (badness 1668) in paragraph at lines 10386--10391 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 1158) in paragraph at lines 10407--10413 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10466--10466 [] \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 10467--10467 [] \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 10468--10468 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2420] [2421] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10652--10652 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2422] Underfull \hbox (badness 1668) in paragraph at lines 10694--10699 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2423] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10791--10791 []\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 10795--10795 []\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 10796--10796 []\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 10801--10801 []\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 10804--10804 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2424] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10827--10827 []\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 10828--10828 []\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)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10854--10854 []\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 10856--10856 [] \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 10858--10858 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] Underfull \vbox (badness 10000) has occurred while \output is active [2425] [2426] Underfull \hbox (badness 10000) in paragraph at lines 10999--11003 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11039 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2427] [2428] Underfull \hbox (badness 10000) in paragraph at lines 11169--11171 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11197--11197 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2429] Underfull \hbox (badness 5036) in paragraph at lines 11225--11227 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a Underfull \hbox (badness 2970) in paragraph at lines 11359--11365 []\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 11359--11365 \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 "lsparseVec tor"\T1/ptm/m/n/10 , [2430] Underfull \hbox (badness 10000) in paragraph at lines 11432--11435 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2431] Underfull \hbox (badness 10000) in paragraph at lines 11450--11455 []\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 11465--11467 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2432] [2433] Underfull \hbox (badness 2698) in paragraph at lines 11590--11596 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2434] Underfull \hbox (badness 10000) in paragraph at lines 11683--11685 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11701--11706 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11701--11706 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other [2435] Underfull \hbox (badness 2591) in paragraph at lines 11709--11714 \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-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or Underfull \hbox (badness 2057) in paragraph at lines 11781--11783 []\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., [2436] [2437] Underfull \hbox (badness 6641) in paragraph at lines 11867--11870 []\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 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11907--11911 []\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 11907--11911 \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 [2438] [2439] Underfull \hbox (badness 7649) in paragraph at lines 12014--12016 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2440] [2441] [2442] Underfull \hbox (badness 7362) in paragraph at lines 12215--12217 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 12253--12253 []\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 12254--12254 []\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)[] [2443] [2444] [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12396--12396 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12409--12409 [] \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 12414--12414 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2446] Underfull \hbox (badness 6910) in paragraph at lines 12590--12592 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2447] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. [2448] [2449]) (./boot-pkg.tex [2450] Chapter 18. [2451] [2452] [2453] [2454] [2455] [2456] [2457] 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"), [2458] 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- [2459] [2460] [2461] 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 boot.c i[][][]\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 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2462] 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 [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2465] 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 [2466] [2467] [2468] [2469] 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- [2470] [2471] [2472] [2473] [2474] 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), [2475] [2476] [2477] Underfull \vbox (badness 10000) has occurred while \output is active [2478] 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),[] [2479] 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. [2480] [2481] [2482] 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 [2483] 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$statis tic \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 , [2484] [2485] 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/10 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/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2486] [2487] [2488] [2489] [2490] 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,[] [2491] [2492] [2493] 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.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/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 , [2494] 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)) [2495] [2496] [2497] 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 [2498] [2499] [2500] [2501] [2502] [2503] [2504] 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)[] [2505] [2506] 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])[] [2507] [2508] [2509] Underfull \hbox (badness 10000) in paragraph at lines 4190--4192 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2510] 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 [2511] [2512] 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-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] 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 [2522] [2523] [2524] [2525] 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 [2526] 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])[] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] 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][] [2535] 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 t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2536] 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 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2537] [2538] [2539] [2540] 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). [2541] [2542] 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[] [2543] [2544] [2545] 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 [2546] [2547] 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),[] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555]) (./class-pkg.tex [2556] Chapter 19. [2557] [2558] [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]) (./cluster-pkg.tex Chapter 20. [2573] Underfull \hbox (badness 1655) in paragraph at lines 134--143 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 134--143 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 134--143 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 134--143 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2574] [2575] 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]))[] [2576] [2577] Underfull \vbox (badness 10000) has occurred while \output is active [2578] [2579] 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, ...)[] [2580] [2581] 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)[] [2582] 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 [2583] [2584] 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-ence s; [][]\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 , [2585] 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 [2586] 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), ...)[] [2587] 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, [2588] [2589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120 [] \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 1137--1137 []\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 [2590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1207--1211 []\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 [2591] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283 [] \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 1289--1289 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2592] [2593] Underfull \hbox (badness 10000) in paragraph at lines 1428--1433 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or [2594] Underfull \hbox (badness 10000) in paragraph at lines 1476--1479 Underfull \hbox (badness 10000) in paragraph at lines 1493--1497 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\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/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/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 1517--1517 []\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 1527--1527 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2595] Underfull \hbox (badness 5741) in paragraph at lines 1567--1570 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2597] [2598] Underfull \hbox (badness 1540) in paragraph at lines 1753--1761 \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 = [2599] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844 []\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 1863--1863 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2600] [2601] [2602] [2603] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2182--2185 Underfull \hbox (badness 3179) in paragraph at lines 2196--2202 [][][]\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/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2605] [2606] Underfull \hbox (badness 10000) in paragraph at lines 2354--2357 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2607] Underfull \hbox (badness 1292) in paragraph at lines 2422--2425 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and [2608] Underfull \hbox (badness 6675) in paragraph at lines 2431--2433 []\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 2454--2457 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\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 , [2609] [2610] [2611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670 []\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 ):[] [2612] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2613] [2614] [2615] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2618] [2619] [2620] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2621] Underfull \hbox (badness 10000) in paragraph at lines 3345--3348 []\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 [2622] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2623] [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 3581--3584 []\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 [2626] Underfull \hbox (badness 10000) in paragraph at lines 3644--3649 [][][]\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.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2627] Underfull \hbox (badness 3884) in paragraph at lines 3706--3711 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/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 3718--3721 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\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/10 hclust[][][]\T 1/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 , [2628] [2629] [2630] Underfull \hbox (badness 10000) in paragraph at lines 3903--3906 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3987--3987 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3998--4000 []\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 [2632] [2633] [2634] [2635] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4191--4191 [] \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 4193--4193 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2636] [2637] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4336--4336 []\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 4345--4345 [] \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 4347--4347 [] \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 4350--4350 []\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 4352--4352 [] \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 4359--4359 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2638] [2639] [2640] [2641] [2642] [2643] [2644] Underfull \hbox (badness 10000) in paragraph at lines 4732--4738 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4748--4750 []\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 4761--4761 []\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 4763--4763 []\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 4773--4773 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2645] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4777--4777 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2646]) (./codetools-pkg.tex 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,[] [2647] 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 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2648] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2649] [2650] [2651]) (./foreign-pkg.tex [2652] 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 . [2653] 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 [2654] [2655] 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 , [2656] 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, [2657] [2658] [2659] 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,[] [2660] 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 10000) 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- Underfull \hbox (badness 6001) in paragraph at lines 505--514 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 , 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 "_dupli cated_"\T1/ptm/m/n/10 ) if [2661] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e n-[]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 [2662] 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,[] [2663] 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="")[] [2664] [2665] 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])[] [2666] 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 . [2667] 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) [2668] 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))) [2669] [2670] 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"))[] [2671] [2672] 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 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2673] 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 side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2674]) (./lattice-pkg.tex Chapter 23. [2675] 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 / [2676] [2677] 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"),[] [2678] 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"),[] [2679] [2680] [2681] [2682] 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 [2683] [2684] [2685] [2686] 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. [2687] 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 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2688] [2689] 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 [2690] [2691] [2692] 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 , [2693] 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/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2694] Underfull \vbox (badness 10000) has occurred while \output is active [2695] 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 [2696] 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\T1/pt m/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 [2697] [2698] [2699] [2700] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2701] 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-fied, t he 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 first ch ecked. If [2702] [2703] [2704] 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"),[] [2705] [2706] [2707] [2708] [2709] 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"),[] [2710] [2711] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2712] 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.rast er[][][]\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[][][] \T 1/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 [2713] 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 [2714] 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),[] [2715] 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"),[] [2716] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2717] [2718] [2719]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} [2720] 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"),[] [2721] [2722] [2723] [2724] [2725] 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))) [2726] [2727] 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 [2728] 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 [2729] 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-rent se t-tings (ob-tained by [2730] 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 trellis .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 [2731] [2732] 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 i s 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 "superpose.p olygon"\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 f or \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 c ol.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 plot .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 pl ot.polygon \T1/ptm/m/n/10 and [2733] [2734] [2735] [2736] [2737] 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")[] [2738] [2739] Underfull \vbox (badness 1092) has occurred while \output is active [2740] 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 . [2741] [2742] 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-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2743] [2744] [2745] [2746] [2747] 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-cally the en-try f or 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],[] [2748] 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 lef t of pan-els us-ing [2749] 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, wh ich is to draw a strip ap-pro-pri-ate for [2750] [2751] 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",[] [2752] 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 [2753] 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-fault 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 , ex-tr a 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 , these are used (in com-bi-na-tion with [2754] [2755] 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 Lattice[ ][][]\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 , [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] 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- [2759] [2760] 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/1 0 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-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2761] 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,[] [2762] [2763] 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/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2764] 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 v alid color. The [2765] [2766] [2767] [2768] [2769] 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 pan el 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 [2770] [2771] 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 this fu nc-tion is passed [2772] [2773] 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 [2774] [2775] 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 [2776] 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))[] [2777] [2778] 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 on 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 be a list of ar-gu-ments to be sup-plied to [2779] 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),[] [2780] 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)[] [2781] [2782] [2783] 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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] 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.superpo se 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 [2792] [2793] 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, ...)[] [2794] 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 [2795] 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 [2796] [2797] 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 [2798] 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)[] [2799] [2800] 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)),[] [2801] Overfull \hbox (46.28876pt too wide) in paragraph at lines 9228--9232 []\T1/ptm/m/n/10 Returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9228--9232 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2802] [2803] [2804] [2805] [2806] [2807] [2808] 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/10 , \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/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2809] [2810] [2811]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} [2812] [2813] [2814] 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 Heart 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),[] [2815] [2816]) (./mgcv-pkg.tex Chapter 24. [2817] [2818] 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,[] [2819] 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. [2820] [2821] [2822] [2823] Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][]\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 378--385 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2824] Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421 []\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)+[] [2825] [2826] [2827] Underfull \hbox (badness 2922) in paragraph at lines 633--634 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2828] [2829] Underfull \hbox (badness 1406) in paragraph at lines 703--704 []\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 [2830] [2831] Underfull \hbox (badness 1158) in paragraph at lines 813--815 []\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 [2832] Underfull \hbox (badness 1259) in paragraph at lines 876--877 []\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). [2833] Underfull \vbox (badness 10000) has occurred while \output is active [2834] [2835] [2836] [2837] [2838] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 []\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 1226--1226 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2839] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \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 1255--1255 []\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 1264--1264 []\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 1266--1266 [] \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 [2840] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1297--1297 []\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)[] [2841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1380--1380 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2842] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1391--1391 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1425--1425 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1931--1931 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2852] [2853] [2854] [2855] [2856] [2857] Underfull \hbox (badness 1052) in paragraph at lines 2319--2327 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2336--2336 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2348--2351 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2361--2365 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2858] Underfull \hbox (badness 1043) in paragraph at lines 2387--2392 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2859] [2860] [2861] Underfull \hbox (badness 1043) in paragraph at lines 2552--2558 \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 [2862] Underfull \hbox (badness 10000) in paragraph at lines 2688--2694 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\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 2688--2694 [][]\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 2688--2694 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2863] [2864] Underfull \vbox (badness 10000) has occurred while \output is active [2865] Underfull \vbox (badness 10000) has occurred while \output is active [2866] [2867] [2868] [2869] [2870] [2871] [2872] [2873] [2874] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3344--3344 [] \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 3347--3347 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] Underfull \hbox (badness 5189) in paragraph at lines 3822--3826 []\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 [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3939--3939 []\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 [2885] [2886] [2887] Underfull \hbox (badness 1184) in paragraph at lines 4108--4112 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2888] [2889] [2890] [2891] [2892] [2893] [2894] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4554--4554 [] \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)+[] [2895] [2896] [2897] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4704--4704 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2898] [2899] Underfull \hbox (badness 1142) in paragraph at lines 4829--4833 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2900] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2901] [2902] Underfull \hbox (badness 5970) in paragraph at lines 5018--5024 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-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 5018--5024 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/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 . [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] [2905] [2906] [2907] Underfull \hbox (badness 1577) in paragraph at lines 5370--5373 []\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 5377--5378 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2908] [2909] [2910] [2911] [2912] [2913] [2914] Underfull \hbox (badness 6708) in paragraph at lines 5766--5767 []\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 [2915] [2916] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5815--5815 [] \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 5840--5840 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2917] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5869--5869 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2918] [2919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5991--5991 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2920] [2921] [2922] [2923] [2924] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6328--6328 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2925] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6330--6330 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2926] [2927] [2928] Underfull \vbox (badness 10000) has occurred while \output is active [2929] [2930] [2931] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6670--6670 []\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) [2932] [2933] [2934] [2935] Underfull \vbox (badness 10000) has occurred while \output is active [2936] Underfull \vbox (badness 10000) has occurred while \output is active [2937] [2938] [2939] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7102--7102 []\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 7129--7129 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] Underfull \hbox (badness 1242) in paragraph at lines 7672--7673 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2949] [2950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2951] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7822--7822 []\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 7841--7841 [] \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 [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] [2972] Underfull \hbox (badness 10000) in paragraph at lines 9061--9064 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\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 9061--9064 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ 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 9061--9064 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2973] Underfull \hbox (badness 10000) in paragraph at lines 9117--9120 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9117--9120 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2974] [2975] [2976] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9337--9337 []\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 9338--9338 [] \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 9341--9341 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2977] [2978] [2979] Underfull \hbox (badness 1629) in paragraph at lines 9499--9504 \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 [2980] [2981] [2982] [2983] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9710--9710 [] \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 9747--9751 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para- Underfull \hbox (badness 1292) in paragraph at lines 9747--9751 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2984] [2985] [2986] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9880--9880 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2987] [2988] [2989] Underfull \vbox (badness 10000) has occurred while \output is active [2990] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10153--10153 [] \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[] [2991] Underfull \hbox (badness 1205) in paragraph at lines 10191--10193 []\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 10191--10193 \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 10197--10202 []\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 [2992] Underfull \hbox (badness 1205) in paragraph at lines 10281--10283 []\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 10281--10283 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2993] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\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 10350--10353 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh 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, [2994] [2995] Underfull \hbox (badness 1253) in paragraph at lines 10480--10482 []\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, [2996] [2997] [2998] [2999] [3000] Underfull \hbox (badness 1946) in paragraph at lines 10733--10740 []\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 10733--10740 \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 10733--10740 \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: s ee [3001] Underfull \hbox (badness 2846) in paragraph at lines 10741--10744 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 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 10741--10744 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3002] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10807--10807 []\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 10817--10817 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] Underfull \hbox (badness 10000) in paragraph at lines 10848--10851 []\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 , [3003] [3004] [3005] [3006] [3007] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11150--11150 []\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) [3008] [3009] [3010] [3011] [3012] [3013] [3014] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11521--11521 [] \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 11535--11535 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] [3015] Underfull \vbox (badness 10000) has occurred while \output is active [3016] Underfull \hbox (badness 3861) in paragraph at lines 11637--11640 []\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 11646--11646 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3017] Underfull \hbox (badness 10000) in paragraph at lines 11703--11707 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3018] [3019] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11847--11847 [] \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 11858--11863 []\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 [3020] [3021] Underfull \hbox (badness 1803) in paragraph at lines 11935--11939 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11947--11959 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11964--11968 \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 11964--11968 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [3022] [3023] [3024] [3025] Underfull \hbox (badness 6876) in paragraph at lines 12159--12165 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 12200--12201 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3026] [3027] Underfull \hbox (badness 10000) in paragraph at lines 12318--12319 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3028] [3029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12372--12372 [] \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 12384--12384 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12396--12396 [] \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 12401--12401 [] \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 12407--12407 [] \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 12408--12408 [] \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:[] [3030] Underfull \hbox (badness 10000) in paragraph at lines 12477--12479 []\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 12477--12479 \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 [3031] [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 12607--12608 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12688--12688 []\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 12689--12689 []\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[] [3035] [3036] [3037] Underfull \hbox (badness 10000) in paragraph at lines 12840--12841 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3038] [3039] [3040] [3041] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13090--13090 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3042] Underfull \hbox (badness 10000) in paragraph at lines 13151--13153 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 13310--13313 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13310--13313 \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 13310--13313 \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" [3046] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3047] Underfull \hbox (badness 10000) in paragraph at lines 13441--13447 []\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 13441--13447 \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- [3048] [3049] [3050] Underfull \vbox (badness 10000) has occurred while \output is active [3051] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13655--13655 []\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 [3052] Underfull \hbox (badness 10000) in paragraph at lines 13758--13766 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [3053] Underfull \hbox (badness 10000) in paragraph at lines 13784--13785 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3054] [3055] [3056] [3057] Underfull \hbox (badness 3396) in paragraph at lines 14044--14047 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [3058] Underfull \hbox (badness 10000) in paragraph at lines 14089--14091 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 14370--14373 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 14370--14373 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3064] Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][][]\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 14403--14407 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][]\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 , [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2158) in paragraph at lines 14693--14693 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3070] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14772--14772 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3071] [3072] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14906--14906 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3073] [3074] Underfull \hbox (badness 4846) in paragraph at lines 15037--15040 []\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 [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3095] [3096] [3097] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441 []\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, [3098] Overfull \hbox (48.78088pt too wide) in paragraph at lines 16443--16443 []\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 16445--16445 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 16465--16466 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16465--16466 \T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected by \T1/pcr/m/n/10 ar.row [3099] [3100] [3101] [3102] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653 []\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 16654--16654 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3103] [3104] [3105]) (./nlme-pkg.tex [3106] Chapter 25. [3107] 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 - fi t-ted) are used; else, if [3108] 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 - fi t-ted) are used; else, if [3109] [3110] [3111] [3112] [3113] 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,[] [3114] [3115] 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 --------------------------- ---------------[] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] 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"),[] [3124] 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.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3125] [3126] [3127] [3128] [3129] [3130] [3131] 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.effe cts.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 , [3132] 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 [3133] [3134] [3135] [3136] [3137] 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 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3138] 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")[] [3139] 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 [3140] [3141] 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 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3142] 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,[] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] 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 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3151] [3152] [3153] [3154] [3155] [3156pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored ...shipout:D \box_use:N \l_shipout_box l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3157] [3158] [3159] [3160] [3161] [3162] 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 corGaus[][ ][]\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 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3187] [3188] [3189] [3190] [3191] [3192] [3193] 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 , [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] 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 [3203] 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 , [3204] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\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 , [3205] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3206] [3207] [3208] [3209] Underfull \hbox (badness 7133) in paragraph at lines 6562--6566 []\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 , [3210] Underfull \hbox (badness 10000) in paragraph at lines 6661--6667 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3211] Underfull \hbox (badness 10000) in paragraph at lines 6726--6728 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3212] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3213] [3214] [3215] Underfull \hbox (badness 10000) in paragraph at lines 6999--7006 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7044--7046 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3217] [3218] [3219] Underfull \hbox (badness 10000) in paragraph at lines 7259--7264 [][][]\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 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3220] [3221] [3222] Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7411--7419 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7434--7437 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3223] [3224] [3225] Underfull \hbox (badness 3354) in paragraph at lines 7650--7652 []\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 [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\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 8205--8205 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8214--8236 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3234] [3235] [3236] [3237] [3238] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8527--8529 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8578 \aliasA{sigma}{lmeObject}{sigma} [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] [3249] [3250] [3251] Underfull \hbox (badness 10000) in paragraph at lines 9330--9337 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3252] Underfull \hbox (badness 6300) in paragraph at lines 9423--9426 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3253] [3254] [3255] [3256]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3257] Underfull \hbox (badness 10000) in paragraph at lines 9712--9715 []\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 9756--9759 []\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 9756--9759 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3258] [3259] [3260] [3261] [3262] [3263] [3264] [3265] Underfull \hbox (badness 7291) in paragraph at lines 10220--10222 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3266] [3267] [3268] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3269] Underfull \hbox (badness 1596) in paragraph at lines 10465--10491 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3270] [3271] [3272] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3273] [3274] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10792--10792 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10803--10808 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3275] Underfull \hbox (badness 8075) in paragraph at lines 10825--10829 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10844--10846 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3276] [3277] [3278] [3279] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136 []\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 11137--11137 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3280] [3281] [3282] [3283] [3284] [3285] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 6268) in paragraph at lines 11914--11924 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] Underfull \hbox (badness 10000) in paragraph at lines 12175--12181 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 6876) in paragraph at lines 12497--12499 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-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 [3301] [3302] Underfull \hbox (badness 2452) in paragraph at lines 12653--12660 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 12718--12724 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3313] [3314] [3315] [3316] [3317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3318] Underfull \hbox (badness 10000) in paragraph at lines 13699--13702 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3319] Underfull \hbox (badness 1838) in paragraph at lines 13742--13749 []\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 13742--13749 \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 13799--13799 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3320] Underfull \hbox (badness 10000) in paragraph at lines 13806--13809 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13806--13809 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13834--13837 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13834--13837 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3321] Underfull \hbox (badness 10000) in paragraph at lines 13914--13917 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3322] Underfull \hbox (badness 1472) in paragraph at lines 13939--13946 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3323] Underfull \hbox (badness 10000) in paragraph at lines 14008--14010 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] Underfull \hbox (badness 1215) in paragraph at lines 14288--14290 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3328] [3329] [3330] [3331] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3332] [3333] [3334] [3335] [3336] [3337] [3338] [3339] [3340]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Underfull \hbox (badness 2126) in paragraph at lines 15825--15829 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833 []\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 15852--15852 [] \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 15853--15853 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3352] Underfull \hbox (badness 1009) in paragraph at lines 15883--15892 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3353] [3354] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 10000) in paragraph at lines 16365--16371 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\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.reStruc t[][][]\T1/ptm/m/n/10 , [3360] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3361] [3362] [3363] [3364] [3365] [3366] [3367] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3368] [3369] [3370] [3371] [3372] Underfull \hbox (badness 1867) in paragraph at lines 17220--17229 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3373] Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17292--17293 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3374] [3375] [3376] [3377] Underfull \hbox (badness 10000) in paragraph at lines 17542--17550 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/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 , [3378] [3379] [3380] [3381] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17814--17814 []\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 17816--17816 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3382] [3383] [3384] [3385] [3386] [3387] Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][][]\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.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][]\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 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3388] Underfull \hbox (badness 3579) in paragraph at lines 18290--18295 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3389] Underfull \hbox (badness 3579) in paragraph at lines 18354--18359 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3390] Underfull \hbox (badness 3579) in paragraph at lines 18417--18422 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3391] Underfull \hbox (badness 1577) in paragraph at lines 18478--18480 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18480--18485 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3392] Underfull \hbox (badness 3579) in paragraph at lines 18543--18548 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18576--18585 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\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 18576--18585 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3393] Underfull \hbox (badness 3579) in paragraph at lines 18615--18620 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3394] [3395] Underfull \hbox (badness 1009) in paragraph at lines 18761--18770 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3396] [3397] Underfull \hbox (badness 1009) in paragraph at lines 18893--18902 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406]) (./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): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3407] 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,[] [3408] [3409] [3410] 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,[] [3411] 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)[] [3412] [3413] 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,[] [3414]) (./rpart-pkg.tex Chapter 27. [3415] [3416] [3417] [3418] 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, ...)[] [3419] [3420] [3421] [3422] 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 will be at the hor-i-zon-tal plot co-or-di-nates of [3423] [3424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3425] [3426] [3427] Overfull \hbox (25.98041pt too wide) in paragraph at lines 914--914 []\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 933--933 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3428] [3429] [3430] [3431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1179--1179 []\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 1180--1180 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1242--1244 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3432] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1286--1286 []\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 1302--1302 []\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 1303--1303 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3433] [3434] [3435] [3436] [3437] [3438] [3439] Underfull \hbox (badness 1565) in paragraph at lines 1759--1762 []\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 ', [3440] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1853--1853 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3441] [3442] [3443]) (./spatial-pkg.tex [3444] Chapter 28. [3445] [3446] [3447] [3448] [3449] [3450] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463]) (./survival-pkg.tex [3464] Chapter 29. [3465] [3466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\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 190--190 []\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 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3467] [3468] Underfull \hbox (badness 6412) in paragraph at lines 282--284 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3469] [3470]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} [3471] Overfull \hbox (9.78043pt too wide) in paragraph at lines 483--483 []\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 485--485 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3472] Overfull \hbox (6.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3473] [3474] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3475] [3476] 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 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"),[] [3477] [3478] 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,[] [3479] [3480] [3481] 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[] [3482] [3483] 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) [3484] 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} [3485] Underfull \hbox (badness 10000) in paragraph at lines 1356--1360 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by 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, ...)[] [3486] [3487] [3488] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575 [] \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 1624--1624 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3489] [3490] [3491] [3492] [3493] Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 []\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 1940--1955 \T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt m/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3494] Underfull \hbox (badness 1337) in paragraph at lines 2024--2028 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3495] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2079--2079 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2651--2651 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2678--2678 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3504] [3505] [3506] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2910--2910 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3507] [3508] [3509] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3251--3251 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3512] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3286--3286 [] \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 3300--3302 []\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 3311--3311 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3513] [3514] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3445--3445 [] \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 )))[] [3515] [3516] Overfull \hbox (467.89665pt too wide) in alignment at lines 3586--3586 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3517] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3518] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3519] [3520] [3521] [3522] [3523] [3524] [3525] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4144--4144 [] \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 )))[] [3526] [3527] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4290--4290 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4295--4295 []\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 4299--4299 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3529] [3530] [3531] Overfull \vbox (11.01616pt too high) has occurred while \output is active [3532] [3533] [3534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4716--4716 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3535] [3536] [3537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3538] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5072--5072 []\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[] [3539] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5080--5080 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3540] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5166--5166 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5244--5244 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3542] Underfull \hbox (badness 1852) in paragraph at lines 5316--5318 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3543] [3544] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5441--5441 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3545] [3546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5543--5543 []\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 5544--5544 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3547] [3548] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5810--5810 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5831--5831 []\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 5833--5833 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3551] [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6348--6348 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3557] [3558] [3559] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6528--6528 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6540--6543 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6848--6848 []\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 6849--6849 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3565] [3566] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7014--7014 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3567] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7088--7088 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicates[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7092 ...ata from a soldering experiment}{solder} [3568] [3569] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7198--7198 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3570] [3571] [3572] [3573] [3574] [3575] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7562--7562 []\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 7563--7563 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3576] [3577] [3578] [3579] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7881--7881 [] \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 ),[] [3580] [3581] [3582] [3583] Underfull \hbox (badness 1253) in paragraph at lines 8170--8173 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3586] Underfull \hbox (badness 10000) in paragraph at lines 8422--8431 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 8422--8431 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3587] [3588] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8518--8518 [] \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 8536--8536 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8578--8584 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3589] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8630--8630 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3590] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8716--8716 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 8941--8946 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3594] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8960--8960 [] \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 8961--8961 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3595] [3596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9171--9171 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3597] [3598] Underfull \hbox (badness 3058) in paragraph at lines 9304--9309 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3599] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9434--9434 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3601] [3602] [3603] [3604] [3605] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9819--9819 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 9860--9864 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3606] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9906--9906 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3607] [3608] Underfull \hbox (badness 2035) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10070--10077 \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, it is [3609] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10150--10150 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3610] [3611] [3612] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10307--10307 [] \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 )[] [3613] [3614] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 [] \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 10442--10442 [] \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 )[] [3615] [3616] [3617] [3618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10751--10751 []\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 10752--10752 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10758--10758 [] \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 10760--10760 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3620] [3621] [3622] [3623] [3624] [3625] [3626] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11201--11201 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3627] [3628] [3629]) [3630] No file fullrefman.ind. (./fullrefman.aux) Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.tree} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.viewports} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.xyplot.zoo} has been referenced but does not ex ist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipsePoints} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.ellipse} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.cluster.stats} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chorizon} has been referenced but does not exis t, replaced by a fixed one pdfTeX warning (dest): name{Rfn.Sobj.Rul.SpatialGrid} has been referenced but d oes not exist, 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2021] (kpathsea + Thai support). Scanning input file fullrefman.idx.............................done (25101 entries accepted, 78 rejected). Sorting entries...........................................................................................................................................................................................................................................................................................done (418554 comparisons). Generating output file fullrefman.ind...........................done (26205 lines written, 106 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2020-10-01> patch level 4 L3 programming layer <2021-02-18> (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2020/04/10 v1.4m 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/base/fontenc.sty) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty (/usr/share/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref-langpatches.def) (/usr/share/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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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 5050) 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 \T1/pt m/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/pcr/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 1668) in paragraph at lines 154--161 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] Underfull \hbox (badness 3009) in paragraph at lines 226--238 \T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1 0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou sly to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 369--372 [][][]\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-lar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 567--573 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 635--635 []\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 636--636 []\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 912--912 []\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 933--933 []\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 962--962 []\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 1578--1584 Underfull \hbox (badness 10000) in paragraph at lines 1591--1593 []\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 1770--1770 [] \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 1799--1802 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1919--1921 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2056--2056 []\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 2094--2096 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e 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 2366--2366 []\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 2408--2408 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] Underfull \hbox (badness 10000) in paragraph at lines 2503--2505 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2506--2511 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [39] Underfull \hbox (badness 1107) in paragraph at lines 2574--2576 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] [42] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2741--2741 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3410--3410 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [52] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3441--3441 []\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 3442--3442 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3449--3449 []\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 3450--3450 [] \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 3453--3453 []\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 3901--3903 []\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 4399--4403 []\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 4399--4403 \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 or [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4483--4483 [] \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 4717--4717 []\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 4748--4754 []\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 4759--4762 []\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 4935--4935 []\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 5191--5193 []\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 10000) in paragraph at lines 5614--5622 []\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 [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6183--6191 []\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 6380--6380 []\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 6382--6382 []\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 6383--6383 []\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 6585--6588 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6589--6592 []\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 6632--6640 []\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 6796--6796 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6848--6851 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC onnection\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 7031--7034 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 7031--7034 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [104] [105] [106] Underfull \hbox (badness 1406) in paragraph at lines 7213--7219 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 7233--7235 []\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 7275--7282 []\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio n = "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 7275--7282 \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 7275--7282 \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] [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7479--7479 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] Underfull \hbox (badness 1231) in paragraph at lines 7604--7610 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7816--7818 []\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 7975--7975 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8208--8208 []\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 8327--8337 []\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 8327--8337 [][]\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] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8359--8364 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8501--8501 [] \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 1629) in paragraph at lines 8850--8862 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8850--8862 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9299--9303 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9390--9390 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9392--9392 []\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 9418--9418 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9419--9419 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] Underfull \hbox (badness 1924) in paragraph at lines 9480--9485 []\T1/ptm/m/n/10 Attributes named \T1/pcr/m/n/10 dim\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 dimnames\T1/ptm/m/n/10 , \T1/pcr/m/n/10 levels\T1/ptm/m/n/10 , \T1/pcr/m/n /10 names \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 are de-parsed to \T1/pcr/m/n/10 .Dim\T1/ptm/m/n/10 , [139] Underfull \hbox (badness 5403) in paragraph at lines 9550--9552 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9569--9571 []\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 9800--9803 []\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 10415--10420 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \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 10470--10470 []\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 10471--10471 []\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 10573--10578 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10613--10619 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10675--10675 []\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 10677--10677 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10797--10802 [][][]$\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 10797--10802 \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 10797--10802 \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 10828--10828 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10902--10902 []\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 11049--11049 []\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 11247--11255 []\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 11256--11258 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11473--11476 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11928--11928 []\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/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12259--12261 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] Underfull \hbox (badness 4569) in paragraph at lines 12396--12400 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 12396--12400 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] Underfull \vbox (badness 10000) has occurred while \output is active [193] [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2221) in paragraph at lines 13820--13829 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13820--13829 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14081--14083 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14201--14203 []\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 14360--14362 []\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 14477--14481 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\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 14488--14491 [][][]$\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 14509--14509 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [210] [211] Underfull \hbox (badness 10000) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\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 14641--14641 []\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 14707--14710 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14724--14724 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14753--14753 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [213] Underfull \hbox (badness 1472) in paragraph at lines 14777--14784 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14777--14784 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14785--14789 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14949--14949 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14950--14950 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15184--15184 []\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 15187--15187 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [220] Underfull \hbox (badness 1168) in paragraph at lines 15271--15275 []\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 15271--15275 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [221] Underfull \hbox (badness 6944) in paragraph at lines 15369--15372 [][][]\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/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15394--15394 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [223] [224] Underfull \hbox (badness 10000) in paragraph at lines 15532--15534 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15552--15552 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15558--15558 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [225] Underfull \hbox (badness 2790) in paragraph at lines 15565--15568 []\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 Underfull \hbox (badness 1024) in paragraph at lines 15596--15603 []\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 [226] Underfull \hbox (badness 10000) in paragraph at lines 15671--15673 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15671--15673 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15693--15698 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15699--15701 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [227] Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15710--15718 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15818--15818 []\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 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [229] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15840--15840 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16669--16669 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] Underfull \hbox (badness 2418) in paragraph at lines 16778--16782 \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/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16785--16788 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [243] Underfull \hbox (badness 2326) in paragraph at lines 16820--16827 [][][]\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[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [244] [245] [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17077--17077 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [247] Underfull \hbox (badness 1867) in paragraph at lines 17105--17112 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17406--17406 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Underfull \vbox (badness 10000) has occurred while \output is active [252] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17435--17435 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [253] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17491--17491 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [254] [255] [256] [257] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17864--17864 []\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))) [258] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17929--17929 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [259] [260] [261] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [262] [263] [264] [265] Underfull \hbox (badness 2285) in paragraph at lines 18461--18463 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / [266] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18469--18469 []\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.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18499--18499 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [267] [268] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18632--18632 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18638--18638 []\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 18641--18641 []\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 18647--18647 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [269] [270] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18774--18774 []\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 18782--18782 []\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):[] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 18987--18989 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [274] [275] [276] [277] [278] Underfull \hbox (badness 10000) in paragraph at lines 19325--19331 Underfull \hbox (badness 10000) in paragraph at lines 19338--19340 []\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 _ [279] [280] [281] Underfull \hbox (badness 4699) in paragraph at lines 19570--19573 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\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 , [282] [283] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19698--19698 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [284] [285] [286] Underfull \hbox (badness 4739) in paragraph at lines 19833--19835 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [287] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19882--19882 []\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 19883--19883 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1975) in paragraph at lines 20494--20497 []\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 [296] [297] [298] [299] [300] [301] [302] Underfull \hbox (badness 1077) in paragraph at lines 20892--20897 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20906--20913 [][][]$\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 / [303] Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec- Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 \T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr /m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o r [304] [305] Underfull \hbox (badness 10000) in paragraph at lines 21135--21139 []\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 21135--21139 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll 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 21140--21147 []\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- [306] [307] Underfull \hbox (badness 10000) in paragraph at lines 21271--21278 [][][]\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 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21392--21396 []\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 [310] Underfull \hbox (badness 5161) in paragraph at lines 21462--21467 []\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 21462--21467 \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 21462--21467 \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 21462--21467 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [311] [312] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21629--21629 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21633--21633 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [313] Underfull \hbox (badness 3343) in paragraph at lines 21694--21698 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \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 [314] [315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21835--21835 [] \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 21846--21846 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [316] [317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21957--21957 []\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 21960--21960 []\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 22005--22010 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [318] [319] Underfull \hbox (badness 2564) in paragraph at lines 22096--22099 []\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 22133--22133 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [320] [321] Underfull \hbox (badness 1400) in paragraph at lines 22301--22305 [][][]\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 do uble[][][] \T1/ptm/m/n/10 (class [322] [323] [324] Underfull \hbox (badness 1824) in paragraph at lines 22471--22479 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. In nu-meric and Underfull \hbox (badness 6758) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1 0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/ m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23137--23137 []\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 23138--23138 [] \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 23141--23141 []\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)[] [335] [336] Underfull \hbox (badness 1655) in paragraph at lines 23270--23274 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [337] [338] [339] Underfull \hbox (badness 2277) in paragraph at lines 23519--23522 []\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 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [340] [341] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0. 0, [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1484) in paragraph at lines 24107--24115 []\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 24107--24115 \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 / [349] [350] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24185--24185 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [351] [352] [353] [354] [355] [356] [357] Underfull \hbox (badness 1448) in paragraph at lines 24699--24707 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [358] [359] Underfull \hbox (badness 3849) in paragraph at lines 24814--24819 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [360] Underfull \hbox (badness 7308) in paragraph at lines 24891--24897 []\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-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24891--24897 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24891--24897 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [361] [362] Underfull \hbox (badness 10000) in paragraph at lines 25054--25056 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [363] [364] [365] Underfull \hbox (badness 6188) in paragraph at lines 25281--25284 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [366] [367] [368] Underfull \hbox (badness 1521) in paragraph at lines 25466--25480 \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- [369] [370] [371] [372] [373] Underfull \hbox (badness 2197) in paragraph at lines 25780--25784 []\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 25780--25784 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 25794--25798 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 25794--25798 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 25836--25836 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [374] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25840--25840 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [375] Underfull \hbox (badness 10000) in paragraph at lines 25888--25894 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25888--25894 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25901--25903 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [376] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25968--25968 [] \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:[] [377] [378] Underfull \hbox (badness 8189) in paragraph at lines 26163--26169 []\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 [][][] [379] [380] [381] Underfull \hbox (badness 1694) in paragraph at lines 26388--26391 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [382] [383] [384] [385] Underfull \hbox (badness 1603) in paragraph at lines 26635--26637 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [386] [387] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26762--26770 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [388] [389] Underfull \hbox (badness 3271) in paragraph at lines 26981--26984 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [390] [391] [392] Underfull \hbox (badness 3138) in paragraph at lines 27287--27293 []\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 27287--27293 \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 27287--27293 \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 [393] Underfull \hbox (badness 1194) in paragraph at lines 27300--27303 []\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/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27326--27328 []\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 27346--27352 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27361--27366 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 27379--27382 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [394] Underfull \hbox (badness 10000) in paragraph at lines 27395--27398 []\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 27403--27409 []\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 27403--27409 \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 27403--27409 \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 27403--27409 \T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina ry.universal" \T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27418--27425 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27418--27425 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27418--27425 \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 27418--27425 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [395] [396] [397] [398] Underfull \vbox (badness 10000) has occurred while \output is active [399] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27765--27765 []\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 27778--27782 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 27778--27782 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27925--27928 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27925--27928 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 28207--28213 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 28207--28213 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and Overfull \hbox (42.18039pt too wide) in paragraph at lines 28229--28229 []\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 28241--28241 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28254--28254 []\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 28258--28258 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [406] [407] [408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28433--28433 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28442--28442 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [409] Underfull \hbox (badness 1360) in paragraph at lines 28497--28501 []\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 = [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 2005) in paragraph at lines 28892--28896 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc r/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 = [416] Underfull \hbox (badness 1796) in paragraph at lines 28960--28963 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [417] [418] [419] [420] Underfull \hbox (badness 10000) in paragraph at lines 29164--29167 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29859--29859 [] \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))[] [431] [432] [433] [434] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30150--30150 []\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 30161--30161 []\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 30167--30167 []\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 30173--30173 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [435] [436] Underfull \hbox (badness 7415) in paragraph at lines 30256--30260 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 30277--30277 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [437] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30323--30323 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [438] Underfull \hbox (badness 3713) in paragraph at lines 30468--30479 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [439] [440] Underfull \hbox (badness 1248) in paragraph at lines 30620--30627 \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 30620--30627 \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 / [441] [442] Underfull \hbox (badness 1533) in paragraph at lines 30738--30741 []\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 [443] [444] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30883--30883 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30901--30912 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [445] [446] [447] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31045--31045 []\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 31047--31047 []\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 31048--31048 []\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 31049--31049 []\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 31050--31050 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31057--31057 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [448] [449] [450] [451] [452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31365--31365 []\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 31367--31367 []\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 31377--31377 []\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 31378--31378 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [453] Underfull \hbox (badness 4048) in paragraph at lines 31473--31478 []\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 31473--31478 \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 31473--31478 \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 , [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 2080) in paragraph at lines 32011--32021 []\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), [462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [463] [464] [465] [466] [467] [468] [469] Underfull \hbox (badness 7558) in paragraph at lines 32564--32568 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32574--32576 []\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 Underfull \hbox (badness 10000) in paragraph at lines 32585--32587 []\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 32588--32592 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht tps : / / www . [470] [471] [472] [473] [474] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32959--32959 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [475] Underfull \hbox (badness 10000) in paragraph at lines 33030--33034 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [476] [477] [478] [479] Underfull \hbox (badness 2302) in paragraph at lines 33256--33261 []\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me nt to the spec-i-fied num-ber of sig-nif-i-cant Underfull \hbox (badness 3769) in paragraph at lines 33256--33261 \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 [480] [481] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33389--33389 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33392--33392 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [482] [483] [484] [485] [486] [487] [488] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33833--33833 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [489] [490] [491] [492] [493] [494] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34270--34270 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [495] Underfull \hbox (badness 1158) in paragraph at lines 34374--34379 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [496] Underfull \hbox (badness 10000) in paragraph at lines 34401--34407 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 34401--34407 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [497] [498] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34559--34559 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [499] [500] [501] Underfull \hbox (badness 8151) in paragraph at lines 34819--34822 []\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 . [502] [503] [504] Underfull \hbox (badness 10000) in paragraph at lines 35034--35039 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by = [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36023--36023 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [520] [521] [522] [523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36277--36277 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36279--36279 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 36322--36328 [][][]\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[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36322--36328 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [524] [525] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36433--36433 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [526] [527] [528] [529] [530] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36774--36774 []\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 36789--36789 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [531] [532] [533] Underfull \hbox (badness 10000) in paragraph at lines 37014--37016 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [534] [535] [536] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37241--37241 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37242--37242 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [537] [538] [539] [540] Overfull \hbox (63.78036pt too wide) in paragraph at lines 37509--37509 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [541] Underfull \hbox (badness 6110) in paragraph at lines 37600--37610 []\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-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 37600--37610 \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 37600--37610 \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 37600--37610 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n 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 37600--37610 \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 [542] Underfull \hbox (badness 10000) in paragraph at lines 37646--37652 []\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 37646--37652 \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 37646--37652 \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 37661--37668 []\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 37661--37668 \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 37661--37668 \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 [543] [544] [545] Underfull \hbox (badness 1484) in paragraph at lines 37893--37897 []\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/ m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [546] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37955--37955 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [547] [548] [549] [550] [551] [552] [553] [554] [555] Overfull \hbox (0.78088pt too wide) in paragraph at lines 38535--38535 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [556] [557] [558] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38785--38785 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [559] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38829--38829 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [560] [561] [562] [563] [564] [565] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39263--39263 []\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 39266--39266 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [566] Underfull \hbox (badness 10000) in paragraph at lines 39317--39324 []\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 39317--39324 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39370--39370 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [568] [569] [570] [571] [572] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39681--39681 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [573] [574] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39846--39846 []\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. [575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39884--39884 []\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 39914--39920 []\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 39914--39920 \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 39933--39938 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 39933--39938 \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 [576] [577] [578] [579] Underfull \hbox (badness 10000) in paragraph at lines 40221--40225 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \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 [580] Underfull \hbox (badness 1584) in paragraph at lines 40236--40239 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \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 [581] [582] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40374--40374 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [583] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40451--40451 []\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 [584] [585] Underfull \hbox (badness 1082) in paragraph at lines 40595--40598 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [586] [587] [588] Underfull \hbox (badness 1038) in paragraph at lines 40786--40789 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [589] [590] [591] [592] [593] Underfull \hbox (badness 1442) in paragraph at lines 41150--41154 \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 = [594] [595] [596] [597] Underfull \hbox (badness 4096) in paragraph at lines 41400--41403 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [598] Underfull \hbox (badness 7888) in paragraph at lines 41514--41518 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\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) > [599] [600] [601] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41668--41668 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (35.4281pt too wide) in paragraph at lines 41670--41670 [] \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 41672--41672 [] \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 41685--41687 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [602] Underfull \hbox (badness 10000) in paragraph at lines 41765--41768 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [603] [604] Underfull \hbox (badness 3872) in paragraph at lines 41883--41886 []\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 . [605] Underfull \hbox (badness 5475) in paragraph at lines 41949--41953 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [606] [607] [608] [609] [610] [611] Underfull \hbox (badness 10000) in paragraph at lines 42373--42380 \T1/ptm/m/n/10 is also 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 4467) in paragraph at lines 42429--42438 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42429--42438 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [612] Underfull \hbox (badness 1082) in paragraph at lines 42439--42451 \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' in that di-rec-tory states the ver-sion. That op-tion is Underfull \hbox (badness 1337) in paragraph at lines 42512--42520 \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 [613] Underfull \hbox (badness 10000) in paragraph at lines 42521--42524 []\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 42575--42578 [][][]$\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 42579--42581 [][][]$\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- Overfull \hbox (31.3804pt too wide) in paragraph at lines 42588--42588 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 42809--42811 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [617] [618] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42931--42931 []\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 42933--42933 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [619] [620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43034--43034 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43036--43036 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [621] [622] [623] Underfull \hbox (badness 6542) in paragraph at lines 43310--43312 []\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 , and [624] [625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43429--43429 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [626] Underfull \hbox (badness 1708) in paragraph at lines 43497--43505 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 43497--43505 \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 [627] Underfull \hbox (badness 4859) in paragraph at lines 43527--43532 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [628] Underfull \hbox (badness 3895) in paragraph at lines 43589--43601 []\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 43589--43601 \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 , [629] [630] [631] [632] [633] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43912--43912 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [634] [635] [636] [637] [638] [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44381--44381 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [640] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44390--44390 []\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 44456--44462 [][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[ ][][]\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 , [641] Underfull \hbox (badness 3861) in paragraph at lines 44465--44470 [][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex ists[][][]\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 , [642] Overfull \hbox (36.7804pt too wide) in paragraph at lines 44558--44558 []\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[] [643] Underfull \hbox (badness 1803) in paragraph at lines 44611--44614 []\T1/ptm/m/n/10 The atomic modes are \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/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 44615--44622 []\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 [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 44830--44832 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44936--44936 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [648] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45011--45011 []\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[] [649] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45019--45019 []\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 ...[] [650] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45113--45113 []\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 45117--45117 []\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 45118--45118 [] \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 45125--45125 []\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 45128--45128 []\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[] [651] Underfull \hbox (badness 6220) in paragraph at lines 45167--45172 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 45167--45172 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 10000) in paragraph at lines 45188--45193 []\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 4229) in paragraph at lines 45188--45193 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [652] Underfull \hbox (badness 2818) in paragraph at lines 45284--45290 []\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 a nd \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 [653] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45319--45319 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 2846) in paragraph at lines 45778--45782 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas Overfull \hbox (4.38043pt too wide) in paragraph at lines 45818--45818 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] [661] Underfull \hbox (badness 3209) in paragraph at lines 45839--45843 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [662]) (./compiler-pkg.tex Chapter 2. [663] 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 be us ed 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 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] 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,[] [672] 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)[] Underfull \vbox (badness 1472) has occurred while \output is active [673] [674] [675] [676] 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)[] [677] Overfull \hbox (48.81013pt too wide) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [678] [679] Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [680] [681] [682] 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. [683] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [684] [685] [686] [687] [688] 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)")[] [689] [690] 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 frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\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-tained from the a bove [691] [692] [693] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [694] 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)[] [695] [696] 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]]))))[] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] [702] [703] Overfull \vbox (4.29591pt too high) has occurred while \output is active [704] [705] [706] [707] [708] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [709] Overfull \vbox (13.87083pt too high) has occurred while \output is active [710] Underfull \vbox (badness 2376) has occurred while \output is active [711] [712] [713] [714] [715] 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 = ".")[] [716] [717] [718] [719] [720] [721] [722] [723] 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:[] [724] [725] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [726] Overfull \vbox (10.49593pt too high) has occurred while \output is active [727] Overfull \vbox (15.49593pt too high) has occurred while \output is active [728] 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 / [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742]) (./grDevices-pkg.tex Chapter 4. [743] [744] [745] [746] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to 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/ptm/m/n/1 0 in [747] [748] Underfull \hbox (badness 10000) in paragraph at lines 382--390 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 382--390 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [749] [750] 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",[] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] 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 [761] [762] [763] 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))[] Underfull \hbox (badness 1173) in paragraph at lines 1405--1408 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [764] [765] [766] [767] [768] [769] [770] [771] Underfull \hbox (badness 1565) in paragraph at lines 1893--1898 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1893--1898 \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 [772] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1976--1976 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2017--2027 []\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 2017--2027 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 2129--2131 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [775] [776] Underfull \hbox (badness 6758) in paragraph at lines 2308--2311 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [777] [778] Underfull \hbox (badness 2326) in paragraph at lines 2426--2436 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2426--2436 \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 2426--2436 \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 2426--2436 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [779] [780] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2529--2529 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2645--2645 []\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 2646--2646 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 2919--2920 Underfull \vbox (badness 10000) has occurred while \output is active [787] [788] [789] [790] [791] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3252--3252 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [792] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3336--3336 []\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 3337--3337 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 3493--3498 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3493--3498 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [795] [796] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3567--3567 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [797] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3651--3651 []\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 3671--3671 []\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 3678--3678 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [798] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3734--3734 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [799] Underfull \hbox (badness 8170) in paragraph at lines 3763--3766 []\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 , [800] Underfull \hbox (badness 2189) in paragraph at lines 3824--3829 []\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we ll for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3862--3866 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [801] Underfull \vbox (badness 10000) has occurred while \output is active [802] Underfull \hbox (badness 5260) in paragraph at lines 3992--3995 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [803] [804] [805] [806] [807] Underfull \hbox (badness 5939) in paragraph at lines 4325--4330 []\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 fa mily\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 , [808] [809] [810] [811] [812] [813] Underfull \hbox (badness 10000) in paragraph at lines 4732--4737 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [814] [815] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4847--4847 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [816] [817] Underfull \hbox (badness 1348) in paragraph at lines 5052--5055 []\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 [818] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5076--5076 []\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 5117--5123 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [819] Underfull \hbox (badness 1112) in paragraph at lines 5150--5154 []\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" [820] Underfull \hbox (badness 1755) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [821] [822] [823] Underfull \hbox (badness 7344) in paragraph at lines 5472--5474 []\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 5483--5487 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [824] [825] Underfull \hbox (badness 1552) in paragraph at lines 5610--5619 \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 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \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/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5620--5622 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5652--5658 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [826] Underfull \hbox (badness 5388) in paragraph at lines 5678--5680 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [827] [828] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5779--5779 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [829] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5891--5891 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 5977--5979 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [832] [833] [834] [835] [836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6344--6344 []\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 6358--6361 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [837] [838] [839] [840] [841] [842] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6693--6693 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6700--6700 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [843] [844] [845] [846] Underfull \hbox (badness 10000) in paragraph at lines 6963--6968 []\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 6963--6968 \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 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6963--6968 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7069--7069 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [848] Underfull \hbox (badness 3590) in paragraph at lines 7108--7111 []\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 7108--7111 \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 7119--7119 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [849] Underfull \hbox (badness 1189) in paragraph at lines 7184--7186 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [850] Underfull \hbox (badness 10000) in paragraph at lines 7289--7291 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [851] Underfull \hbox (badness 10000) in paragraph at lines 7335--7342 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7335--7342 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [852] Underfull \hbox (badness 5607) in paragraph at lines 7419--7423 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [853] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7471--7471 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [854] [855] Underfull \hbox (badness 5637) in paragraph at lines 7603--7609 \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 7636--7639 []\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 / [856] [857] [858] Underfull \hbox (badness 1231) in paragraph at lines 7805--7807 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [859] [860]) (./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 = [861] [862] [863] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [864] [865] [866] [867] 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 [868] [869] 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[] [870] 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 \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [871] [872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \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 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [873] [874] [875] Underfull \hbox (badness 10000) in paragraph at lines 964--968 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able. Overfull \hbox (133.98029pt too wide) in paragraph at lines 981--981 [] \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 983--983 []\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 985--985 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [876] [877] [878] [879] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [880] [881] [882] Underfull \hbox (badness 2503) in paragraph at lines 1431--1440 \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 1466--1468 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [883] [884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1540--1540 []\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 1541--1541 []\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 1547--1547 []\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 1548--1548 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [885] [886] [887] [888] [889] Underfull \hbox (badness 10000) in paragraph at lines 1851--1857 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.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 1871--1871 []\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 1883--1883 []\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 1899--1899 []\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 1908--1908 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [890] [891] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1993--1993 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [892] [893] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2122--2122 []\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 2127--2127 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [894] [895] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2301--2301 []\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 2302--2302 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [896] Underfull \hbox (badness 1430) in paragraph at lines 2333--2335 []\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 [897] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2414--2414 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2426--2433 \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 [898] Underfull \hbox (badness 7273) in paragraph at lines 2508--2512 [][][]\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[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and [899] [900] [901] [902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2756--2756 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [903] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2793--2793 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [904] [905] Underfull \hbox (badness 1226) in paragraph at lines 2918--2922 \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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 2971--2971 []\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 :[] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2975--2975 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] Underfull \hbox (badness 10000) in paragraph at lines 3027--3030 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [907] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3232--3232 []\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 3237--3237 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 [][]\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 3379--3384 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [912] [913] [914] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3565--3565 []\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 3584--3584 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [915] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [916] [917] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3765--3765 [] \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 3766--3766 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [918] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3805--3805 [] \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 [919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3865--3865 []\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 3867--3867 []\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 3875--3875 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [920] Underfull \hbox (badness 10000) in paragraph at lines 3938--3942 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [921] [922] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4050--4050 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [923] [924] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4204--4204 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [925] Underfull \hbox (badness 3930) in paragraph at lines 4283--4285 []\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 [926] [927] [928] [929] [930] Underfull \hbox (badness 1286) in paragraph at lines 4594--4597 \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 4602--4607 []\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 [931] [932] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4699--4699 []\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 4704--4704 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [933] Underfull \hbox (badness 1264) in paragraph at lines 4895--4908 \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/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 5032--5038 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 5163--5166 [938 ] Underfull \hbox (badness 10000) in paragraph at lines 5224--5226 [939 ] [940] Underfull \hbox (badness 10000) in paragraph at lines 5414--5416 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [941] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5470--5470 []\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 5471--5471 [] \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 [942] [943] [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5836--5836 []\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 5837--5837 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5896 \aliasA{plot}{plot.default}{plot} [949] [950] [951] [952] [953] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6234--6234 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 6664--6666 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [960] [961] Underfull \hbox (badness 1028) in paragraph at lines 6758--6760 []\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 6801--6802 [][] [962 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6895--6895 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [963] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6926--6926 [] \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 [964] [965] Underfull \hbox (badness 10000) in paragraph at lines 7048--7050 []\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 7075--7075 [] \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 7081--7081 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [966] Underfull \hbox (badness 2600) in paragraph at lines 7138--7140 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7370--7370 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [971] [972] [973] [974] [975] [976] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7757--7757 []\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 7761--7761 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [977] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [978] [979] [980] [981] [982] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8122--8122 []\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 8125--8125 []\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 8129--8129 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [983] [984] [985] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\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 8301--8301 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [986] [987] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8405--8405 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8416--8421 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [988] Underfull \hbox (badness 1112) in paragraph at lines 8464--8468 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [989] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8524--8524 []\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 8539--8539 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [990] [991] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8676--8676 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [992] [993] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8861--8861 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [994] Underfull \hbox (badness 10000) in paragraph at lines 8889--8891 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8891--8893 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8923--8929 []\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 are \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 [995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8971 \HeaderA{units}{Graphical Units}{units} [996] Underfull \hbox (badness 1205) in paragraph at lines 9036--9038 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [997] [998] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9155--9155 []\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)[] [999]) (./grid-pkg.tex [1000] Chapter 6. [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 10000) in paragraph at lines 479--485 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 479--485 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [1009] Underfull \hbox (badness 4859) in paragraph at lines 565--568 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1010] [1011] [1012] [1013] [1014] [1015] Overfull \hbox (31.3804pt too wide) in paragraph at lines 959--959 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1016] [1017] [1018] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1164--1164 [] \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 1165--1165 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1166--1166 [] \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 1167--1167 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1168--1168 [] \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 1169--1169 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1019] Underfull \hbox (badness 1430) in paragraph at lines 1214--1219 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1020] [1021] [1022] Underfull \hbox (badness 3219) in paragraph at lines 1428--1431 []\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 [1023] [1024] [1025] [1026] [1027] [1028] [1029] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1816--1816 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1030] [1031] [1032] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2030--2030 []\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 2031--2031 []\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 2032--2032 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1033] Underfull \hbox (badness 2961) in paragraph at lines 2067--2072 []\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 , [1034] Underfull \hbox (badness 1430) in paragraph at lines 2126--2131 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2155--2158 []\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 [1035] [1036] [1037] Underfull \hbox (badness 2894) in paragraph at lines 2362--2369 []\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 [1038] [1039] [1040] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2518--2518 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2530--2535 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1041] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1042] [1043] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2741--2741 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1044] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2773--2773 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1045] [1046] [1047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3015--3015 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1048] [1049] [1050] [1051] [1052] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3330--3330 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1053] [1054] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3426--3426 []\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 3460--3466 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1055] [1056] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3552--3552 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3559--3559 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1057] [1058] [1059] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3760--3760 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1060] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3796--3796 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Underfull \hbox (badness 1067) in paragraph at lines 4537--4540 []\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 [1073] Underfull \hbox (badness 1430) in paragraph at lines 4583--4588 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1074] [1075] [1076] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] Underfull \hbox (badness 7256) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 5419--5421 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 6859) in paragraph at lines 6206--6212 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1099] [1100] [1101] [1102] [1103] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6484--6484 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1104] Underfull \hbox (badness 1867) in paragraph at lines 6584--6586 []\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 [1105] Underfull \hbox (badness 10000) in paragraph at lines 6621--6627 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1106] [1107] Underfull \hbox (badness 1371) in paragraph at lines 6753--6756 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1108] Underfull \vbox (badness 10000) has occurred while \output is active [1109] [1110] [1111] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1112]) (./methods-pkg.tex Chapter 7. [1113] [1114] 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 c o-erce meth-ods work. Use [1115] [1116] [1117] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1118] [1119] 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[] [1120] 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 [1121] 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 [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] 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[] [1137] [1138] 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 c an be an ob-ject of class [1139] [1140] [1141] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\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 = [1142] [1143] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\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 [1144] [1145] [1146] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\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 [1147] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1148] [1149] [1150] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1151] [1152] [1153] [1154] [1155] [1156] [1157] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1160] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1163] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\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 [1164] [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1167] [1168] [1169] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1171] [1172] [1173] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\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 , [1174] [1175] [1176] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\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 [1177] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1181] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\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 5237--5237 []\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 [1182] [1183] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1184] [1185] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1186] [1187] [1188] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1189] [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1195] [1196] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \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 [1197] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1198] [1199] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\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 6647--6656 [][]\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 [1200] Underfull \vbox (badness 10000) has occurred while \output is active [1201] [1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1204] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1205] [1206] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\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 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1208] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/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 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/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 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1209] [1210] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\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 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1211] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7517--7517 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1212] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1225] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1230] [1231] [1232] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1233] [1234] [1235] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1236] [1237] [1238] [1239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1240] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\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 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1251] [1252] [1253]) (./parallel-pkg.tex [1254] 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/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1255] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1256] [1257] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\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 [1258] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 444--446 []\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 [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 1917) in paragraph at lines 778--787 []\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 778--787 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1266] [1267] Overfull \hbox (60.78088pt too wide) in paragraph at lines 871--871 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1268] [1269] [1270] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1062--1062 []\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 1066--1066 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1271] Underfull \hbox (badness 5388) in paragraph at lines 1181--1186 []\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 [1272] Underfull \hbox (badness 10000) in paragraph at lines 1205--1213 []\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 1242--1242 []\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)[] [1273] [1274] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1358--1358 [] \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 1372--1372 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1275] Underfull \hbox (badness 1577) in paragraph at lines 1401--1404 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1448--1450 []\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 [1276] [1277]) (./splines-pkg.tex [1278] 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 [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] 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))[] [1287] Underfull \hbox (badness 1424) 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(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1288] [1289] 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)))[] [1290] [1291] [1292]) (./stats-pkg.tex Chapter 10. [1293] 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 o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/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[] [1294] [1295] [1296] [1297] [1298] 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[] [1299] 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) [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 1024) in paragraph at lines 888--890 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1316] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1626--1626 [] \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 1629--1629 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1317] [1318] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1776--1776 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1319] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1788--1788 []\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 :[ ] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2806--2806 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1334] [1335] [1336] [1337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3046--3046 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1338] [1339] [1340] Underfull \hbox (badness 10000) in paragraph at lines 3257--3259 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3306--3306 []\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 3307--3307 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1342] [1343] [1344] [1345] [1346] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1347] [1348] [1349] [1350] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3980--3980 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1351] [1352] [1353] [1354] [1355] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4269--4269 []\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 4270--4270 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1356] [1357] [1358] [1359] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4510--4510 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1360] [1361] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4685--4685 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1362] [1363] Underfull \hbox (badness 3989) in paragraph at lines 4779--4786 []\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 = [1364] [1365] [1366] [1367] [1368] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5164--5164 []\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 5166--5166 []\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))[] [1369] [1370] [1371] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5387--5387 []\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 5405--5405 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1372] Underfull \hbox (badness 2680) in paragraph at lines 5432--5434 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1373] [1374] [1375] Underfull \hbox (badness 1436) in paragraph at lines 5615--5620 []\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 5615--5620 \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 5615--5620 \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 , [1376] [1377] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1378] [1379] [1380] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5985--5985 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1381] [1382] [1383] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6170--6170 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1384] [1385] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6278--6278 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1386] Underfull \hbox (badness 10000) in paragraph at lines 6345--6350 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1387] [1388] [1389] Underfull \hbox (badness 5954) in paragraph at lines 6541--6543 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1390] Underfull \hbox (badness 2503) in paragraph at lines 6623--6626 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can 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 6627--6629 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \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 6630--6635 \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, [1391] Underfull \hbox (badness 7238) in paragraph at lines 6666--6669 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6678--6678 []\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 6701--6701 []\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 6716--6716 []\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):[] [1392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6731--6731 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1393] [1394] [1395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6976--6976 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1396] [1397] [1398] Underfull \vbox (badness 10000) has occurred while \output is active [1399] [1400] [1401] [1402] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 \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 "binary" \T1/ptm/ m/n/10 or [1403] Underfull \hbox (badness 6493) in paragraph at lines 7474--7477 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1404] [1405] Underfull \hbox (badness 10000) in paragraph at lines 7611--7614 []\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 = [1406] [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 10000) in paragraph at lines 8023--8028 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1412] [1413] [1414] [1415] [1416] [1417] Underfull \hbox (badness 1210) in paragraph at lines 8378--8380 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1418] [1419] [1420] [1421] [1422] [1423] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8841--8841 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1424] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8886--8886 []\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 8889--8889 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1425] [1426] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9027--9027 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1427] [1428] [1429] [1430] [1431] [1432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9454--9454 [] \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 9455--9455 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1433] [1434] [1435] Underfull \hbox (badness 7291) in paragraph at lines 9634--9636 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1436] [1437] [1438] [1439] [1440] [1441] [1442] Underfull \hbox (badness 6944) in paragraph at lines 10122--10128 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1443] [1444] [1445] Underfull \hbox (badness 3758) in paragraph at lines 10336--10339 []\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 [1446] [1447] [1448] [1449] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10580--10580 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10606--10611 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1450] Underfull \hbox (badness 4132) in paragraph at lines 10645--10649 []\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 10699--10705 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1451] Underfull \hbox (badness 10000) in paragraph at lines 10750--10753 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\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 [1452] [1453] [1454] Underfull \hbox (badness 2142) in paragraph at lines 10967--10970 []\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 ^^@ [1455] Underfull \hbox (badness 1708) in paragraph at lines 11048--11052 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1456] Underfull \hbox (badness 10000) in paragraph at lines 11090--11096 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11128--11133 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1457] [1458] Underfull \hbox (badness 2635) in paragraph at lines 11261--11264 \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/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1459] [1460] [1461] Underfull \hbox (badness 1694) in paragraph at lines 11444--11447 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1462] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11545--11545 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1463] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11578--11578 [] \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 11591--11595 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1464] [1465] [1466] [1467] [1468] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11913--11913 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11928 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11988--11988 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1470] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12000--12000 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12053--12058 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12070--12072 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1471] [1472] [1473] [1474] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12324--12324 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12325--12325 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1475] [1476] [1477] [1478] [1479] [1480] Underfull \hbox (badness 10000) in paragraph at lines 12669--12671 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12692--12694 []\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 [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 6910) in paragraph at lines 12999--13001 []\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 13005--13009 []\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 13005--13009 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13611--13611 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1495] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13712--13712 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13760--13765 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] Underfull \hbox (badness 1275) in paragraph at lines 13869--13871 []\T1/pcr/m/n/10 lm \T1/ptm/m/n/10 re-turns an ob-ject of [][]\T1/pcr/m/n/10 cl ass[][][] "lm" \T1/ptm/m/n/10 or for mul-ti-vari-ate (`mul-ti-ple') re-sponses of class [1498] [1499] Underfull \hbox (badness 10000) in paragraph at lines 13967--13971 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 1163) in paragraph at lines 14301--14309 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1505] [1506] Underfull \hbox (badness 4518) in paragraph at lines 14421--14426 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1507] [1508] [1509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14609--14609 []\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 14610--14610 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1510] [1511] [1512] [1513] [1514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14953--14953 []\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 14954--14954 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1515] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15047--15047 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 2726) in paragraph at lines 15456--15459 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/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 , [1523] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15550--15550 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16178--16178 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1534] [1535] Underfull \hbox (badness 1490) in paragraph at lines 16325--16330 \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 [1536] Underfull \hbox (badness 1648) in paragraph at lines 16391--16393 []\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 2591) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1537] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16476--16476 []\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 16477--16477 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17034--17034 []\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[] [1547] [1548] [1549] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17266--17266 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \vbox (badness 10000) has occurred while \output is active [1560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 17988--17988 []\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 [1561] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18006--18006 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc urate numerical[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18007--18007 []\T1/pcr/m/n/9 ## differentiation; the first fit gives Error: "step factor .. reduced below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/ m/n/9 .."[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18010--18010 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central diff. typically work:[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 18011--18011 [] \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral =TRUE, warnOnly=TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18013--18013 []\T1/pcr/m/n/9 ## 2nd fit still fails on some (less accurate) platforms => us ing warnOnly[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18043--18043 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1562] [1563] [1564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18219--18219 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1565] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18266--18266 []\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 18313--18313 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1566] [1567] [1568] [1569] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18519--18519 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1248) in paragraph at lines 18834--18837 []\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 18847--18851 []\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 18855--18859 \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 [1575] Underfull \hbox (badness 2042) in paragraph at lines 18913--18915 []\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 [1576] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19019--19019 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1577] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19062--19062 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19080--19080 []\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 19083--19083 []\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 19103--19103 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1578] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19141--19152 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19141--19152 \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 [1579] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19204--19204 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1580] [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19431--19431 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1583] [1584] Underfull \hbox (badness 1337) in paragraph at lines 19542--19545 []\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 [1585] [1586] [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19861--19861 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1590] [1591] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19949--19949 [] \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 19951--19951 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19953--19953 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1592] Underfull \hbox (badness 10000) in paragraph at lines 19999--20005 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 3049) in paragraph at lines 20040--20044 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1593] [1594] [1595] [1596] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20293--20293 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20303--20306 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1597] Underfull \hbox (badness 1107) in paragraph at lines 20361--20363 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1598] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20416--20416 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20423--20423 []\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)[] [1600] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20517--20517 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1601] [1602] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20646--20646 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1603] Underfull \hbox (badness 7740) in paragraph at lines 20709--20711 []\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 [1604] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20757--20757 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1605] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20849--20849 [] \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 20854--20854 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21709--21709 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1619] Underfull \hbox (badness 6859) in paragraph at lines 21776--21783 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21787--21793 []\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/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22533--22533 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22817--22817 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22818--22818 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1337) in paragraph at lines 23144--23150 []\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 [1642] [1643] [1644] [1645] [1646] [1647] [1648] Underfull \hbox (badness 2913) in paragraph at lines 23569--23572 []\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th e pre-ci-sion to use when for-mat- Underfull \hbox (badness 1152) in paragraph at lines 23569--23572 \T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s ions up to 4.0.x, this had been set to [1649] Underfull \hbox (badness 10000) in paragraph at lines 23703--23705 []\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 23703--23705 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23710--23711 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1650] [1651] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23821--23821 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1652] Underfull \hbox (badness 1028) in paragraph at lines 23879--23882 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1653] [1654] Underfull \hbox (badness 10000) in paragraph at lines 23994--23997 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7944) in paragraph at lines 24049--24051 []\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,levels = [1655] Underfull \hbox (badness 7944) in paragraph at lines 24111--24113 []\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,levels = [1656] [1657] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24213--24213 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1658] [1659] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24330--24330 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24331--24331 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24332--24332 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24333--24333 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 24493--24498 [][][]\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 re-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 24493--24498 [][]\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 24504--24504 []\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 24505--24505 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] [1662] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24524--24524 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1663] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24628--24628 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1664] Underfull \hbox (badness 1033) in paragraph at lines 24671--24677 \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 24692--24695 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1665] Underfull \hbox (badness 2134) in paragraph at lines 24761--24765 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24774--24774 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24803--24803 []\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 24815--24815 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1667] [1668] [1669] [1670] [1671] [1672] [1673] Underfull \hbox (badness 6268) in paragraph at lines 25273--25278 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/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 , [1674] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25301--25301 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1675] [1676] [1677] Underfull \hbox (badness 1867) in paragraph at lines 25478--25480 []\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 25493--25497 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25493--25497 \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 25529--25529 []\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 25536--25536 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1678] [1679] [1680] Underfull \hbox (badness 2495) in paragraph at lines 25719--25728 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1681] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25801--25801 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1682] Underfull \hbox (badness 1412) in paragraph at lines 25808--25810 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1683] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25895--25895 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25920--25920 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25923--25923 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1684] [1685] [1686] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26147--26147 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26151--26157 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26197--26197 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26218--26218 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1688] Underfull \hbox (badness 1019) in paragraph at lines 26280--26285 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1689] [1690] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26410--26410 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1691] [1692] [1693] [1694] [1695] [1696] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1697] [1698] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26971--26971 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1699] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26977--26977 []\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 26986--26986 []\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 26987--26987 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1700] Underfull \hbox (badness 2922) in paragraph at lines 27056--27061 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27093--27093 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1701] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27096--27096 [] \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 27105--27105 [] \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 27106--27106 [] \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 27110--27110 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1702] Underfull \hbox (badness 3240) in paragraph at lines 27164--27167 [][][]\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 grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 27185--27185 [] \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 27188--27188 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1703] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27271--27271 [] \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 27275--27275 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1704] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27285--27285 [] \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 27290--27290 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27326--27332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27364--27364 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27380--27380 [] \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 27383--27383 []\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 27385--27385 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1706] [1707] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27497--27497 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1708] Underfull \hbox (badness 2922) in paragraph at lines 27559--27564 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1709] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27597--27597 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 27646--27651 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27677--27677 []\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 27711--27716 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27736--27736 []\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 27740--27740 []\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 27760--27760 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1712] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27770--27770 [] \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[] Underfull \hbox (badness 2922) in paragraph at lines 27805--27810 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27827--27827 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1713] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27845--27845 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1714] Underfull \hbox (badness 6493) in paragraph at lines 27897--27902 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27925--27925 []\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 27928--27928 []\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 27931--27931 []\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 27934--27934 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] Underfull \hbox (badness 3396) in paragraph at lines 28817--28819 []\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 [1729] [1730] Underfull \hbox (badness 2237) in paragraph at lines 28994--28996 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1731] [1732] [1733] Underfull \hbox (badness 2591) in paragraph at lines 29158--29160 []\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 [1734] Underfull \hbox (badness 2237) in paragraph at lines 29204--29207 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1735] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1736] Underfull \hbox (badness 3407) in paragraph at lines 29386--29390 []\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) [1737] [1738] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29456--29456 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1739] Underfull \hbox (badness 1337) in paragraph at lines 29519--29523 []\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 [1740] [1741] [1742] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29777--29777 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1743] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29805--29805 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 29831--29834 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1744] [1745] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29910--29910 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29988--29988 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1747] Underfull \hbox (badness 2205) in paragraph at lines 30077--30082 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30676--30676 []\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 30677--30677 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1757] [1758] [1759] [1760] [1761] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30977--30977 [] \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 30978--30978 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1762] [1763] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31104--31104 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\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 [1764] [1765] [1766] Underfull \hbox (badness 1337) in paragraph at lines 31330--31334 []\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 [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 1337) in paragraph at lines 31859--31863 []\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 Underfull \hbox (badness 5878) in paragraph at lines 31873--31875 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i -tive nu-meric tol-er-ance, used in [1776] [1777] [1778] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32066--32066 []\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 32068--32068 []\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)[] [1779] [1780] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32227--32227 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32312--32312 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1782] Underfull \hbox (badness 6775) in paragraph at lines 32369--32374 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1783] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32445--32445 []\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 "")[] [1784] [1785]) (./stats4-pkg.tex [1786] Chapter 11. [1787] [1788] [1789] 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 [1790] 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[] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797]) (./tcltk-pkg.tex [1798] Chapter 12. [1799] [1800] [1801] [1802] 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[] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] 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-ing any Tk or Tcl com-mand by sim-ply run-ning [1807] [1808] [1809] [1810] [1811] [1812] 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"))))[] [1813] [1814] [1815] [1816] [1817] 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-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1818]) (./tools-pkg.tex Chapter 13. [1819] 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.[] [1820] Underfull \hbox (badness 10000) in paragraph at lines 141--143 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via 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 b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1821] 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)[] [1822] 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/1 0 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/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1823] 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-gine to use. Over-rides any [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1831] [1832] 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")[] [1833] [1834] [1835] 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, ...)[] [1836] 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/p tm/m/n/10 and [1837] 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-he r-it-ing from class [1838] [1839] 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/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and [1840] [1841] [1842] [1843] [1844] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1700--1700 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1707--1715 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1707--1715 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 1707--1715 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1845] [1846] [1847]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1919 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig nored \relax l.1920 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1848] [1849] [1850] [1851] Underfull \hbox (badness 1142) in paragraph at lines 2188--2194 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2222--2222 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1852] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2223--2223 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2250--2257 []\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 2250--2257 \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 2250--2257 \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 [1853] Underfull \hbox (badness 1342) in paragraph at lines 2302--2308 \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 [1854] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2391--2399 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2391--2399 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 2391--2399 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1855] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2427--2427 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2460--2460 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1856] [1857] [1858] [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2744--2744 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1860] Underfull \hbox (badness 2486) in paragraph at lines 2789--2797 []\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 [1861] [1862] [1863] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3001--3001 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3005--3005 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1864] [1865] [1866] Underfull \hbox (badness 1072) in paragraph at lines 3177--3179 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1867] [1868] [1869] [1870] [1871] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1872] [1873] [1874] [1875] Underfull \hbox (badness 4108) in paragraph at lines 3758--3765 []\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 [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3858--3858 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] [1877] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3861--3861 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3878--3880 []\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 3895--3901 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1878] [1879] Underfull \hbox (badness 7832) in paragraph at lines 4017--4020 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1880] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4093--4093 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] Underfull \hbox (badness 1137) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1881] [1882] [1883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4304--4304 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1884] [1885] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) [1886] Underfull \hbox (badness 10000) in paragraph at lines 4477--4480 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4493--4498 []\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/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4501--4507 []\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 4501--4507 \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 [1887] [1888] [1889] [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4758--4758 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4759--4759 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4772--4775 []\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 4776--4786 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4814--4820 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4814--4820 \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 ', [1891] Underfull \hbox (badness 1571) in paragraph at lines 4842--4846 []\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 4868--4873 \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 [1892] [1893] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5008--5008 []\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 '[] [1894]) (./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 `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1895] [1896] [1897] [1898] 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[] [1899] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1900] 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 [1901] 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"))),[] [1902] [1903] [1904] Overfull \hbox (0.78088pt too wide) in paragraph at lines 677--677 []\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 683--683 []\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 684--684 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 685--685 []\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 686--686 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 720--726 []\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 720--726 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1905] [1906] Underfull \hbox (badness 4505) in paragraph at lines 857--863 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1907] [1908] [1909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1043--1043 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1910] Underfull \hbox (badness 1748) in paragraph at lines 1108--1116 []\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 1108--1116 \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 1661) in paragraph at lines 1108--1116 \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 1108--1116 \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 1120--1122 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1911] Underfull \hbox (badness 10000) in paragraph at lines 1228--1231 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1912] [1913] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1311--1311 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1914] [1915] [1916] [1917] [1918] [1919] [1920] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1813--1813 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1921] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1848--1848 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1922] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1994--1994 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1923] Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 []\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm /m/n/10 4.1.0. A less di-rect way to ex-am-ine char- Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 \T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use some-thing like [1924] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2096--2096 []\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 2098--2098 []\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 2106--2106 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2254--2254 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1928] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2306--2306 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1929] [1930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2475--2475 [] \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")[] [1931] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1933] Underfull \hbox (badness 1082) in paragraph at lines 2692--2696 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2697 ... the Clipboard in MS Windows}{clipboard} [1934] Underfull \hbox (badness 1163) in paragraph at lines 2728--2730 []\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 . [1935] Underfull \hbox (badness 10000) in paragraph at lines 2816--2818 []\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 [1936] [1937] [1938] [1939] Underfull \hbox (badness 10000) in paragraph at lines 3034--3036 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1940] [1941] [1942] [1943] Underfull \hbox (badness 1762) in paragraph at lines 3327--3330 []\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 = [1944] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3419--3419 []\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 3420--3420 []\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 '[] [1945] Underfull \hbox (badness 2452) in paragraph at lines 3496--3499 []\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 [1946] [1947] [1948] [1949] [1950] [1951] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 4062--4070 []\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 [1954] Underfull \hbox (badness 1231) in paragraph at lines 4139--4151 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 4152--4157 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1955] [1956] Underfull \hbox (badness 4660) in paragraph at lines 4272--4275 \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 Underfull \hbox (badness 10000) in paragraph at lines 4296--4298 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1957] [1958] [1959] Underfull \hbox (badness 1565) in paragraph at lines 4481--4485 []\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 [1960] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4564--4564 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1961] Underfull \hbox (badness 1931) in paragraph at lines 4599--4606 []\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) [1962] [1963] [1964] [1965] [1966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4923--4923 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1967]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} [1968] [1969] [1970] [1971] [1972] [1973] [1974] [1975] Underfull \hbox (badness 1622) in paragraph at lines 5513--5517 []\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 [1976] [1977] [1978] [1979] [1980] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5835--5835 []\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 5847--5847 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1981] [1982] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5980--5980 [] \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 5981--5981 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1983] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6191--6191 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1986] Underfull \hbox (badness 10000) in paragraph at lines 6275--6277 []\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 [1987] Underfull \hbox (badness 1502) in paragraph at lines 6324--6329 []\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 6324--6329 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 6497--6506 []\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 6497--6506 \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 [1990] Underfull \hbox (badness 2150) in paragraph at lines 6561--6564 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6577--6580 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1991] [1992] Underfull \hbox (badness 3118) in paragraph at lines 6700--6702 []\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 [1993] [1994] Underfull \hbox (badness 5091) in paragraph at lines 6875--6877 []\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 [1995] Underfull \hbox (badness 5331) in paragraph at lines 6891--6897 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6891--6897 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6891--6897 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6905--6912 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") Underfull \hbox (badness 1270) in paragraph at lines 6920--6930 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If [1996] Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., Underfull \hbox (badness 1424) in paragraph at lines 6971--6974 []\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 [1997] Underfull \hbox (badness 2376) in paragraph at lines 7042--7049 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7042--7049 \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 7042--7049 \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 7050--7053 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1998] Underfull \hbox (badness 1314) in paragraph at lines 7129--7136 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 7176--7179 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac kages(filters = Underfull \hbox (badness 1314) in paragraph at lines 7176--7179 \T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/ 10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n /10 ver-sion (for Underfull \hbox (badness 10000) in paragraph at lines 7209--7214 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , [1999] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7232--7232 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7268--7272 []\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 7282--7285 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2000] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7329--7329 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2001] [2002] Underfull \hbox (badness 4132) in paragraph at lines 7453--7455 []\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 [2003] [2004] [2005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7620--7620 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2006] [2007] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7763--7763 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2008] Underfull \hbox (badness 10000) in paragraph at lines 7803--7805 []\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 [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 7991--7993 []\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 7996--7998 []\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 [2011] [2012] [2013] [2014] Underfull \hbox (badness 1859) in paragraph at lines 8224--8227 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [2015] Underfull \hbox (badness 1655) in paragraph at lines 8318--8321 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \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 8329--8329 []\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 8337--8337 []\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):[] [2016] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8345--8345 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2017] Underfull \hbox (badness 1917) in paragraph at lines 8432--8434 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [2018] [2019] [2020] [2021] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8704--8704 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8705--8705 [] \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 8706--8706 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2022] Underfull \hbox (badness 10000) in paragraph at lines 8734--8736 []\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 8748--8750 []\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 8756--8761 []\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, [2023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8802--8802 [] \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 8803--8803 [] \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[] [2024] [2025] Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8932--8937 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8939--8942 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [2026] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9055--9055 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9056--9056 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2027] [2028] [2029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9229--9229 [] \T1/pcr/m/n/9 "S original, "),[] [2030] Underfull \hbox (badness 1789) in paragraph at lines 9362--9364 []\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 [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 5203) in paragraph at lines 9935--9938 []\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 [2040] [2041] Underfull \hbox (badness 1394) in paragraph at lines 10161--10168 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [2042] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10185--10185 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2043] [2044] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10346--10346 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2045] [2046] [2047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10527--10527 []\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[] [2048] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10613--10613 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10616--10616 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10621--10621 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2049] Underfull \hbox (badness 2027) in paragraph at lines 10693--10696 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2050] [2051] [2052] [2053] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10972--10972 []\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 10973--10973 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10980--10985 []\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 10980--10985 \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 10980--10985 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2054] [2055] [2056] [2057] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11213--11213 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11474--11478 \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 11492--11492 []\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 11497--11497 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2062] [2063] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11630--11630 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11631--11631 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2064] [2065] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2066] Underfull \hbox (badness 1917) in paragraph at lines 11890--11893 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11890--11893 \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 [2067] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11913--11913 []\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 '[] [2068] Underfull \hbox (badness 10000) in paragraph at lines 11976--11978 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [2069] Underfull \hbox (badness 6725) in paragraph at lines 12026--12035 \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 6428) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 12026--12035 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2070] Underfull \hbox (badness 1377) in paragraph at lines 12126--12129 []\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 [2071] Underfull \hbox (badness 3646) in paragraph at lines 12161--12163 [][][]$\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 12199--12199 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 12380--12384 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12411--12417 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2075] [2076] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12587--12587 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2077] Underfull \hbox (badness 1009) in paragraph at lines 12605--12617 []\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 12645--12647 []\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 [2078] Underfull \hbox (badness 1043) in paragraph at lines 12688--12693 []\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 [2079] [2080] [2081] [2082] Underfull \hbox (badness 1888) in paragraph at lines 12981--12984 []\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 12998--13001 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2083] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13044--13044 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2084] Underfull \hbox (badness 2158) in paragraph at lines 13099--13102 []\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 13147--13147 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2085] [2086] [2087] Underfull \hbox (badness 2302) in paragraph at lines 13304--13306 []\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 [2088] Underfull \hbox (badness 3333) in paragraph at lines 13411--13413 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2089] [2090] [2091] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13578--13578 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13602--13607 []\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 have Underfull \hbox (badness 5970) in paragraph at lines 13611--13614 []\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 13611--13614 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2092] Underfull \hbox (badness 1442) in paragraph at lines 13638--13642 []\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 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 13684--13684 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2093] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13715--13715 []\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 13722--13722 []\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 13724--13724 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] Underfull \vbox (badness 10000) has occurred while \output is active [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 13892--13894 []\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 [2097] [2098] Underfull \hbox (badness 6300) in paragraph at lines 14049--14056 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14049--14056 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14049--14056 \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$"\T1/ptm/m/n/10 ) and [2099] [2100] Underfull \hbox (badness 2020) in paragraph at lines 14218--14234 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 14218--14234 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2101] [2102] Underfull \hbox (badness 5022) in paragraph at lines 14357--14361 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 14364--14367 [][][]$\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 14364--14367 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14528--14528 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2106] [2107] [2108] [2109] [2110] [2111] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14969--14969 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14975--14975 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14996--14998 []\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 15011--15015 \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 Underfull \hbox (badness 1694) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 \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 15031--15036 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15037--15039 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2112] Underfull \hbox (badness 10000) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault 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 15088--15093 []\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 Underfull \hbox (badness 10000) in paragraph at lines 15096--15099 [][][]\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.packages[] [][]\T1/ptm/m/n/10 , [2113] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15150--15150 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2114] [2115] [2116] Underfull \hbox (badness 10000) in paragraph at lines 15357--15360 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 15357--15360 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2117] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15373--15373 []\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:[] [2118] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15440--15440 [] \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 15462--15462 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2119] [2120] Underfull \hbox (badness 1297) in paragraph at lines 15593--15595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2121] Underfull \hbox (badness 4036) in paragraph at lines 15640--15642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2122] [2123] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2124] Underfull \hbox (badness 1715) in paragraph at lines 15829--15832 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/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 15874--15876 []\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 = [2125] [2126] [2127]) [2128] [2129] [2130] (./KernSmooth-pkg.tex Chapter 15. [2131] 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) [2132] [2133] [2134] [2135] [2136] 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, [2137] [2138] [2139] [2140]) (./MASS-pkg.tex Chapter 16. [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2419--2419 []\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 2423--2423 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2175] [2176] [2177] [2178] Underfull \hbox (badness 6559) in paragraph at lines 2703--2706 []\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 [2179] [2180] [2181] Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 , [2182] [2183] Underfull \hbox (badness 4686) in paragraph at lines 3041--3043 []\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 [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3236--3236 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2187] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3366--3366 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1845) in paragraph at lines 4154--4156 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2200] [2201] [2202] [2203] [2204] [2205] [2206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4650--4650 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2207] [2208] [2209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4872--4872 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2224] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5985--5985 []\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") [2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} [2227] [2228] Underfull \hbox (badness 1783) in paragraph at lines 6266--6270 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2229] [2230] [2231] [2232] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6566--6566 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6654--6654 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2234] [2235] [2236] [2237] [2238] [2239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7093--7093 []\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 7110--7110 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2240] Underfull \hbox (badness 10000) in paragraph at lines 7133--7135 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7188--7194 []\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 ) = [2241] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7258--7258 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2242] [2243] Underfull \hbox (badness 5091) in paragraph at lines 7367--7370 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2244] [2245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2246] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7562--7562 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 4686) in paragraph at lines 8000--8002 []\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 [2253] [2254] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8119--8119 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8143--8147 []\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 [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] [2274] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9527--9527 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2275] Underfull \hbox (badness 2035) in paragraph at lines 9639--9641 []\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 9654--9657 []\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-larly), [2276] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9736--9736 []\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 9738--9738 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9741--9741 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289]) (./Matrix-pkg.tex [2290] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\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 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2291] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\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 [2292] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\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 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2293] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\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 [2294] [2295] Overfull \hbox (15.18042pt too wide) in paragraph at lines 471--471 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2296] Underfull \hbox (badness 5147) in paragraph at lines 501--504 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in Underfull \hbox (badness 5119) in paragraph at lines 514--518 []\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 518--523 [][][]\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/pcr/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 548--548 []\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 550--550 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 559--559 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2297] [2298] Overfull \hbox (52.98038pt too wide) in paragraph at lines 673--673 []\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 674--674 []\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 675--675 []\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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 688--688 [] \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 689--689 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 763--767 \T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc r/m/n/10 https : / / www . netlib . org / lapack / double / [2300] [2301] Underfull \hbox (badness 3536) in paragraph at lines 882--887 []\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c at-ing if the re-sult should be sparse, i.e., for- Underfull \hbox (badness 7777) in paragraph at lines 882--887 \T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]" \T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de- Underfull \hbox (badness 6188) in paragraph at lines 882--887 \T1/ptm/m/n/10 cides from the ``spar-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 [2302] Underfull \hbox (badness 10000) in paragraph at lines 925--930 []\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 meth-ods: [2303] Overfull \hbox (72.78088pt too wide) in paragraph at lines 986--986 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2304] [2305]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} [2306] Underfull \hbox (badness 2285) in paragraph at lines 1259--1264 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2307] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1305--1305 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2308] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1400--1400 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1428--1431 []\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 [2309] Underfull \hbox (badness 1609) in paragraph at lines 1475--1479 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra Overfull \hbox (4.38043pt too wide) in paragraph at lines 1502--1502 []\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 1516--1516 []\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[] [2310] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1524--1524 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Underfull \hbox (badness 10000) in paragraph at lines 1571--1578 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1571--1578 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or [2311] Underfull \hbox (badness 1783) in paragraph at lines 1606--1610 []\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 Underfull \hbox (badness 1221) in paragraph at lines 1622--1628 \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 . Hen ce, 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.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1664 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1685 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1696 \aliasA{rowSums}{colSums}{rowSums} [2312] 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 from 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/10 , since [2313] [2314] [2315] 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 [2316] [2317] [2318] [2319] Underfull \hbox (badness 1484) in paragraph at lines 2277--2279 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2320] Underfull \hbox (badness 7379) in paragraph at lines 2373--2375 []\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 [2321] [2322] [2323] Underfull \hbox (badness 4846) in paragraph at lines 2649--2653 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2654--2658 []\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 2661--2664 []\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 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2708--2708 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2717--2719 []\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 2721--2726 []\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 2721--2726 [][]\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 [2325] Underfull \hbox (badness 1097) in paragraph at lines 2744--2747 []\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 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2757--2762 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2326] Underfull \hbox (badness 3646) in paragraph at lines 2996--2999 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 3028--3030 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 3031--3035 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 3040--3046 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2327] Underfull \hbox (badness 10000) in paragraph at lines 3047--3051 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3057--3061 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 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 [2328] [2329] Underfull \hbox (badness 10000) in paragraph at lines 3241--3243 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3288--3290 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2330] Underfull \hbox (badness 2469) in paragraph at lines 3408--3411 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3573--3577 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3573--3577 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2333] Underfull \hbox (badness 2285) in paragraph at lines 3623--3626 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2334] [2335] Underfull \hbox (badness 10000) in paragraph at lines 3770--3775 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3770--3775 \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 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3782--3785 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2336] Underfull \hbox (badness 10000) in paragraph at lines 3858--3860 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3945--3945 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2338] [2339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4078--4078 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2340] Underfull \hbox (badness 3635) in paragraph at lines 4146--4150 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4155--4158 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4155--4158 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4160--4164 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2341] [2342] Underfull \hbox (badness 3158) in paragraph at lines 4343--4347 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2343] [2344] [2345] [2346] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4593--4593 []\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 4600--4600 [] \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 4604--4604 []\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 4607--4607 []\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 4617--4617 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2347] [2348] [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 4919--4924 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2351] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5000--5000 []\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 5002--5002 [] \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 5006--5006 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2352] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5013--5013 [] \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 '[] [2353] [2354] Underfull \hbox (badness 4120) in paragraph at lines 5157--5160 []\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 (15.18042pt too wide) in paragraph at lines 5194--5194 []\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 5200--5200 [] \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 5201--5201 [] \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 5205--5205 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5207--5207 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2355] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5214--5214 []\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 5217--5217 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2356] Underfull \hbox (badness 1817) in paragraph at lines 5306--5315 []\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 within the Underfull \hbox (badness 10000) in paragraph at lines 5348--5350 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5350--5353 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5363--5366 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2357] Underfull \hbox (badness 4765) in paragraph at lines 5381--5384 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2358] [2359] [2360] [2361] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2362] Underfull \hbox (badness 10000) in paragraph at lines 5782--5785 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5793--5793 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2363] Underfull \hbox (badness 1622) in paragraph at lines 5830--5835 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5830--5835 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2364] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5891--5891 []\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 5892--5892 [] \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 5899--5899 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2365] [2366] Underfull \hbox (badness 1062) in paragraph at lines 6028--6031 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 6057--6060 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2367] Underfull \hbox (badness 2635) in paragraph at lines 6169--6174 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6169--6174 \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 "Matrix"\T1/ptm/ m/n/10 , by class [2368] Underfull \hbox (badness 10000) in paragraph at lines 6177--6180 []\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 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6287--6297 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6287--6297 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2369] Underfull \hbox (badness 3179) in paragraph at lines 6369--6372 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2370] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\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., [2371] Underfull \hbox (badness 10000) in paragraph at lines 6542--6545 []\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., [2372] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6558--6558 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6597--6603 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6597--6603 [][]\T1/pcr/m/n/10 stop[][][]\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, Underfull \hbox (badness 1675) in paragraph at lines 6618--6621 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2373] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6688--6688 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2374] [2375] Underfull \hbox (badness 10000) in paragraph at lines 6829--6832 []\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 [2376] Underfull \hbox (badness 1490) in paragraph at lines 6851--6853 []\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[][][] \T 1/ptm/m/n/10 and (one case of) [2377] Underfull \hbox (badness 5036) in paragraph at lines 6931--6935 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6931--6935 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2378]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.7030 \aliasA{det}{Matrix-class}{det} [2379] Underfull \hbox (badness 10000) in paragraph at lines 7133--7136 Underfull \hbox (badness 10000) in paragraph at lines 7143--7145 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2380]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7206 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7314 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7413 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7510--7516 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2381] Underfull \hbox (badness 10000) in paragraph at lines 7583--7586 []\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 1199) in paragraph at lines 7583--7586 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7586--7591 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7586--7591 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7591--7595 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7591--7595 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7601--7602 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2382] [2383] Underfull \hbox (badness 1009) in paragraph at lines 7737--7739 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see [2384] Underfull \hbox (badness 1062) in paragraph at lines 7782--7785 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 7816--7819 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2385] Underfull \hbox (badness 10000) in paragraph at lines 7872--7874 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7974--7974 [] \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 8014--8014 []\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 [2388] Underfull \hbox (badness 2635) in paragraph at lines 8079--8084 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8079--8084 \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 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8087--8090 []\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 ); us e, e.g., [2389] Underfull \hbox (badness 3482) in paragraph at lines 8161--8167 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2390] Underfull \hbox (badness 1867) in paragraph at lines 8281--8283 []\T1/ptm/m/n/10 fast sim- [2391]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} [2392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8408--8408 []\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 8409--8409 []\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 8410--8410 []\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 8523--8533 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2393] Underfull \hbox (badness 3179) in paragraph at lines 8594--8597 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 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 8684--8687 []\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 8760--8763 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8776--8776 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2397] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8888--8891 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8894--8901 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2398] [2399] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8987--8987 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8990--8990 []\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 8992--8992 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8996--8996 []\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 8997--8997 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 9022--9032 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9022--9032 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2400] [2401]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9123 \aliasA{qr}{qr-methods}{qr} [2402] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9196--9196 []\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 9207--9207 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9227--9227 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9235--9235 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2403] Underfull \hbox (badness 10000) in paragraph at lines 9292--9298 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9309--9312 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2404] [2405] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9408--9408 []\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 9424--9424 []\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 9430--9430 []\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 9431--9431 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9449 ... the Reciprocal Condition Number}{rcond} [2406] [2407] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9562--9562 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2408] [2409] [2410] Underfull \hbox (badness 2351) in paragraph at lines 9753--9761 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9753--9761 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2411] [2412] Underfull \hbox (badness 1558) in paragraph at lines 9900--9903 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2413] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9962--9962 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9966--9966 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2414]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.10028 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10125--10125 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10132--10132 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2415] Underfull \hbox (badness 1616) in paragraph at lines 10167--10179 []\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 10184--10187 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 10193--10200 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10206--10216 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10206--10216 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10233--10237 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's [2416] Underfull \hbox (badness 10000) in paragraph at lines 10240--10242 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10263--10264 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10269--10271 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10273--10274 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10281--10284 [][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10299--10299 []\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 10303--10303 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2417] Underfull \hbox (badness 10000) in paragraph at lines 10324--10327 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10352--10354 []\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 10360--10363 []\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 10360--10363 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10371--10375 []\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 10371--10375 \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 [2418] Underfull \hbox (badness 1668) in paragraph at lines 10386--10391 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 1158) in paragraph at lines 10407--10413 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10466--10466 [] \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 10467--10467 [] \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 10468--10468 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2420] [2421] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10652--10652 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2422] Underfull \hbox (badness 1668) in paragraph at lines 10694--10699 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2423] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10791--10791 []\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 10795--10795 []\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 10796--10796 []\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 10801--10801 []\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 10804--10804 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2424] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10827--10827 []\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 10828--10828 []\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)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10854--10854 []\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 10856--10856 [] \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 10858--10858 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] Underfull \vbox (badness 10000) has occurred while \output is active [2425] [2426] Underfull \hbox (badness 10000) in paragraph at lines 10999--11003 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11039 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2427] [2428] Underfull \hbox (badness 10000) in paragraph at lines 11169--11171 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11197--11197 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2429] Underfull \hbox (badness 5036) in paragraph at lines 11225--11227 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a Underfull \hbox (badness 2970) in paragraph at lines 11359--11365 []\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 11359--11365 \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 "lsparseVec tor"\T1/ptm/m/n/10 , [2430] Underfull \hbox (badness 10000) in paragraph at lines 11432--11435 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2431] Underfull \hbox (badness 10000) in paragraph at lines 11450--11455 []\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 11465--11467 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2432] [2433] Underfull \hbox (badness 2698) in paragraph at lines 11590--11596 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2434] Underfull \hbox (badness 10000) in paragraph at lines 11683--11685 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11701--11706 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11701--11706 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other [2435] Underfull \hbox (badness 2591) in paragraph at lines 11709--11714 \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-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or Underfull \hbox (badness 2057) in paragraph at lines 11781--11783 []\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., [2436] [2437] Underfull \hbox (badness 6641) in paragraph at lines 11867--11870 []\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 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11907--11911 []\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 11907--11911 \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 [2438] [2439] Underfull \hbox (badness 7649) in paragraph at lines 12014--12016 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2440] [2441] [2442] Underfull \hbox (badness 7362) in paragraph at lines 12215--12217 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 12253--12253 []\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 12254--12254 []\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)[] [2443] [2444] [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12396--12396 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12409--12409 [] \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 12414--12414 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2446] Underfull \hbox (badness 6910) in paragraph at lines 12590--12592 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2447] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. [2448] [2449]) (./boot-pkg.tex [2450] Chapter 18. [2451] [2452] [2453] [2454] [2455] [2456] [2457] 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"), [2458] 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- [2459] [2460] [2461] 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 boot.c i[][][]\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 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2462] 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 [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2465] 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 [2466] [2467] [2468] [2469] 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- [2470] [2471] [2472] [2473] [2474] 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), [2475] [2476] [2477] Underfull \vbox (badness 10000) has occurred while \output is active [2478] 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),[] [2479] 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. [2480] [2481] [2482] 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 [2483] 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$statis tic \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 , [2484] [2485] 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/10 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/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2486] [2487] [2488] [2489] [2490] 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,[] [2491] [2492] [2493] 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.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/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 , [2494] 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)) [2495] [2496] [2497] 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 [2498] [2499] [2500] [2501] [2502] [2503] [2504] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2505] [2506] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2507] [2508] [2509] Underfull \hbox (badness 10000) in paragraph at lines 4190--4192 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2510] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2511] [2512] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2522] [2523] [2524] [2525] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2526] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2535] 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 t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2536] 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 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2537] [2538] [2539] [2540] 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). [2541] [2542] 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[] [2543] [2544] [2545] 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 [2546] [2547] 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),[] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555]) (./class-pkg.tex [2556] Chapter 19. [2557] [2558] [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]) (./cluster-pkg.tex Chapter 20. [2573] Underfull \hbox (badness 1655) in paragraph at lines 134--143 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 134--143 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 134--143 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 134--143 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2574] [2575] 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]))[] [2576] [2577] Underfull \vbox (badness 10000) has occurred while \output is active [2578] [2579] 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, ...)[] [2580] [2581] 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)[] [2582] 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 [2583] [2584] 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-ence s; [][]\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 , [2585] 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 [2586] 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), ...)[] [2587] 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, [2588] [2589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120 [] \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 1137--1137 []\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 [2590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1207--1211 []\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 [2591] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283 [] \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 1289--1289 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2592] [2593] Underfull \hbox (badness 10000) in paragraph at lines 1428--1433 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or [2594] Underfull \hbox (badness 10000) in paragraph at lines 1476--1479 Underfull \hbox (badness 10000) in paragraph at lines 1493--1497 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\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/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/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 1517--1517 []\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 1527--1527 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2595] Underfull \hbox (badness 5741) in paragraph at lines 1567--1570 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2597] [2598] Underfull \hbox (badness 1540) in paragraph at lines 1753--1761 \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 = [2599] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844 []\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 1863--1863 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2600] [2601] [2602] [2603] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2182--2185 Underfull \hbox (badness 3179) in paragraph at lines 2196--2202 [][][]\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/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2605] [2606] Underfull \hbox (badness 10000) in paragraph at lines 2354--2357 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2607] Underfull \hbox (badness 1292) in paragraph at lines 2422--2425 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and [2608] Underfull \hbox (badness 6675) in paragraph at lines 2431--2433 []\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 2454--2457 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\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 , [2609] [2610] [2611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670 []\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 ):[] [2612] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2613] [2614] [2615] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2618] [2619] [2620] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2621] Underfull \hbox (badness 10000) in paragraph at lines 3345--3348 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2622] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2623] [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 3581--3584 []\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 [2626] Underfull \hbox (badness 10000) in paragraph at lines 3644--3649 [][][]\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.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2627] Underfull \hbox (badness 3884) in paragraph at lines 3706--3711 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/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 3718--3721 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\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/10 hclust[][][]\T 1/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 , [2628] [2629] [2630] Underfull \hbox (badness 10000) in paragraph at lines 3903--3906 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3987--3987 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3998--4000 []\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 [2632] [2633] [2634] [2635] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4191--4191 [] \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 4193--4193 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2636] [2637] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4336--4336 []\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 4345--4345 [] \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 4347--4347 [] \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 4350--4350 []\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 4352--4352 [] \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 4359--4359 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2638] [2639] [2640] [2641] [2642] [2643] [2644] Underfull \hbox (badness 10000) in paragraph at lines 4732--4738 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4748--4750 []\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 4761--4761 []\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 4763--4763 []\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)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4773--4773 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2645] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4777--4777 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2646]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2647] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2648] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2649] [2650] [2651]) (./foreign-pkg.tex [2652] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\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 . [2653] 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 [2654] [2655] 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 , [2656] 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, [2657] [2658] [2659] 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,[] [2660] 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 10000) 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- Underfull \hbox (badness 6001) in paragraph at lines 505--514 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 , 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 "_dupli cated_"\T1/ptm/m/n/10 ) if [2661] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e n-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 568--574 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2662] Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2663] Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2664] [2665] Underfull \hbox (badness 10000) in paragraph at lines 812--813 Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2666] Underfull \hbox (badness 10000) in paragraph at lines 869--873 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\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 . [2667] 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) [2668] 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))) [2669] [2670] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2671] [2672] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2673] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2674]) (./lattice-pkg.tex Chapter 23. [2675] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\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 / [2676] [2677] 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"),[] [2678] 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"),[] [2679] [2680] [2681] [2682] 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 [2683] [2684] [2685] [2686] 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. [2687] 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 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2688] [2689] 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 [2690] [2691] [2692] 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 , [2693] 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/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2694] Underfull \vbox (badness 10000) has occurred while \output is active [2695] 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 [2696] 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\T1/pt m/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 [2697] [2698] [2699] [2700] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2701] 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-fied, t he 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 first ch ecked. If [2702] [2703] [2704] 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"),[] [2705] [2706] [2707] [2708] [2709] 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"),[] [2710] [2711] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2712] 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.rast er[][][]\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[][][] \T 1/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 [2713] 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 [2714] 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),[] [2715] 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"),[] [2716] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2717] [2718] [2719]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} [2720] 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"),[] [2721] [2722] [2723] [2724] [2725] 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))) [2726] [2727] 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 [2728] 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 [2729] 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-rent se t-tings (ob-tained by [2730] 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 trellis .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 [2731] [2732] 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 i s 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 "superpose.p olygon"\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 f or \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 c ol.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 plot .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 pl ot.polygon \T1/ptm/m/n/10 and [2733] [2734] [2735] [2736] [2737] 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")[] [2738] [2739] Underfull \vbox (badness 1092) has occurred while \output is active [2740] 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 . [2741] [2742] 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-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2743] [2744] [2745] [2746] [2747] 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-cally the en-try f or 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],[] [2748] 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 lef t of pan-els us-ing [2749] 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, wh ich is to draw a strip ap-pro-pri-ate for [2750] [2751] 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",[] [2752] 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 [2753] 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-fault 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 , ex-tr a 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 , these are used (in com-bi-na-tion with [2754] [2755] 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 Lattice[ ][][]\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 , [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] 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- [2759] [2760] 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/1 0 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-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2761] 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,[] [2762] [2763] 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/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2764] 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 v alid color. The [2765] [2766] [2767] [2768] [2769] 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 pan el 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 [2770] [2771] 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 this fu nc-tion is passed [2772] [2773] 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 [2774] [2775] 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 [2776] 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))[] [2777] [2778] 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 on 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 be a list of ar-gu-ments to be sup-plied to [2779] 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),[] [2780] 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)[] [2781] [2782] [2783] 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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] 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.superpo se 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 [2792] [2793] 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, ...)[] [2794] 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 [2795] 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 [2796] [2797] 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 [2798] 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)[] [2799] [2800] 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)),[] [2801] Overfull \hbox (46.28876pt too wide) in paragraph at lines 9228--9232 []\T1/ptm/m/n/10 Returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9228--9232 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2802] [2803] [2804] [2805] [2806] [2807] [2808] 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/10 , \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/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2809] [2810] [2811]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} [2812] [2813] [2814] 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 Heart 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),[] [2815] [2816]) (./mgcv-pkg.tex Chapter 24. [2817] [2818] 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,[] [2819] 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. [2820] [2821] [2822] [2823] Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][]\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 378--385 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2824] Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421 []\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)+[] [2825] [2826] [2827] Underfull \hbox (badness 2922) in paragraph at lines 633--634 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2828] [2829] Underfull \hbox (badness 1406) in paragraph at lines 703--704 []\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 [2830] [2831] Underfull \hbox (badness 1158) in paragraph at lines 813--815 []\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 [2832] Underfull \hbox (badness 1259) in paragraph at lines 876--877 []\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). [2833] Underfull \vbox (badness 10000) has occurred while \output is active [2834] [2835] [2836] [2837] [2838] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 []\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 1226--1226 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2839] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1255--1255 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1264--1264 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1266--1266 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2840] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1297--1297 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1380--1380 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2842] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1391--1391 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1425--1425 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1931--1931 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2852] [2853] [2854] [2855] [2856] [2857] Underfull \hbox (badness 1052) in paragraph at lines 2319--2327 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2336--2336 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2348--2351 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2361--2365 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2858] Underfull \hbox (badness 1043) in paragraph at lines 2387--2392 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2859] [2860] [2861] Underfull \hbox (badness 1043) in paragraph at lines 2552--2558 \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 [2862] Underfull \hbox (badness 10000) in paragraph at lines 2688--2694 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\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 2688--2694 [][]\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 2688--2694 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2863] [2864] Underfull \vbox (badness 10000) has occurred while \output is active [2865] Underfull \vbox (badness 10000) has occurred while \output is active [2866] [2867] [2868] [2869] [2870] [2871] [2872] [2873] [2874] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3344--3344 [] \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 3347--3347 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] Underfull \hbox (badness 5189) in paragraph at lines 3822--3826 []\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 [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3939--3939 []\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 [2885] [2886] [2887] Underfull \hbox (badness 1184) in paragraph at lines 4108--4112 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2888] [2889] [2890] [2891] [2892] [2893] [2894] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4554--4554 [] \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)+[] [2895] [2896] [2897] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4704--4704 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2898] [2899] Underfull \hbox (badness 1142) in paragraph at lines 4829--4833 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2900] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2901] [2902] Underfull \hbox (badness 5970) in paragraph at lines 5018--5024 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-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 5018--5024 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/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 . [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] [2905] [2906] [2907] Underfull \hbox (badness 1577) in paragraph at lines 5370--5373 []\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 5377--5378 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2908] [2909] [2910] [2911] [2912] [2913] [2914] Underfull \hbox (badness 6708) in paragraph at lines 5766--5767 []\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 [2915] [2916] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5815--5815 [] \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 5840--5840 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2917] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5869--5869 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2918] [2919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5991--5991 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2920] [2921] [2922] [2923] [2924] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6328--6328 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2925] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6330--6330 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2926] [2927] [2928] Underfull \vbox (badness 10000) has occurred while \output is active [2929] [2930] [2931] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6670--6670 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2932] [2933] [2934] [2935] Underfull \vbox (badness 10000) has occurred while \output is active [2936] Underfull \vbox (badness 10000) has occurred while \output is active [2937] [2938] [2939] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7102--7102 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7129--7129 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] Underfull \hbox (badness 1242) in paragraph at lines 7672--7673 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2949] [2950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2951] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7822--7822 []\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 7841--7841 [] \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 [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] [2972] Underfull \hbox (badness 10000) in paragraph at lines 9061--9064 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\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 9061--9064 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ 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 9061--9064 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2973] Underfull \hbox (badness 10000) in paragraph at lines 9117--9120 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9117--9120 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2974] [2975] [2976] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9337--9337 []\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 9338--9338 [] \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 9341--9341 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2977] [2978] [2979] Underfull \hbox (badness 1629) in paragraph at lines 9499--9504 \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 [2980] [2981] [2982] [2983] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9710--9710 [] \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 9747--9751 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para- Underfull \hbox (badness 1292) in paragraph at lines 9747--9751 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2984] [2985] [2986] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9880--9880 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2987] [2988] [2989] Underfull \vbox (badness 10000) has occurred while \output is active [2990] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10153--10153 [] \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[] [2991] Underfull \hbox (badness 1205) in paragraph at lines 10191--10193 []\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 10191--10193 \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 10197--10202 []\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 [2992] Underfull \hbox (badness 1205) in paragraph at lines 10281--10283 []\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 10281--10283 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2993] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\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 10350--10353 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh 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, [2994] [2995] Underfull \hbox (badness 1253) in paragraph at lines 10480--10482 []\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, [2996] [2997] [2998] [2999] [3000] Underfull \hbox (badness 1946) in paragraph at lines 10733--10740 []\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 10733--10740 \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 10733--10740 \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: s ee [3001] Underfull \hbox (badness 2846) in paragraph at lines 10741--10744 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 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 10741--10744 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3002] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10807--10807 []\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 10817--10817 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] Underfull \hbox (badness 10000) in paragraph at lines 10848--10851 []\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 , [3003] [3004] [3005] [3006] [3007] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11150--11150 []\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) [3008] [3009] [3010] [3011] [3012] [3013] [3014] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11521--11521 [] \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 11535--11535 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] [3015] Underfull \vbox (badness 10000) has occurred while \output is active [3016] Underfull \hbox (badness 3861) in paragraph at lines 11637--11640 []\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 11646--11646 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3017] Underfull \hbox (badness 10000) in paragraph at lines 11703--11707 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3018] [3019] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11847--11847 [] \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 11858--11863 []\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 [3020] [3021] Underfull \hbox (badness 1803) in paragraph at lines 11935--11939 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11947--11959 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11964--11968 \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 11964--11968 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [3022] [3023] [3024] [3025] Underfull \hbox (badness 6876) in paragraph at lines 12159--12165 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 12200--12201 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3026] [3027] Underfull \hbox (badness 10000) in paragraph at lines 12318--12319 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3028] [3029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12372--12372 [] \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 12384--12384 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12396--12396 [] \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 12401--12401 [] \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 12407--12407 [] \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 12408--12408 [] \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:[] [3030] Underfull \hbox (badness 10000) in paragraph at lines 12477--12479 []\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 12477--12479 \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 [3031] [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 12607--12608 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12688--12688 []\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 12689--12689 []\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[] [3035] [3036] [3037] Underfull \hbox (badness 10000) in paragraph at lines 12840--12841 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3038] [3039] [3040] [3041] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13090--13090 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3042] Underfull \hbox (badness 10000) in paragraph at lines 13151--13153 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 13310--13313 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13310--13313 \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 13310--13313 \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" [3046] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3047] Underfull \hbox (badness 10000) in paragraph at lines 13441--13447 []\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 13441--13447 \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- [3048] [3049] [3050] Underfull \vbox (badness 10000) has occurred while \output is active [3051] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13655--13655 []\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 [3052] Underfull \hbox (badness 10000) in paragraph at lines 13758--13766 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [3053] Underfull \hbox (badness 10000) in paragraph at lines 13784--13785 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3054] [3055] [3056] [3057] Underfull \hbox (badness 3396) in paragraph at lines 14044--14047 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [3058] Underfull \hbox (badness 10000) in paragraph at lines 14089--14091 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 14370--14373 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 14370--14373 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3064] Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][][]\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 14403--14407 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][]\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 , [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2158) in paragraph at lines 14693--14693 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3070] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14772--14772 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3071] [3072] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14906--14906 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3073] [3074] Underfull \hbox (badness 4846) in paragraph at lines 15037--15040 []\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 [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3095] [3096] [3097] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441 []\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, [3098] Overfull \hbox (48.78088pt too wide) in paragraph at lines 16443--16443 []\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 16445--16445 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 16465--16466 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16465--16466 \T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected by \T1/pcr/m/n/10 ar.row [3099] [3100] [3101] [3102] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653 []\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 16654--16654 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3103] [3104] [3105]) (./nlme-pkg.tex [3106] Chapter 25. [3107] 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 - fi t-ted) are used; else, if [3108] 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 - fi t-ted) are used; else, if [3109] [3110] [3111] [3112] [3113] 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,[] [3114] [3115] 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 --------------------------- ---------------[] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] 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"),[] [3124] 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.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3125] [3126] [3127] [3128] [3129] [3130] [3131] 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.effe cts.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 , [3132] 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 [3133] [3134] [3135] [3136] [3137] 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 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3138] 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")[] [3139] 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 [3140] [3141] 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 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3142] 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,[] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] 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 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3151] [3152] [3153] [3154] [3155] [3156pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored ...shipout:D \box_use:N \l_shipout_box l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3157] [3158] [3159] [3160] [3161] [3162] 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 corGaus[][ ][]\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 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3187] [3188] [3189] [3190] [3191] [3192] [3193] 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 , [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] 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 [3203] 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 , [3204] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\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 , [3205] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3206] [3207] [3208] [3209] Underfull \hbox (badness 7133) in paragraph at lines 6562--6566 []\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 , [3210] Underfull \hbox (badness 10000) in paragraph at lines 6661--6667 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3211] Underfull \hbox (badness 10000) in paragraph at lines 6726--6728 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3212] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3213] [3214] [3215] Underfull \hbox (badness 10000) in paragraph at lines 6999--7006 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7044--7046 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3217] [3218] [3219] Underfull \hbox (badness 10000) in paragraph at lines 7259--7264 [][][]\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 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3220] [3221] [3222] Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7411--7419 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7434--7437 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3223] [3224] [3225] Underfull \hbox (badness 3354) in paragraph at lines 7650--7652 []\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 [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\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 8205--8205 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8214--8236 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3234] [3235] [3236] [3237] [3238] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8527--8529 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8578 \aliasA{sigma}{lmeObject}{sigma} [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] [3249] [3250] [3251] Underfull \hbox (badness 10000) in paragraph at lines 9330--9337 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3252] Underfull \hbox (badness 6300) in paragraph at lines 9423--9426 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3253] [3254] [3255] [3256]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3257] Underfull \hbox (badness 10000) in paragraph at lines 9712--9715 []\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 9756--9759 []\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 9756--9759 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3258] [3259] [3260] [3261] [3262] [3263] [3264] [3265] Underfull \hbox (badness 7291) in paragraph at lines 10220--10222 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3266] [3267] [3268] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3269] Underfull \hbox (badness 1596) in paragraph at lines 10465--10491 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3270] [3271] [3272] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3273] [3274] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10792--10792 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10803--10808 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3275] Underfull \hbox (badness 8075) in paragraph at lines 10825--10829 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10844--10846 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3276] [3277] [3278] [3279] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136 []\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 11137--11137 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3280] [3281] [3282] [3283] [3284] [3285] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 6268) in paragraph at lines 11914--11924 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] Underfull \hbox (badness 10000) in paragraph at lines 12175--12181 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 6876) in paragraph at lines 12497--12499 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-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 [3301] [3302] Underfull \hbox (badness 2452) in paragraph at lines 12653--12660 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 12718--12724 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3313] [3314] [3315] [3316] [3317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3318] Underfull \hbox (badness 10000) in paragraph at lines 13699--13702 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3319] Underfull \hbox (badness 1838) in paragraph at lines 13742--13749 []\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 13742--13749 \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 13799--13799 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3320] Underfull \hbox (badness 10000) in paragraph at lines 13806--13809 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13806--13809 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13834--13837 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13834--13837 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3321] Underfull \hbox (badness 10000) in paragraph at lines 13914--13917 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3322] Underfull \hbox (badness 1472) in paragraph at lines 13939--13946 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3323] Underfull \hbox (badness 10000) in paragraph at lines 14008--14010 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] Underfull \hbox (badness 1215) in paragraph at lines 14288--14290 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3328] [3329] [3330] [3331] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3332] [3333] [3334] [3335] [3336] [3337] [3338] [3339] [3340]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Underfull \hbox (badness 2126) in paragraph at lines 15825--15829 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833 []\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 15852--15852 [] \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 15853--15853 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3352] Underfull \hbox (badness 1009) in paragraph at lines 15883--15892 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3353] [3354] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 10000) in paragraph at lines 16365--16371 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\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.reStruc t[][][]\T1/ptm/m/n/10 , [3360] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3361] [3362] [3363] [3364] [3365] [3366] [3367] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3368] [3369] [3370] [3371] [3372] Underfull \hbox (badness 1867) in paragraph at lines 17220--17229 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3373] Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17292--17293 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3374] [3375] [3376] [3377] Underfull \hbox (badness 10000) in paragraph at lines 17542--17550 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/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 , [3378] [3379] [3380] [3381] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17814--17814 []\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 17816--17816 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3382] [3383] [3384] [3385] [3386] [3387] Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][][]\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.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][]\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 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3388] Underfull \hbox (badness 3579) in paragraph at lines 18290--18295 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3389] Underfull \hbox (badness 3579) in paragraph at lines 18354--18359 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3390] Underfull \hbox (badness 3579) in paragraph at lines 18417--18422 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3391] Underfull \hbox (badness 1577) in paragraph at lines 18478--18480 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18480--18485 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3392] Underfull \hbox (badness 3579) in paragraph at lines 18543--18548 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18576--18585 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\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 18576--18585 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3393] Underfull \hbox (badness 3579) in paragraph at lines 18615--18620 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3394] [3395] Underfull \hbox (badness 1009) in paragraph at lines 18761--18770 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3396] [3397] Underfull \hbox (badness 1009) in paragraph at lines 18893--18902 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406]) (./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): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3407] 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,[] [3408] [3409] [3410] 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,[] [3411] 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)[] [3412] [3413] 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,[] [3414]) (./rpart-pkg.tex Chapter 27. [3415] [3416] [3417] [3418] 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, ...)[] [3419] [3420] [3421] [3422] 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 will be at the hor-i-zon-tal plot co-or-di-nates of [3423] [3424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3425] [3426] [3427] Overfull \hbox (25.98041pt too wide) in paragraph at lines 914--914 []\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 933--933 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3428] [3429] [3430] [3431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1179--1179 []\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 1180--1180 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1242--1244 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3432] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1286--1286 []\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 1302--1302 []\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 1303--1303 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3433] [3434] [3435] [3436] [3437] [3438] [3439] Underfull \hbox (badness 1565) in paragraph at lines 1759--1762 []\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 ', [3440] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1853--1853 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3441] [3442] [3443]) (./spatial-pkg.tex [3444] Chapter 28. [3445] [3446] [3447] [3448] [3449] [3450] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463]) (./survival-pkg.tex [3464] Chapter 29. [3465] [3466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\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 190--190 []\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 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3467] [3468] Underfull \hbox (badness 6412) in paragraph at lines 282--284 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3469] [3470]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} [3471] Overfull \hbox (9.78043pt too wide) in paragraph at lines 483--483 []\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 485--485 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3472] Overfull \hbox (6.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3473] [3474] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3475] [3476] 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 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"),[] [3477] [3478] 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,[] [3479] [3480] [3481] 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[] [3482] [3483] 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) [3484] 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} [3485] Underfull \hbox (badness 10000) in paragraph at lines 1356--1360 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by 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, ...)[] [3486] [3487] [3488] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575 [] \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 1624--1624 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3489] [3490] [3491] [3492] [3493] Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 []\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 1940--1955 \T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt m/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3494] Underfull \hbox (badness 1337) in paragraph at lines 2024--2028 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3495] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2079--2079 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2651--2651 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2678--2678 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3504] [3505] [3506] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2910--2910 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3507] [3508] [3509] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3251--3251 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3512] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3286--3286 [] \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 3300--3302 []\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 3311--3311 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3513] [3514] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3445--3445 [] \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 )))[] [3515] [3516] Overfull \hbox (467.89665pt too wide) in alignment at lines 3586--3586 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3517] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3518] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3519] [3520] [3521] [3522] [3523] [3524] [3525] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4144--4144 [] \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 )))[] [3526] [3527] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4290--4290 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4295--4295 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4299--4299 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3529] [3530] [3531] Overfull \vbox (11.01616pt too high) has occurred while \output is active [3532] [3533] [3534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4716--4716 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3535] [3536] [3537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3538] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5072--5072 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3539] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5080--5080 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3540] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5166--5166 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5244--5244 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3542] Underfull \hbox (badness 1852) in paragraph at lines 5316--5318 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3543] [3544] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5441--5441 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3545] [3546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5543--5543 []\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 5544--5544 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3547] [3548] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5810--5810 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5831--5831 []\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 5833--5833 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3551] [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6348--6348 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3557] [3558] [3559] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6528--6528 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6540--6543 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6848--6848 []\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 6849--6849 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3565] [3566] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7014--7014 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3567] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7088--7088 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicates[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7092 ...ata from a soldering experiment}{solder} [3568] [3569] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7198--7198 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3570] [3571] [3572] [3573] [3574] [3575] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7562--7562 []\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 7563--7563 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3576] [3577] [3578] [3579] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7881--7881 [] \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 ),[] [3580] [3581] [3582] [3583] Underfull \hbox (badness 1253) in paragraph at lines 8170--8173 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3586] Underfull \hbox (badness 10000) in paragraph at lines 8422--8431 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 8422--8431 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3587] [3588] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8518--8518 [] \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 8536--8536 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8578--8584 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3589] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8630--8630 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3590] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8716--8716 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 8941--8946 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3594] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8960--8960 [] \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 8961--8961 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3595] [3596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9171--9171 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3597] [3598] Underfull \hbox (badness 3058) in paragraph at lines 9304--9309 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3599] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9434--9434 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3601] [3602] [3603] [3604] [3605] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9819--9819 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 9860--9864 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3606] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9906--9906 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3607] [3608] Underfull \hbox (badness 2035) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10070--10077 \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, it is [3609] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10150--10150 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3610] [3611] [3612] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10307--10307 [] \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 )[] [3613] [3614] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 [] \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 10442--10442 [] \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 )[] [3615] [3616] [3617] [3618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10751--10751 []\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 10752--10752 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10758--10758 [] \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 10760--10760 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3620] [3621] [3622] [3623] [3624] [3625] [3626] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11201--11201 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3627] [3628] [3629]) [3630] (./fullrefman.ind [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640] [3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] [3652] [3653] [3654] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2583--2585 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , [3655] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2585--2587 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2587--2589 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2589--2591 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2591--2593 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2593--2595 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2595--2597 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2597--2599 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2599--2601 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 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paragraph at lines 3236--3238 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 3238--3240 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3240--3242 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 3242--3244 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3244--3246 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3662] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3399--3401 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3663] [3664] [3665] [3666] [3667] [3668] [3669] [3670] [3671] Overfull \hbox (62.8567pt too wide) in paragraph at lines 4506--4508 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox 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paragraph at lines 4766--4768 []\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 4768--4770 []\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4770--4772 []\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 4772--4774 []\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 4774--4776 []\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method Overfull \hbox (98.8567pt too wide) in paragraph at lines 4776--4778 []\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method Overfull \hbox (98.8567pt too wide) in paragraph at lines 4778--4780 []\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 4780--4782 []\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method [3674] Overfull \hbox (104.8567pt too wide) in paragraph at lines 4782--4784 []\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValueSp-method Overfull \hbox (146.8567pt too wide) in paragraph at lines 4784--4786 []\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValueSp-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4866--4868 []\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4868--4870 []\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 4870--4872 []\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 4874--4876 []\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4892--4894 []\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4900--4902 []\T1/pcr/m/n/10 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cbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7276--7278 []\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7278--7280 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3690] [3691] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7534--7536 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3692] [3693] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8035--8037 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8037--8039 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8039--8041 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method [3694] Overfull \hbox (26.8567pt too wide) in paragraph at lines 8045--8047 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox 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in paragraph at lines 11633--11635 \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 , [3719] [3720] Overfull \hbox (56.8567pt too wide) in paragraph at lines 11975--11977 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11977--11979 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11979--11981 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11981--11983 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11983--11985 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11985--11987 []\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11987--11989 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[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14533--14535 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14535--14537 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 14537--14539 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14539--14541 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14541--14543 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method [3733] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14543--14545 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14545--14547 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 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in paragraph at lines 17473--17475 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17477--17479 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17479--17481 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 17481--17483 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17501--17503 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method [3748] Overfull \hbox (38.8567pt too wide) in paragraph at lines 17503--17505 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17505--17507 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 17507--17509 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17511--17513 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17515--17517 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17519--17521 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method Overfull \hbox (46.01662pt too wide) in paragraph at lines 17727--17729 \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 , [3749] Overfull \hbox (77.3567pt too wide) in paragraph at lines 17755--17757 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3750] [3751] [3752] [3753] [3754] Overfull \hbox (46.01662pt too wide) in paragraph at lines 19060--19062 \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 19063--19065 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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(\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 19077--19079 \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 19079--19081 \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 19083--19085 \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 19085--19087 \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 (4.01662pt too wide) in paragraph at lines 19087--19089 \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 19089--19091 \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 19091--19093 \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 19093--19095 \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 , [3756] [3757] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19445--19447 \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 19519--19521 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3758] [3759] [3760] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19990--19992 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19999--20001 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20001--20003 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20003--20005 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20005--20007 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20017--20019 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20027--20029 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20042--20044 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20048--20050 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3761] Overfull \hbox (62.8567pt too wide) in paragraph at lines 20169--20171 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3762] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20383--20385 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20385--20387 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20387--20389 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20389--20391 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20393--20395 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20395--20397 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20397--20399 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20399--20401 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20401--20403 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20403--20405 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20405--20407 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20411--20413 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20415--20417 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20425--20427 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method [3763] Overfull \hbox (8.8567pt too wide) in paragraph at lines 20429--20431 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20431--20433 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20433--20435 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20435--20437 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20437--20439 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20439--20441 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 20441--20443 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20470--20472 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20472--20474 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20474--20476 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20476--20478 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20480--20482 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20484--20486 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20488--20490 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20492--20494 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20496--20498 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20500--20502 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20504--20506 []\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 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Schur,symmetricMatrix,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21512--21514 []\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21514--21516 []\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method [3769] [3770] Overfull \hbox (26.8567pt too wide) in paragraph at lines 21902--21904 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21906--21908 \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 21910--21912 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 21914--21916 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21924--21926 []\T1/pcr/m/n/10 show,refClassRepresentation-method [3771] [3772] Overfull \hbox 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22196--22198 \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 22199--22203 []\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 22204--22206 \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 22252--22254 \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 (20.8567pt too wide) in paragraph at lines 22291--22293 []\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 22293--22295 []\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22295--22297 []\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method [3773] Overfull \hbox (2.8567pt too wide) in paragraph at lines 22305--22307 []\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22307--22309 []\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 22309--22311 []\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 22311--22313 []\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22315--22317 []\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22317--22319 []\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22323--22325 []\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22329--22331 []\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in 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22417--22419 []\T1/pcr/m/n/10 solve,Matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22419--22421 []\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22421--22423 []\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22423--22425 []\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22435--22437 []\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method Overfull \hbox (52.01662pt too wide) in paragraph at lines 22582--22584 \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 , [3775] [3776] Overfull \hbox (44.8567pt too wide) in paragraph at lines 23025--23027 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends Overfull \hbox (44.8567pt too wide) in paragraph at lines 23027--23029 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results Overfull \hbox (44.8567pt too wide) in paragraph at lines 23029--23031 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings [3777] [3778] [3779] [3780] [3781] Overfull \hbox (32.8567pt too wide) in paragraph at lines 23916--23918 []\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 23918--23920 []\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 23920--23922 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method [3782] Overfull \hbox (74.8567pt too wide) in paragraph at lines 23922--23924 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 23924--23926 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 23926--23928 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method Overfull 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tcrossprod,ddenseMatrix,lsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 23944--23946 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 23946--23948 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 23948--23950 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ndenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 23950--23952 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 23952--23954 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 23954--23956 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 23956--23958 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 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Typ-i-cally, it is equal to [5] Underfull \hbox (badness 3009) in paragraph at lines 226--238 \T1/pcr/m/n/10 *.exponent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 *.min.exp\T1/ptm/m/n/1 0 , and \T1/pcr/m/n/10 *.max.exp\T1/ptm/m/n/10 , com-puted en-tirely anal-o-gou sly to their [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 369--372 [][][]\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-lar, [8] [9] [10] Underfull \hbox (badness 1072) in paragraph at lines 567--573 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [11] Overfull \hbox (4.38043pt too wide) in paragraph at lines 635--635 []\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 636--636 []\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 912--912 []\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 933--933 []\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 962--962 []\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 1578--1584 Underfull \hbox (badness 10000) in paragraph at lines 1591--1593 []\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 1770--1770 [] \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 1799--1802 []\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] Underfull \hbox (badness 10000) in paragraph at lines 1919--1921 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [31] [32] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2056--2056 []\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 2094--2096 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e 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 2366--2366 []\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 2408--2408 [] \T1/pcr/m/n/9 tmp <- read.delim(file.path(R.home("share"), "zoneinfo", "zo ne1970.tab"),[] [38] Underfull \hbox (badness 10000) in paragraph at lines 2503--2505 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2506--2511 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [39] Underfull \hbox (badness 1107) in paragraph at lines 2574--2576 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [40] [41] [42] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2741--2741 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3410--3410 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] [52] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3441--3441 []\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 3442--3442 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3449--3449 []\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 3450--3450 [] \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 3453--3453 []\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 3901--3903 []\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 4399--4403 []\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 4399--4403 \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 or [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4483--4483 [] \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 4717--4717 []\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 4748--4754 []\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 4759--4762 []\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 4935--4935 []\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 5191--5193 []\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 10000) in paragraph at lines 5614--5622 []\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 [84] [85] [86] [87] [88] [89] [90] [91] [92] Underfull \hbox (badness 1796) in paragraph at lines 6183--6191 []\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 6380--6380 []\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 6382--6382 []\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 6383--6383 []\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 6585--6588 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6589--6592 []\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 6632--6640 []\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 6796--6796 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [101] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6848--6851 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [102] [103] Underfull \hbox (badness 1997) in paragraph at lines 6990--6995 []\T1/pcr/m/n/10 file\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pipe\T1/ptm/m/n/10 , \T1/p cr/m/n/10 fifo\T1/ptm/m/n/10 , \T1/pcr/m/n/10 url\T1/ptm/m/n/10 , \T1/pcr/m/n/1 0 gzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 bzfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x zfile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 unz\T1/ptm/m/n/10 , \T1/pcr/m/n/10 socketC onnection\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 7031--7034 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 7031--7034 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [104] [105] [106] Underfull \hbox (badness 1406) in paragraph at lines 7213--7219 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 7213--7219 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 7233--7235 []\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 7275--7282 []\T1/pcr/m/n/10 file \T1/ptm/m/n/10 can be used with \T1/pcr/m/n/10 descriptio n = "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 7275--7282 \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 7275--7282 \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] [109] Underfull \vbox (badness 10000) has occurred while \output is active [110] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7479--7479 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [111] Underfull \hbox (badness 1231) in paragraph at lines 7604--7610 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [112] [113] [114] Underfull \hbox (badness 10000) in paragraph at lines 7816--7818 []\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 7975--7975 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [118] [119] [120] [121] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8208--8208 []\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 8327--8337 []\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 8327--8337 [][]\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] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8359--8364 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [124] [125] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8501--8501 [] \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 1629) in paragraph at lines 8850--8862 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8850--8862 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [130] [131] [132] [133] [134] [135] Underfull \hbox (badness 10000) in paragraph at lines 9299--9303 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [136] [137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9390--9390 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9392--9392 []\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 9418--9418 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9419--9419 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [138] Underfull \hbox (badness 1924) in paragraph at lines 9480--9485 []\T1/ptm/m/n/10 Attributes named \T1/pcr/m/n/10 dim\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 dimnames\T1/ptm/m/n/10 , \T1/pcr/m/n/10 levels\T1/ptm/m/n/10 , \T1/pcr/m/n /10 names \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tsp \T1/ptm/m/n/10 are de-parsed to \T1/pcr/m/n/10 .Dim\T1/ptm/m/n/10 , [139] Underfull \hbox (badness 5403) in paragraph at lines 9550--9552 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9569--9571 []\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 9800--9803 []\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 10415--10420 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \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 10470--10470 []\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 10471--10471 []\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 10573--10578 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10613--10619 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as [155] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10675--10675 []\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 10677--10677 []\T1/pcr/m/n/9 chk.n2 <- function(...) stopifnot(identical(print(...names()), names(list(...))))[] [156] [157] Underfull \hbox (badness 2828) in paragraph at lines 10797--10802 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10797--10802 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10797--10802 \T1/pcr/m/n/10 754-[]2019$[][]\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 10828--10828 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [158] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10902--10902 []\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 11049--11049 []\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 11247--11255 []\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 11256--11258 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [164] [165] [166] Underfull \hbox (badness 10000) in paragraph at lines 11473--11476 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [167] [168] [169] [170] [171] [172] [173] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11928--11928 []\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/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and [177] Underfull \hbox (badness 10000) in paragraph at lines 12259--12261 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [178] [179] Underfull \hbox (badness 4569) in paragraph at lines 12396--12400 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 12396--12400 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [180] [181] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13357--13357 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] Underfull \vbox (badness 10000) has occurred while \output is active [193] [194] [195] [196] [197] [198] [199] Underfull \hbox (badness 2221) in paragraph at lines 13820--13829 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13820--13829 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [200] [201] [202] [203] Underfull \hbox (badness 2253) in paragraph at lines 14081--14083 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [204] [205] Underfull \hbox (badness 2573) in paragraph at lines 14201--14203 []\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 14360--14362 []\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 14477--14481 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\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 14488--14491 [][][]$\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 14509--14509 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14534--14534 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [210] [211] Underfull \hbox (badness 10000) in paragraph at lines 14631--14634 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\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 14641--14641 []\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 14707--14710 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14724--14724 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14753--14753 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, [213] Underfull \hbox (badness 1472) in paragraph at lines 14777--14784 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14777--14784 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14785--14789 []\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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14949--14949 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) [216] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14950--14950 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [217] [218] [219] Overfull \hbox (63.78036pt too wide) in paragraph at lines 15184--15184 []\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 15187--15187 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [220] Underfull \hbox (badness 1168) in paragraph at lines 15271--15275 []\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 15271--15275 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [221] Underfull \hbox (badness 6944) in paragraph at lines 15369--15372 [][][]\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/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15394--15394 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [223] [224] Underfull \hbox (badness 10000) in paragraph at lines 15532--15534 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15552--15552 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15558--15558 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [225] Underfull \hbox (badness 2790) in paragraph at lines 15565--15568 []\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 Underfull \hbox (badness 1024) in paragraph at lines 15596--15603 []\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 [226] Underfull \hbox (badness 10000) in paragraph at lines 15671--15673 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15671--15673 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15693--15698 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15699--15701 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [227] Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15705--15709 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15710--15718 []\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] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15818--15818 []\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 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [229] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15840--15840 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16669--16669 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [242] Underfull \hbox (badness 2418) in paragraph at lines 16778--16782 \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/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16785--16788 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [243] Underfull \hbox (badness 2326) in paragraph at lines 16820--16827 [][][]\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[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [244] [245] [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17077--17077 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [247] Underfull \hbox (badness 1867) in paragraph at lines 17105--17112 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [248] [249] [250] [251] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17406--17406 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Underfull \vbox (badness 10000) has occurred while \output is active [252] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17435--17435 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] [253] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17491--17491 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [254] [255] [256] [257] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17864--17864 []\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))) [258] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17929--17929 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [259] [260] [261] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18119--18119 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [262] [263] [264] [265] Underfull \hbox (badness 2285) in paragraph at lines 18461--18463 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / [266] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18469--18469 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18499--18499 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [267] [268] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18632--18632 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18638--18638 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18641--18641 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18647--18647 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [269] [270] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18774--18774 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18782--18782 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [271] [272] [273] Underfull \hbox (badness 10000) in paragraph at lines 18987--18989 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [274] [275] [276] [277] [278] Underfull \hbox (badness 10000) in paragraph at lines 19325--19331 Underfull \hbox (badness 10000) in paragraph at lines 19338--19340 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [279] [280] [281] Underfull \hbox (badness 4699) in paragraph at lines 19570--19573 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\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 , [282] [283] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19698--19698 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [284] [285] [286] Underfull \hbox (badness 4739) in paragraph at lines 19833--19835 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [287] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19882--19882 []\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 19883--19883 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [288] [289] [290] [291] [292] [293] [294] [295] Underfull \hbox (badness 1975) in paragraph at lines 20494--20497 []\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 [296] [297] [298] [299] [300] [301] [302] Underfull \hbox (badness 1077) in paragraph at lines 20892--20897 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 20906--20913 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [303] Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec- Underfull \hbox (badness 10000) in paragraph at lines 20986--20990 \T1/ptm/m/n/10 tory `\T1/pcr/m/n/10 R/\T1/ptm/m/sl/10 R.version$platform\T1/pcr /m/n/10 -library/\T1/ptm/m/sl/10 x.y\T1/ptm/m/n/10 ' of the home di-rec-tory (o r [304] [305] Underfull \hbox (badness 10000) in paragraph at lines 21135--21139 []\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 21135--21139 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll 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 21140--21147 []\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- [306] [307] Underfull \hbox (badness 10000) in paragraph at lines 21271--21278 [][][]\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 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [308] [309] Underfull \hbox (badness 10000) in paragraph at lines 21392--21396 []\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 [310] Underfull \hbox (badness 5161) in paragraph at lines 21462--21467 []\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 21462--21467 \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 21462--21467 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21462--21467 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [311] [312] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21629--21629 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21633--21633 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [313] Underfull \hbox (badness 3343) in paragraph at lines 21694--21698 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [314] [315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21835--21835 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 21846--21846 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, prob = 0.2))),[] [316] [317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21957--21957 []\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 21960--21960 []\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 22005--22010 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [318] [319] Underfull \hbox (badness 2564) in paragraph at lines 22096--22099 []\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 22133--22133 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [320] [321] Underfull \hbox (badness 1400) in paragraph at lines 22301--22305 [][][]\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 do uble[][][] \T1/ptm/m/n/10 (class [322] [323] [324] Underfull \hbox (badness 1824) in paragraph at lines 22471--22479 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. In nu-meric and Underfull \hbox (badness 6758) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 com-plex vec-tors, ze-ros are \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/1 0 and non-zero val-ues are \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 . For [][]\T1/pcr/ m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 22471--22479 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] Overfull \hbox (52.98038pt too wide) in paragraph at lines 23137--23137 []\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 23138--23138 [] \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 23141--23141 []\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)[] [335] [336] Underfull \hbox (badness 1655) in paragraph at lines 23270--23274 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [337] [338] [339] Underfull \hbox (badness 2277) in paragraph at lines 23519--23522 []\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 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [340] [341] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 A ma-trix is the spe-cial case of a two-dimensional [][]\T1/pc r/m/n/10 array[][][]\T1/ptm/m/n/10 . Since \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.0. 0, [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1484) in paragraph at lines 24107--24115 []\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 24107--24115 \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 / [349] [350] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24185--24185 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [351] [352] [353] [354] [355] [356] [357] Underfull \hbox (badness 1448) in paragraph at lines 24699--24707 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [358] [359] Underfull \hbox (badness 3849) in paragraph at lines 24814--24819 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [360] Underfull \hbox (badness 7308) in paragraph at lines 24891--24897 []\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-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24891--24897 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24891--24897 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24901--24904 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [361] [362] Underfull \hbox (badness 10000) in paragraph at lines 25054--25056 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [363] [364] [365] Underfull \hbox (badness 6188) in paragraph at lines 25281--25284 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [366] [367] [368] Underfull \hbox (badness 1521) in paragraph at lines 25466--25480 \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- [369] [370] [371] [372] [373] Underfull \hbox (badness 2197) in paragraph at lines 25780--25784 []\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 25780--25784 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 25794--25798 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 25794--25798 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 25836--25836 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [374] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25840--25840 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [375] Underfull \hbox (badness 10000) in paragraph at lines 25888--25894 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25888--25894 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25901--25903 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [376] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25968--25968 [] \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:[] [377] [378] Underfull \hbox (badness 8189) in paragraph at lines 26163--26169 []\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 [][][] [379] [380] [381] Underfull \hbox (badness 1694) in paragraph at lines 26388--26391 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [382] [383] [384] [385] Underfull \hbox (badness 1603) in paragraph at lines 26635--26637 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [386] [387] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26762--26770 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [388] [389] Underfull \hbox (badness 3271) in paragraph at lines 26981--26984 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [390] [391] [392] Underfull \hbox (badness 3138) in paragraph at lines 27287--27293 []\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 27287--27293 \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 27287--27293 \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 [393] Underfull \hbox (badness 1194) in paragraph at lines 27300--27303 []\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/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 27326--27328 []\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 27346--27352 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27361--27366 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 27379--27382 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [394] Underfull \hbox (badness 10000) in paragraph at lines 27395--27398 []\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 27403--27409 []\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 27403--27409 \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 27403--27409 \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 27403--27409 \T1/pcr/m/n/10 "mac.binary.leopard" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "mac.bina ry.universal" \T1/ptm/m/n/10 are no longer Underfull \hbox (badness 10000) in paragraph at lines 27418--27425 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 27418--27425 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 27418--27425 \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 27418--27425 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [395] [396] [397] [398] Underfull \vbox (badness 10000) has occurred while \output is active [399] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27765--27765 []\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 27778--27782 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 27778--27782 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27925--27928 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27925--27928 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [402] [403] [404] [405] Underfull \hbox (badness 10000) in paragraph at lines 28207--28213 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 28207--28213 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and Overfull \hbox (42.18039pt too wide) in paragraph at lines 28229--28229 []\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 28241--28241 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 28254--28254 []\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 28258--28258 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [406] [407] [408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28433--28433 []\T1/pcr/m/n/9 mtcars |> subset(cyl == 4) |> nrow() # same as nrow(subset(mt cars, cyl == 4))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28442--28442 []\T1/pcr/m/n/9 stop() |> (function(...) {})() # stop() is not used on RHS so is not evaluated[] [409] Underfull \hbox (badness 1360) in paragraph at lines 28497--28501 []\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 = [410] [411] [412] [413] [414] [415] Underfull \hbox (badness 2005) in paragraph at lines 28892--28896 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/cmtt/m/n/10 `\T1/pc r/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 = [416] Underfull \hbox (badness 1796) in paragraph at lines 28960--28963 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [417] [418] [419] [420] Underfull \hbox (badness 10000) in paragraph at lines 29164--29167 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [421] [422] [423] [424] [425] [426] [427] [428] [429] [430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29859--29859 [] \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))[] [431] [432] [433] [434] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30150--30150 []\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 30161--30161 []\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 30167--30167 []\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 30173--30173 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] Underfull \vbox (badness 10000) has occurred while \output is active [435] [436] Underfull \hbox (badness 7415) in paragraph at lines 30256--30260 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use Overfull \hbox (42.18039pt too wide) in paragraph at lines 30277--30277 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [437] Overfull \hbox (6.78088pt too wide) in paragraph at lines 30323--30323 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [438] Underfull \hbox (badness 3713) in paragraph at lines 30468--30479 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [439] [440] Underfull \hbox (badness 1248) in paragraph at lines 30620--30627 \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 30620--30627 \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 / [441] [442] Underfull \hbox (badness 1533) in paragraph at lines 30738--30741 []\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 [443] [444] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30883--30883 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30901--30912 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [445] [446] [447] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31045--31045 []\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 31047--31047 []\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 31048--31048 []\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 31049--31049 []\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 31050--31050 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 31057--31057 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [448] [449] [450] [451] [452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 31365--31365 []\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 31367--31367 []\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 31377--31377 []\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 31378--31378 []\T1/pcr/m/n/9 d2b <- function(x) vapply(as.double(x), function(x) numToBits(x) , raw(64L))[] [453] Underfull \hbox (badness 4048) in paragraph at lines 31473--31478 []\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 31473--31478 \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 31473--31478 \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 , [454] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 2080) in paragraph at lines 32011--32021 []\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), [462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32045--32045 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [463] [464] [465] [466] [467] [468] [469] Underfull \hbox (badness 7558) in paragraph at lines 32564--32568 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 32574--32576 []\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 Underfull \hbox (badness 10000) in paragraph at lines 32585--32587 []\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 32588--32592 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 pcre2pattern \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 pcrepattern man \T1/ptm/m/n/10 page (found as part of [][]$\T1/pcr/m/n/10 ht tps : / / www . [470] [471] [472] [473] [474] Overfull \hbox (4.38043pt too wide) in paragraph at lines 32959--32959 []\T1/pcr/m/n/9 rep(1:4, each = 2, times = 3) # length 24, 3 complete replications[] [475] Underfull \hbox (badness 10000) in paragraph at lines 33030--33034 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [476] [477] [478] [479] Underfull \hbox (badness 2302) in paragraph at lines 33256--33261 []\T1/pcr/m/n/10 signif \T1/ptm/m/n/10 rounds the val-ues in its first ar-gu-me nt to the spec-i-fied num-ber of sig-nif-i-cant Underfull \hbox (badness 3769) in paragraph at lines 33256--33261 \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 [480] [481] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33389--33389 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33392--33392 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [482] [483] [484] [485] [486] [487] [488] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33833--33833 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [489] [490] [491] [492] [493] [494] Overfull \hbox (12.78088pt too wide) in paragraph at lines 34270--34270 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [495] Underfull \hbox (badness 1158) in paragraph at lines 34374--34379 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [496] Underfull \hbox (badness 10000) in paragraph at lines 34401--34407 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 34401--34407 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [497] [498] Overfull \hbox (15.18042pt too wide) in paragraph at lines 34559--34559 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [499] [500] [501] Underfull \hbox (badness 8151) in paragraph at lines 34819--34822 []\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 . [502] [503] [504] Underfull \hbox (badness 10000) in paragraph at lines 35034--35039 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 sequence \T1/ptm/m/n/10 gen-er-ates the se-quence [][]\T1/pcr/m/n/10 seq[][][](from[i],by = [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] Overfull \hbox (66.78088pt too wide) in paragraph at lines 36023--36023 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [520] [521] [522] [523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36277--36277 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 36279--36279 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] Underfull \hbox (badness 4954) in paragraph at lines 36322--36328 [][][]\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[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 36322--36328 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [524] [525] Overfull \hbox (20.58041pt too wide) in paragraph at lines 36433--36433 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [526] [527] [528] [529] [530] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36774--36774 []\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 36789--36789 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [531] [532] [533] Underfull \hbox (badness 10000) in paragraph at lines 37014--37016 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [534] [535] [536] Overfull \hbox (12.78088pt too wide) in paragraph at lines 37241--37241 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 37242--37242 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [537] [538] [539] [540] Overfull \hbox (63.78036pt too wide) in paragraph at lines 37509--37509 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [541] Underfull \hbox (badness 6110) in paragraph at lines 37600--37610 []\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-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 37600--37610 \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 37600--37610 \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 37600--37610 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n 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 37600--37610 \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 [542] Underfull \hbox (badness 10000) in paragraph at lines 37646--37652 []\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 37646--37652 \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 37646--37652 \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 37661--37668 []\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 37661--37668 \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 37661--37668 \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 [543] [544] [545] Underfull \hbox (badness 1484) in paragraph at lines 37893--37897 []\T1/ptm/m/n/10 alternative to \T1/pcr/m/n/10 exprs \T1/ptm/m/n/10 or \T1/pcr/ m/n/10 ...\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [546] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37955--37955 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [547] [548] [549] [550] [551] [552] [553] [554] [555] Overfull \hbox (0.78088pt too wide) in paragraph at lines 38535--38535 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [556] [557] [558] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38785--38785 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [559] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38829--38829 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [560] [561] [562] [563] [564] [565] Overfull \hbox (52.98038pt too wide) in paragraph at lines 39263--39263 []\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 39266--39266 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [566] Underfull \hbox (badness 10000) in paragraph at lines 39317--39324 []\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 39317--39324 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [567] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39370--39370 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [568] [569] [570] [571] [572] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39681--39681 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [573] [574] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39846--39846 []\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. [575] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39884--39884 []\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 39914--39920 []\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 39914--39920 \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 39933--39938 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 39933--39938 \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 [576] [577] [578] [579] Underfull \hbox (badness 10000) in paragraph at lines 40221--40225 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \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 [580] Underfull \hbox (badness 1584) in paragraph at lines 40236--40239 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \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 [581] [582] Overfull \hbox (25.98041pt too wide) in paragraph at lines 40374--40374 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [583] Overfull \hbox (19.22812pt too wide) in paragraph at lines 40451--40451 []\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 [584] [585] Underfull \hbox (badness 1082) in paragraph at lines 40595--40598 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [586] [587] [588] Underfull \hbox (badness 1038) in paragraph at lines 40786--40789 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [589] [590] [591] [592] [593] Underfull \hbox (badness 1442) in paragraph at lines 41150--41154 \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 = [594] [595] [596] [597] Underfull \hbox (badness 4096) in paragraph at lines 41400--41403 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [598] Underfull \hbox (badness 7888) in paragraph at lines 41514--41518 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10 length(bin) > [599] [600] [601] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41668--41668 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (35.4281pt too wide) in paragraph at lines 41670--41670 [] \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 41672--41672 [] \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 41685--41687 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [602] Underfull \hbox (badness 10000) in paragraph at lines 41765--41768 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [603] [604] Underfull \hbox (badness 3872) in paragraph at lines 41883--41886 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [605] Underfull \hbox (badness 5475) in paragraph at lines 41949--41953 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [606] [607] [608] [609] [610] [611] Underfull \hbox (badness 10000) in paragraph at lines 42373--42380 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 42429--42438 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 42429--42438 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [612] Underfull \hbox (badness 1082) in paragraph at lines 42439--42451 \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' in that di-rec-tory states the ver-sion. That op-tion is Underfull \hbox (badness 1337) in paragraph at lines 42512--42520 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or [613] Underfull \hbox (badness 10000) in paragraph at lines 42521--42524 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 42575--42578 [][][]$\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 42579--42581 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 42588--42588 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [614] [615] [616] Underfull \hbox (badness 10000) in paragraph at lines 42809--42811 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [617] [618] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42931--42931 []\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 42933--42933 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [619] [620] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43034--43034 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 43036--43036 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [621] [622] [623] Underfull \hbox (badness 6542) in paragraph at lines 43310--43312 []\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 , and [624] [625] Overfull \hbox (30.78088pt too wide) in paragraph at lines 43429--43429 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [626] Underfull \hbox (badness 1708) in paragraph at lines 43497--43505 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 43497--43505 \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 [627] Underfull \hbox (badness 4859) in paragraph at lines 43527--43532 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [628] Underfull \hbox (badness 3895) in paragraph at lines 43589--43601 []\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 43589--43601 \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 , [629] [630] [631] [632] [633] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43912--43912 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [634] [635] [636] [637] [638] [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44381--44381 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [640] Overfull \hbox (25.98041pt too wide) in paragraph at lines 44390--44390 []\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 44456--44462 [][][]\T1/pcr/m/n/10 file[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.access[ ][][]\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 , [641] Underfull \hbox (badness 3861) in paragraph at lines 44465--44470 [][][]\T1/pcr/m/n/10 dir.create[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dir.ex ists[][][]\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 , [642] Overfull \hbox (36.7804pt too wide) in paragraph at lines 44558--44558 []\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[] [643] Underfull \hbox (badness 1803) in paragraph at lines 44611--44614 []\T1/ptm/m/n/10 The atomic modes are \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/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 3471) in paragraph at lines 44615--44622 []\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 [644] [645] [646] Underfull \hbox (badness 3668) in paragraph at lines 44830--44832 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [647] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44936--44936 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [648] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45011--45011 []\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[] [649] Overfull \hbox (90.78033pt too wide) in paragraph at lines 45019--45019 []\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 ...[] [650] Overfull \hbox (25.98041pt too wide) in paragraph at lines 45113--45113 []\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 45117--45117 []\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 45118--45118 [] \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 45125--45125 []\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 45128--45128 []\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[] [651] Underfull \hbox (badness 6220) in paragraph at lines 45167--45172 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 45167--45172 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 10000) in paragraph at lines 45188--45193 []\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 4229) in paragraph at lines 45188--45193 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [652] Underfull \hbox (badness 2818) in paragraph at lines 45284--45290 []\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 a nd \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 [653] Overfull \hbox (15.18042pt too wide) in paragraph at lines 45319--45319 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [654] [655] [656] [657] [658] [659] [660] Underfull \hbox (badness 2846) in paragraph at lines 45778--45782 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas Overfull \hbox (4.38043pt too wide) in paragraph at lines 45818--45818 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] [661] Underfull \hbox (badness 3209) in paragraph at lines 45839--45843 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [662]) (./compiler-pkg.tex Chapter 2. [663] 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 be us ed 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 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [664] [665] [666]) (./datasets-pkg.tex Chapter 3. [667] [668] [669] [670] [671] 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,[] [672] 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)[] Underfull \vbox (badness 1472) has occurred while \output is active [673] [674] [675] [676] 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)[] [677] Overfull \hbox (48.81013pt too wide) in paragraph at lines 704--707 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [678] [679] Overfull \hbox (48.81013pt too wide) in paragraph at lines 837--840 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [680] [681] [682] 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. [683] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1152--1155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [684] [685] [686] [687] [688] 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)")[] [689] [690] 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 frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\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-tained from the a bove [691] [692] [693] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1738--1741 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [694] 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)[] [695] [696] 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]]))))[] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2160--2163 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] [702] [703] Overfull \vbox (4.29591pt too high) has occurred while \output is active [704] [705] [706] [707] [708] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2725--2728 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [709] Overfull \vbox (13.87083pt too high) has occurred while \output is active [710] Underfull \vbox (badness 2376) has occurred while \output is active [711] [712] [713] [714] [715] 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 = ".")[] [716] [717] [718] [719] [720] [721] [722] [723] 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:[] [724] [725] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3759--3762 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [726] Overfull \vbox (10.49593pt too high) has occurred while \output is active [727] Overfull \vbox (15.49593pt too high) has occurred while \output is active [728] 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 / [729] [730] [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742]) (./grDevices-pkg.tex Chapter 4. [743] [744] [745] [746] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to 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/ptm/m/n/1 0 in [747] [748] Underfull \hbox (badness 10000) in paragraph at lines 382--390 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 382--390 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [749] [750] 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",[] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] 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 [761] [762] [763] 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))[] Underfull \hbox (badness 1173) in paragraph at lines 1405--1408 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [764] [765] [766] [767] [768] [769] [770] [771] Underfull \hbox (badness 1565) in paragraph at lines 1893--1898 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1893--1898 \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 [772] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1976--1976 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2017--2027 []\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 2017--2027 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [773] [774] Underfull \hbox (badness 10000) in paragraph at lines 2129--2131 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [775] [776] Underfull \hbox (badness 6758) in paragraph at lines 2308--2311 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [777] [778] Underfull \hbox (badness 2326) in paragraph at lines 2426--2436 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2426--2436 \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 2426--2436 \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 2426--2436 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [779] [780] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2529--2529 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [781] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2645--2645 []\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 2646--2646 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [782] [783] [784] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 2919--2920 Underfull \vbox (badness 10000) has occurred while \output is active [787] [788] [789] [790] [791] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3252--3252 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [792] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3336--3336 []\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 3337--3337 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [793] [794] Underfull \hbox (badness 10000) in paragraph at lines 3493--3498 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3493--3498 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [795] [796] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3567--3567 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [797] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3651--3651 []\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 3671--3671 []\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 3678--3678 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [798] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3734--3734 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [799] Underfull \hbox (badness 8170) in paragraph at lines 3763--3766 []\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 , [800] Underfull \hbox (badness 2189) in paragraph at lines 3824--3829 []\T1/ptm/m/n/10 For ex-am-ple, \T1/pcr/m/n/10 "Dark 3" \T1/ptm/m/n/10 works we ll for shad-ing points or lines in up to five groups, Underfull \hbox (badness 10000) in paragraph at lines 3862--3866 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [801] Underfull \vbox (badness 10000) has occurred while \output is active [802] Underfull \hbox (badness 5260) in paragraph at lines 3992--3995 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [803] [804] [805] [806] [807] Underfull \hbox (badness 5939) in paragraph at lines 4325--4330 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [808] [809] [810] [811] [812] [813] Underfull \hbox (badness 10000) in paragraph at lines 4732--4737 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [814] [815] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4847--4847 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [816] [817] Underfull \hbox (badness 1348) in paragraph at lines 5052--5055 []\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 [818] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5076--5076 []\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 5117--5123 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [819] Underfull \hbox (badness 1112) in paragraph at lines 5150--5154 []\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" [820] Underfull \hbox (badness 1755) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [821] [822] [823] Underfull \hbox (badness 7344) in paragraph at lines 5472--5474 []\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 5483--5487 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [824] [825] Underfull \hbox (badness 1552) in paragraph at lines 5610--5619 \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 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5610--5619 \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/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5620--5622 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5652--5658 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [826] Underfull \hbox (badness 5388) in paragraph at lines 5678--5680 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 https : / / ftp . gnu . org / pub / non-[]gnu / [827] [828] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5779--5779 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [829] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5891--5891 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [830] [831] Underfull \hbox (badness 10000) in paragraph at lines 5977--5979 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [832] [833] [834] [835] [836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6344--6344 []\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 6358--6361 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [837] [838] [839] [840] [841] [842] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6693--6693 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6700--6700 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [843] [844] [845] [846] Underfull \hbox (badness 10000) in paragraph at lines 6963--6968 []\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 6963--6968 \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 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6963--6968 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [847] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7069--7069 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [848] Underfull \hbox (badness 3590) in paragraph at lines 7108--7111 []\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 7108--7111 \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 7119--7119 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [849] Underfull \hbox (badness 1189) in paragraph at lines 7184--7186 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [850] Underfull \hbox (badness 10000) in paragraph at lines 7289--7291 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [851] Underfull \hbox (badness 10000) in paragraph at lines 7335--7342 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7335--7342 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [852] Underfull \hbox (badness 5607) in paragraph at lines 7419--7423 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and [853] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7471--7471 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [854] [855] Underfull \hbox (badness 5637) in paragraph at lines 7603--7609 \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 7636--7639 []\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 / [856] [857] [858] Underfull \hbox (badness 1231) in paragraph at lines 7805--7807 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [859] [860]) (./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 = [861] [862] [863] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [864] [865] [866] [867] 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 [868] [869] 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[] [870] 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 \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [871] [872] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \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 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [873] [874] [875] Underfull \hbox (badness 10000) in paragraph at lines 964--968 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/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-able. Overfull \hbox (133.98029pt too wide) in paragraph at lines 981--981 [] \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 983--983 []\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 985--985 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [876] [877] [878] [879] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1269--1269 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [880] [881] [882] Underfull \hbox (badness 2503) in paragraph at lines 1431--1440 \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 1466--1468 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [883] [884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1540--1540 []\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 1541--1541 []\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 1547--1547 []\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 1548--1548 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [885] [886] [887] [888] [889] Underfull \hbox (badness 10000) in paragraph at lines 1851--1857 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.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 1871--1871 []\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 1883--1883 []\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 1899--1899 []\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 1908--1908 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [890] [891] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1993--1993 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [892] [893] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2122--2122 []\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 2127--2127 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [894] [895] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2301--2301 []\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 2302--2302 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [896] Underfull \hbox (badness 1430) in paragraph at lines 2333--2335 []\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 [897] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2414--2414 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2426--2433 \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 [898] Underfull \hbox (badness 7273) in paragraph at lines 2508--2512 [][][]\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[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and [899] [900] [901] [902] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2756--2756 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [903] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2793--2793 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [904] [905] Underfull \hbox (badness 1226) in paragraph at lines 2918--2922 \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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 2971--2971 []\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 :[] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2975--2975 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] Underfull \hbox (badness 10000) in paragraph at lines 3027--3030 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [907] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3232--3232 []\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 3237--3237 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3379--3384 [][]\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 3379--3384 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [912] [913] [914] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3565--3565 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3584--3584 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [915] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3588--3588 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [916] [917] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3765--3765 [] \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 3766--3766 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [918] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3805--3805 [] \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 [919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3857--3857 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3865--3865 []\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 3867--3867 []\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 3875--3875 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [920] Underfull \hbox (badness 10000) in paragraph at lines 3938--3942 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [921] [922] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4050--4050 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [923] [924] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4204--4204 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [925] Underfull \hbox (badness 3930) in paragraph at lines 4283--4285 []\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 [926] [927] [928] [929] [930] Underfull \hbox (badness 1286) in paragraph at lines 4594--4597 \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 4602--4607 []\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 [931] [932] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4699--4699 []\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 4704--4704 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [933] Underfull \hbox (badness 1264) in paragraph at lines 4895--4908 \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/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [934] [935] Underfull \hbox (badness 10000) in paragraph at lines 5032--5038 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [936] [937] Underfull \hbox (badness 10000) in paragraph at lines 5163--5166 [938 ] Underfull \hbox (badness 10000) in paragraph at lines 5224--5226 [939 ] [940] Underfull \hbox (badness 10000) in paragraph at lines 5414--5416 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [941] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5470--5470 []\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 5471--5471 [] \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 [942] [943] [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5836--5836 []\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 5837--5837 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [948]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5896 \aliasA{plot}{plot.default}{plot} [949] [950] [951] [952] [953] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6234--6234 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [954] [955] [956] [957] [958] [959] Underfull \hbox (badness 10000) in paragraph at lines 6664--6666 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [960] [961] Underfull \hbox (badness 1028) in paragraph at lines 6758--6760 []\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 6801--6802 [][] [962 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6895--6895 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [963] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6926--6926 [] \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 [964] [965] Underfull \hbox (badness 10000) in paragraph at lines 7048--7050 []\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 7075--7075 [] \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 7081--7081 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [966] Underfull \hbox (badness 2600) in paragraph at lines 7138--7140 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7370--7370 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [971] [972] [973] [974] [975] [976] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7757--7757 []\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 7761--7761 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [977] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7773--7773 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [978] [979] [980] [981] [982] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8122--8122 []\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 8125--8125 []\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 8129--8129 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [983] [984] [985] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\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 8301--8301 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [986] [987] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8405--8405 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8416--8421 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [988] Underfull \hbox (badness 1112) in paragraph at lines 8464--8468 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [989] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8524--8524 []\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 8539--8539 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [990] [991] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8676--8676 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [992] [993] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8861--8861 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [994] Underfull \hbox (badness 10000) in paragraph at lines 8889--8891 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8891--8893 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8923--8929 []\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 are \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 [995]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8971 \HeaderA{units}{Graphical Units}{units} [996] Underfull \hbox (badness 1205) in paragraph at lines 9036--9038 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [997] [998] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9155--9155 []\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)[] [999]) (./grid-pkg.tex [1000] Chapter 6. [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] Underfull \hbox (badness 10000) in paragraph at lines 479--485 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 479--485 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [1009] Underfull \hbox (badness 4859) in paragraph at lines 565--568 []\T1/ptm/m/n/10 Modification of the view-port (should all be valid ar-gu-ments to the [1010] [1011] [1012] [1013] [1014] [1015] Overfull \hbox (31.3804pt too wide) in paragraph at lines 959--959 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] [1016] [1017] [1018] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1164--1164 [] \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 1165--1165 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1166--1166 [] \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 1167--1167 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1168--1168 [] \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 1169--1169 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] [1019] Underfull \hbox (badness 1430) in paragraph at lines 1214--1219 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1020] [1021] [1022] Underfull \hbox (badness 3219) in paragraph at lines 1428--1431 []\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 [1023] [1024] [1025] [1026] [1027] [1028] [1029] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1816--1816 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1030] [1031] [1032] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2030--2030 []\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 2031--2031 []\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 2032--2032 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1033] Underfull \hbox (badness 2961) in paragraph at lines 2067--2072 []\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 , [1034] Underfull \hbox (badness 1430) in paragraph at lines 2126--2131 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2155--2158 []\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 [1035] [1036] [1037] Underfull \hbox (badness 2894) in paragraph at lines 2362--2369 []\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 [1038] [1039] [1040] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2518--2518 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2530--2535 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1041] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2589--2589 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1042] [1043] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2741--2741 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1044] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2773--2773 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1045] [1046] [1047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3015--3015 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1048] [1049] [1050] [1051] [1052] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3330--3330 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1053] [1054] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3426--3426 []\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 3460--3466 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1055] [1056] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3552--3552 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3559--3559 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1057] [1058] [1059] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3760--3760 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3775--3775 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1060] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3796--3796 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] Underfull \hbox (badness 1067) in paragraph at lines 4537--4540 []\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 [1073] Underfull \hbox (badness 1430) in paragraph at lines 4583--4588 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1074] [1075] [1076] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4753--4753 [] \T1/pcr/m/n/9 width=unit(1, "inches"), height=un it(1, "inches")))[] Underfull \hbox (badness 7256) in paragraph at lines 4782--4784 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] Underfull \hbox (badness 10000) in paragraph at lines 5419--5421 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 6859) in paragraph at lines 6206--6212 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6206--6212 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1099] [1100] [1101] [1102] [1103] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6484--6484 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1104] Underfull \hbox (badness 1867) in paragraph at lines 6584--6586 []\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 [1105] Underfull \hbox (badness 10000) in paragraph at lines 6621--6627 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1106] [1107] Underfull \hbox (badness 1371) in paragraph at lines 6753--6756 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1108] Underfull \vbox (badness 10000) has occurred while \output is active [1109] [1110] [1111] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6957--6957 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1112]) (./methods-pkg.tex Chapter 7. [1113] [1114] 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 c o-erce meth-ods work. Use [1115] [1116] [1117] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1118] [1119] 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[] [1120] 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 [1121] 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 [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131] [1132] [1133] [1134] [1135] [1136] 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[] [1137] [1138] 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 c an be an ob-ject of class [1139] [1140] [1141] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\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 = [1142] [1143] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\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 [1144] [1145] [1146] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\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 [1147] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1148] [1149] [1150] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1151] [1152] [1153] [1154] [1155] [1156] [1157] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1158] [1159] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1160] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1163] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\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 [1164] [1165] [1166] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1167] [1168] [1169] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1171] [1172] [1173] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\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 , [1174] [1175] [1176] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\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 [1177] [1178] [1179] [1180] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1181] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\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 5237--5237 []\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 [1182] [1183] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1184] [1185] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1186] [1187] [1188] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\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 [1189] [1190] [1191] [1192] [1193] [1194] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1195] [1196] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \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 [1197] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1198] [1199] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\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 6647--6656 [][]\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 [1200] Underfull \vbox (badness 10000) has occurred while \output is active [1201] [1202] [1203]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1204] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] [1205] [1206] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\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 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1207]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\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 [1208] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/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 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/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 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1209] [1210] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\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 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1211] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7517--7517 []\T1/pcr/m/n/9 selectSuperClasses("C", dropVirtual=TRUE, directOnly=FALSE)# d itto w/o "Root"[] [1212] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1224] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1225] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1230] [1231] [1232] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1233] [1234] [1235] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1236] [1237] [1238] [1239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1240] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\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 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249] [1250] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\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 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1251] [1252] [1253]) (./parallel-pkg.tex [1254] 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/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1255] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1256] [1257] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\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 [1258] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1259] [1260] Underfull \hbox (badness 10000) in paragraph at lines 444--446 []\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 [1261] [1262] [1263] [1264] [1265] Underfull \hbox (badness 1917) in paragraph at lines 778--787 []\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 778--787 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1266] [1267] Overfull \hbox (60.78088pt too wide) in paragraph at lines 871--871 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1268] [1269] [1270] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1062--1062 []\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 1066--1066 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1271] Underfull \hbox (badness 5388) in paragraph at lines 1181--1186 []\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 [1272] Underfull \hbox (badness 10000) in paragraph at lines 1205--1213 []\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 1242--1242 []\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)[] [1273] [1274] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1358--1358 [] \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 1372--1372 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1275] Underfull \hbox (badness 1577) in paragraph at lines 1401--1404 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1448--1450 []\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 [1276] [1277]) (./splines-pkg.tex [1278] 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 [1279] [1280] [1281] [1282] [1283] [1284] [1285] [1286] 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))[] [1287] Underfull \hbox (badness 1424) 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(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1288] [1289] 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)))[] [1290] [1291] [1292]) (./stats-pkg.tex Chapter 10. [1293] 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 o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/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[] [1294] [1295] [1296] [1297] [1298] 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[] [1299] 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) [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 1024) in paragraph at lines 888--890 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1550--1554 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1316] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1626--1626 [] \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 1629--1629 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1317] [1318] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1776--1776 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1319] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1788--1788 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[ ] [1320] [1321] [1322] [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2806--2806 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1334] [1335] [1336] [1337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3046--3046 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1338] [1339] [1340] Underfull \hbox (badness 10000) in paragraph at lines 3257--3259 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3306--3306 []\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 3307--3307 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1342] [1343] [1344] [1345] [1346] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1347] [1348] [1349] [1350] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3980--3980 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1351] [1352] [1353] [1354] [1355] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4269--4269 []\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 4270--4270 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1356] [1357] [1358] [1359] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4510--4510 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1360] [1361] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4685--4685 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1362] [1363] Underfull \hbox (badness 3989) in paragraph at lines 4779--4786 []\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 = [1364] [1365] [1366] [1367] [1368] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5164--5164 []\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 5166--5166 []\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))[] [1369] [1370] [1371] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5387--5387 []\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 5405--5405 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1372] Underfull \hbox (badness 2680) in paragraph at lines 5432--5434 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1373] [1374] [1375] Underfull \hbox (badness 1436) in paragraph at lines 5615--5620 []\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 5615--5620 \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 5615--5620 \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 , [1376] [1377] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5818--5818 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1378] [1379] [1380] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5985--5985 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1381] [1382] [1383] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6170--6170 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1384] [1385] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6278--6278 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1386] Underfull \hbox (badness 10000) in paragraph at lines 6345--6350 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1387] [1388] [1389] Underfull \hbox (badness 5954) in paragraph at lines 6541--6543 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1390] Underfull \hbox (badness 2503) in paragraph at lines 6623--6626 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can 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 6627--6629 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \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 6630--6635 \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, [1391] Underfull \hbox (badness 7238) in paragraph at lines 6666--6669 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and Overfull \hbox (4.38043pt too wide) in paragraph at lines 6678--6678 []\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 6701--6701 []\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 6716--6716 []\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):[] [1392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6731--6731 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1393] [1394] [1395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6976--6976 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1396] [1397] [1398] Underfull \vbox (badness 10000) has occurred while \output is active [1399] [1400] [1401] [1402] Underfull \hbox (badness 10000) in paragraph at lines 7375--7379 \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 "binary" \T1/ptm/ m/n/10 or [1403] Underfull \hbox (badness 6493) in paragraph at lines 7474--7477 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1404] [1405] Underfull \hbox (badness 10000) in paragraph at lines 7611--7614 []\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 = [1406] [1407] [1408] [1409] [1410] [1411] Underfull \hbox (badness 10000) in paragraph at lines 8023--8028 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1412] [1413] [1414] [1415] [1416] [1417] Underfull \hbox (badness 1210) in paragraph at lines 8378--8380 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1418] [1419] [1420] [1421] [1422] [1423] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8841--8841 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1424] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8886--8886 []\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 8889--8889 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1425] [1426] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9027--9027 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1427] [1428] [1429] [1430] [1431] [1432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9454--9454 [] \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 9455--9455 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1433] [1434] [1435] Underfull \hbox (badness 7291) in paragraph at lines 9634--9636 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1436] [1437] [1438] [1439] [1440] [1441] [1442] Underfull \hbox (badness 6944) in paragraph at lines 10122--10128 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1443] [1444] [1445] Underfull \hbox (badness 3758) in paragraph at lines 10336--10339 []\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 [1446] [1447] [1448] [1449] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10580--10580 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10606--10611 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1450] Underfull \hbox (badness 4132) in paragraph at lines 10645--10649 []\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 10699--10705 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1451] Underfull \hbox (badness 10000) in paragraph at lines 10750--10753 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\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 [1452] [1453] [1454] Underfull \hbox (badness 2142) in paragraph at lines 10967--10970 []\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 ^^@ [1455] Underfull \hbox (badness 1708) in paragraph at lines 11048--11052 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1456] Underfull \hbox (badness 10000) in paragraph at lines 11090--11096 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 11128--11133 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1457] [1458] Underfull \hbox (badness 2635) in paragraph at lines 11261--11264 \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/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1459] [1460] [1461] Underfull \hbox (badness 1694) in paragraph at lines 11444--11447 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1462] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11545--11545 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1463] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11578--11578 [] \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 11591--11595 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1464] [1465] [1466] [1467] [1468] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11913--11913 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1469]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11928 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11988--11988 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1470] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12000--12000 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12053--12058 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 12070--12072 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1471] [1472] [1473] [1474] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12324--12324 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12325--12325 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1475] [1476] [1477] [1478] [1479] [1480] Underfull \hbox (badness 10000) in paragraph at lines 12669--12671 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12692--12694 []\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 [1481] [1482] [1483] [1484] [1485] Underfull \hbox (badness 6910) in paragraph at lines 12999--13001 []\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 13005--13009 []\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 13005--13009 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1486] [1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13611--13611 []\T1/pcr/m/n/9 lag.plot(sqrt(sunspots), set.lags = c(1:4, 9:12), pch = ".", c ol = "gold")[] [1495] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13712--13712 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1496] Underfull \hbox (badness 4518) in paragraph at lines 13760--13765 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1497] Underfull \hbox (badness 1275) in paragraph at lines 13869--13871 []\T1/pcr/m/n/10 lm \T1/ptm/m/n/10 re-turns an ob-ject of [][]\T1/pcr/m/n/10 cl ass[][][] "lm" \T1/ptm/m/n/10 or for mul-ti-vari-ate (`mul-ti-ple') re-sponses of class [1498] [1499] Underfull \hbox (badness 10000) in paragraph at lines 13967--13971 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1500] [1501] [1502] [1503] [1504] Underfull \hbox (badness 1163) in paragraph at lines 14301--14309 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1505] [1506] Underfull \hbox (badness 4518) in paragraph at lines 14421--14426 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1507] [1508] [1509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14609--14609 []\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 14610--14610 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1510] [1511] [1512] [1513] [1514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14953--14953 []\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 14954--14954 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1515] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15047--15047 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1516] [1517] [1518] [1519] [1520] [1521] [1522] Underfull \hbox (badness 2726) in paragraph at lines 15456--15459 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/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 , [1523] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15550--15550 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1524] [1525] [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16178--16178 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1534] [1535] Underfull \hbox (badness 1490) in paragraph at lines 16325--16330 \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 [1536] Underfull \hbox (badness 1648) in paragraph at lines 16391--16393 []\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 2591) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16406--16415 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1537] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16476--16476 []\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 16477--16477 []\T1/pcr/m/n/9 m.orth <- model.matrix(~a+b, dd, contrasts.arg = list(a = "con tr.helmert"))[] [1538] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17034--17034 []\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[] [1547] [1548] [1549] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17266--17266 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1550] [1551] [1552] [1553] [1554] [1555] [1556] [1557] [1558] [1559] Underfull \vbox (badness 10000) has occurred while \output is active [1560] Overfull \hbox (42.18039pt too wide) in paragraph at lines 17988--17988 []\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 [1561] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18006--18006 []\T1/pcr/m/n/9 ## Here, requiring close convergence, you need to use more acc urate numerical[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18007--18007 []\T1/pcr/m/n/9 ## differentiation; the first fit gives Error: "step factor .. reduced below \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 minFactor\TS1/pcr/m/n/9 ' \T1/pcr/ m/n/9 .."[] Overfull \hbox (101.58032pt too wide) in paragraph at lines 18010--18010 []\T1/pcr/m/n/9 try(nlm1 <- update(nlmod, control = list(tol = 1e-7))) # where central diff. typically work:[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 18011--18011 [] \T1/pcr/m/n/9 (nlm2 <- update(nlmod, control = list(tol = 8e-8, nDcentral =TRUE, warnOnly=TRUE),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18013--18013 []\T1/pcr/m/n/9 ## 2nd fit still fails on some (less accurate) platforms => us ing warnOnly[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18043--18043 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1562] [1563] [1564] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18219--18219 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] [1565] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18266--18266 []\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 18313--18313 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1566] [1567] [1568] [1569] Overfull \hbox (102.78088pt too wide) in paragraph at lines 18519--18519 [] \T1/pcr/m/n/10 eps = .Machine$double.eps ^ (1/if(central) 3 els e 2), central = FALSE)[] [1570] [1571] [1572] [1573] [1574] Underfull \hbox (badness 1248) in paragraph at lines 18834--18837 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18847--18851 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 1478) in paragraph at lines 18855--18859 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$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 [1575] Underfull \hbox (badness 2042) in paragraph at lines 18913--18915 []\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 [1576] Overfull \hbox (15.18042pt too wide) in paragraph at lines 19019--19019 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] [1577] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19062--19062 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 19080--19080 []\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 19083--19083 []\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 19103--19103 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), [1578] Overfull \hbox (36.78088pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] Underfull \hbox (badness 2564) in paragraph at lines 19141--19152 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 19141--19152 \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 [1579] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19204--19204 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1580] [1581] [1582] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19431--19431 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1583] [1584] Underfull \hbox (badness 1337) in paragraph at lines 19542--19545 []\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 [1585] [1586] [1587] [1588] [1589] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19861--19861 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1590] [1591] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19949--19949 [] \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 19951--19951 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19953--19953 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1592] Underfull \hbox (badness 10000) in paragraph at lines 19999--20005 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 3049) in paragraph at lines 20040--20044 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1593] [1594] [1595] [1596] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20293--20293 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20303--20306 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1597] Underfull \hbox (badness 1107) in paragraph at lines 20361--20363 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to [1598] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20416--20416 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1599] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20423--20423 []\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)[] [1600] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20517--20517 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1601] [1602] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20646--20646 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1603] Underfull \hbox (badness 7740) in paragraph at lines 20709--20711 []\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 [1604] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20757--20757 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1605] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20849--20849 [] \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 20854--20854 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1606] [1607] [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] Overfull \hbox (58.38037pt too wide) in paragraph at lines 21709--21709 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tolerance = 1e-15)) # e xactly equal typically[] [1619] Underfull \hbox (badness 6859) in paragraph at lines 21776--21783 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21787--21793 []\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/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1620] [1621] [1622] [1623] [1624] [1625] [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22533--22533 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1632] [1633] [1634] [1635] [1636] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22817--22817 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22818--22818 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1637] [1638] [1639] [1640] [1641] Underfull \hbox (badness 1337) in paragraph at lines 23144--23150 []\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 [1642] [1643] [1644] [1645] [1646] [1647] [1648] Underfull \hbox (badness 2913) in paragraph at lines 23569--23572 []\T1/ptm/m/n/10 used only when \T1/pcr/m/n/10 names \T1/ptm/m/n/10 is true: th e pre-ci-sion to use when for-mat- Underfull \hbox (badness 1152) in paragraph at lines 23569--23572 \T1/ptm/m/n/10 ting the per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-s ions up to 4.0.x, this had been set to [1649] Underfull \hbox (badness 10000) in paragraph at lines 23703--23705 []\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 23703--23705 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23710--23711 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1650] [1651] Overfull \hbox (48.78088pt too wide) in paragraph at lines 23821--23821 [] \T1/pcr/m/n/10 method = c("non.compact", "row.compact", "col.compact" , "compact"),[] [1652] Underfull \hbox (badness 1028) in paragraph at lines 23879--23882 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1653] [1654] Underfull \hbox (badness 10000) in paragraph at lines 23994--23997 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 7944) in paragraph at lines 24049--24051 []\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,levels = [1655] Underfull \hbox (badness 7944) in paragraph at lines 24111--24113 []\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,levels = [1656] [1657] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24213--24213 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1658] [1659] Overfull \hbox (0.78088pt too wide) in paragraph at lines 24330--24330 []\T1/pcr/m/n/10 # varying = ___, # list / matrix / vector (use with care)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 24331--24331 []\T1/pcr/m/n/10 # v.names = ___, # vector of variable names in long format[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 24332--24332 []\T1/pcr/m/n/10 # timevar, times, # name / values of constructed time variable[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 24333--24333 []\T1/pcr/m/n/10 # idvar, ids) # name / values of constructed id v ariable[] [1660] [1661] Underfull \hbox (badness 10000) in paragraph at lines 24493--24498 [][][]\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 re-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 24493--24498 [][]\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 24504--24504 []\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 24505--24505 []\T1/pcr/m/n/9 reshape(Indometh, direction = "wide", idvar = "Subject", timev ar = "time")[] [1662] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24524--24524 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1663] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24628--24628 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] [1664] Underfull \hbox (badness 1033) in paragraph at lines 24671--24677 \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 24692--24695 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1665] Underfull \hbox (badness 2134) in paragraph at lines 24761--24765 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24774--24774 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1666] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24803--24803 []\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 24815--24815 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1667] [1668] [1669] [1670] [1671] [1672] [1673] Underfull \hbox (badness 6268) in paragraph at lines 25273--25278 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/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 , [1674] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25301--25301 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1675] [1676] [1677] Underfull \hbox (badness 1867) in paragraph at lines 25478--25480 []\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 25493--25497 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = use.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 25493--25497 \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 25529--25529 []\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 25536--25536 []\T1/pcr/m/n/9 stopifnot(all.equal(sigma(fm.DN1), summary(fm.DN1)$sigma, tole rance=1e-15))[] [1678] [1679] [1680] Underfull \hbox (badness 2495) in paragraph at lines 25719--25728 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1681] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25801--25801 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1682] Underfull \hbox (badness 1412) in paragraph at lines 25808--25810 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1683] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25895--25895 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25920--25920 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25923--25923 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1684] [1685] [1686] Overfull \hbox (6.78088pt too wide) in paragraph at lines 26147--26147 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 26151--26157 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26197--26197 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26218--26218 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1688] Underfull \hbox (badness 1019) in paragraph at lines 26280--26285 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1689] [1690] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26410--26410 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1691] [1692] [1693] [1694] [1695] [1696] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1697] [1698] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26971--26971 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1699] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26977--26977 []\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 26986--26986 []\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 26987--26987 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1700] Underfull \hbox (badness 2922) in paragraph at lines 27056--27061 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (9.78043pt too wide) in paragraph at lines 27093--27093 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1701] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27096--27096 [] \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 27105--27105 [] \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 27106--27106 [] \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 27110--27110 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1702] Underfull \hbox (badness 3240) in paragraph at lines 27164--27167 [][][]\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 grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 27185--27185 [] \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 27188--27188 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1703] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27271--27271 [] \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 27275--27275 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1704] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27285--27285 [] \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 27290--27290 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 2922) in paragraph at lines 27326--27332 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1705] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27364--27364 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27380--27380 [] \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 27383--27383 []\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 27385--27385 [] \T1/pcr/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol=1 e-11, nDcentral=TRUE), trace=TRUE)[] [1706] [1707] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27497--27497 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1708] Underfull \hbox (badness 2922) in paragraph at lines 27559--27564 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1709] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27597--27597 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] Underfull \hbox (badness 2922) in paragraph at lines 27646--27651 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1710] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27677--27677 []\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 27711--27716 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1711] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27736--27736 []\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 27740--27740 []\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 27760--27760 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1712] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27770--27770 [] \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[] Underfull \hbox (badness 2922) in paragraph at lines 27805--27810 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27827--27827 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1713] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27845--27845 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1714] Underfull \hbox (badness 6493) in paragraph at lines 27897--27902 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27925--27925 []\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 27928--27928 []\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 27931--27931 []\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 27934--27934 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1715] [1716] [1717] [1718] [1719] [1720] [1721] [1722] [1723] [1724] [1725] [1726] [1727] [1728] Underfull \hbox (badness 3396) in paragraph at lines 28817--28819 []\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 [1729] [1730] Underfull \hbox (badness 2237) in paragraph at lines 28994--28996 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1731] [1732] [1733] Underfull \hbox (badness 2591) in paragraph at lines 29158--29160 []\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 [1734] Underfull \hbox (badness 2237) in paragraph at lines 29204--29207 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1735] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29277--29277 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1736] Underfull \hbox (badness 3407) in paragraph at lines 29386--29390 []\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) [1737] [1738] Overfull \hbox (47.58038pt too wide) in paragraph at lines 29456--29456 []\T1/pcr/m/n/9 symnum(ii, cutpoints = 2*(0:4), symbols = c(".", "-", "+", "$ "), show.max = TRUE)[] [1739] Underfull \hbox (badness 1337) in paragraph at lines 29519--29523 []\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 [1740] [1741] [1742] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29777--29777 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] [1743] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29805--29805 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] Underfull \hbox (badness 1616) in paragraph at lines 29831--29834 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1744] [1745] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29910--29910 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29988--29988 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1747] Underfull \hbox (badness 2205) in paragraph at lines 30077--30082 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] [1756] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30676--30676 []\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 30677--30677 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1757] [1758] [1759] [1760] [1761] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30977--30977 [] \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 30978--30978 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1762] [1763] Overfull \hbox (31.3804pt too wide) in paragraph at lines 31104--31104 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 31113--31113 []\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 [1764] [1765] [1766] Underfull \hbox (badness 1337) in paragraph at lines 31330--31334 []\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 [1767] [1768] [1769] [1770] [1771] [1772] [1773] [1774] [1775] Underfull \hbox (badness 1337) in paragraph at lines 31859--31863 []\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 Underfull \hbox (badness 5878) in paragraph at lines 31873--31875 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 conf.int \T1/ptm/m/n/10 is true:) a pos-i -tive nu-meric tol-er-ance, used in [1776] [1777] [1778] Overfull \hbox (117.7803pt too wide) in paragraph at lines 32066--32066 []\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 32068--32068 []\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)[] [1779] [1780] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32227--32227 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1781] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32312--32312 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1782] Underfull \hbox (badness 6775) in paragraph at lines 32369--32374 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1783] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32445--32445 []\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 "")[] [1784] [1785]) (./stats4-pkg.tex [1786] Chapter 11. [1787] [1788] [1789] 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 [1790] 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[] [1791] [1792] [1793] [1794]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1795] [1796] [1797]) (./tcltk-pkg.tex [1798] Chapter 12. [1799] [1800] [1801] [1802] 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[] [1803] [1804] [1805] Underfull \vbox (badness 10000) has occurred while \output is active [1806] 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-ing any Tk or Tcl com-mand by sim-ply run-ning [1807] [1808] [1809] [1810] [1811] [1812] 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"))))[] [1813] [1814] [1815] [1816] [1817] 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-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1818]) (./tools-pkg.tex Chapter 13. [1819] 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.[] [1820] Underfull \hbox (badness 10000) in paragraph at lines 141--143 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via 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 b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1821] 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)[] [1822] 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/1 0 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/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1823] 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-gine to use. Over-rides any [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1831] [1832] 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")[] [1833] [1834] [1835] 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, ...)[] [1836] 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/p tm/m/n/10 and [1837] 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-he r-it-ing from class [1838] [1839] 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/p tm/m/n/10 re-turn ob-jects of class \T1/pcr/m/n/10 "codocClasses" \T1/ptm/m/n/1 0 and [1840] [1841] [1842] [1843] [1844] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1700--1700 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1707--1715 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1707--1715 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 1707--1715 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1845] [1846] [1847]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1919 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ig nored \relax l.1920 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1848] [1849] [1850] [1851] Underfull \hbox (badness 1142) in paragraph at lines 2188--2194 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2222--2222 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1852] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2223--2223 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2250--2257 []\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 2250--2257 \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 2250--2257 \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 [1853] Underfull \hbox (badness 1342) in paragraph at lines 2302--2308 \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 [1854] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 package_dependencies(packages = NULL, db = NULL, which = "str ong", Underfull \hbox (badness 7981) in paragraph at lines 2391--2399 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2391--2399 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Underfull \hbox (badness 1178) in paragraph at lines 2391--2399 \T1/ptm/m/n/10 for the same vec-tor with-out \T1/pcr/m/n/10 "Enhances"\T1/ptm/m /n/10 , char-ac-ter string \T1/pcr/m/n/10 "strong" [1855] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2427--2427 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2460--2460 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1856] [1857] [1858] [1859] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2744--2744 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1860] Underfull \hbox (badness 2486) in paragraph at lines 2789--2797 []\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 [1861] [1862] [1863] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3001--3001 []\T1/pcr/m/n/10 checkDocFiles (package, dir, lib.loc = NULL, chkInternal = FALSE) Overfull \hbox (6.78088pt too wide) in paragraph at lines 3005--3005 []\T1/pcr/m/n/10 checkRdContents (package, dir, lib.loc = NULL, chkInternal = FALSE)[] [1864] [1865] [1866] Underfull \hbox (badness 1072) in paragraph at lines 3177--3179 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1867] [1868] [1869] [1870] [1871] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1872] [1873] [1874] [1875] Underfull \hbox (badness 4108) in paragraph at lines 3758--3765 []\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 [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3858--3858 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] [1877] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3861--3861 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3878--3880 []\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 3895--3901 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1878] [1879] Underfull \hbox (badness 7832) in paragraph at lines 4017--4020 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1880] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4093--4093 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] Underfull \hbox (badness 1137) in paragraph at lines 4119--4121 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1881] [1882] [1883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4304--4304 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1884] [1885] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) [1886] Underfull \hbox (badness 10000) in paragraph at lines 4477--4480 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4493--4498 []\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/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4501--4507 []\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 4501--4507 \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 [1887] [1888] [1889] [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4758--4758 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4759--4759 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz",[] Underfull \hbox (badness 3240) in paragraph at lines 4772--4775 []\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 4776--4786 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4814--4820 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4814--4820 \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 ', [1891] Underfull \hbox (badness 1571) in paragraph at lines 4842--4846 []\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 4868--4873 \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 [1892] [1893] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5008--5008 []\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 '[] [1894]) (./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 `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1895] [1896] [1897] [1898] 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[] [1899] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1900] 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 [1901] 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"))),[] [1902] [1903] [1904] Overfull \hbox (0.78088pt too wide) in paragraph at lines 677--677 []\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 683--683 []\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 684--684 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 685--685 []\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 686--686 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 720--726 []\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 720--726 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1905] [1906] Underfull \hbox (badness 4505) in paragraph at lines 857--863 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1907] [1908] [1909] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1043--1043 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1910] Underfull \hbox (badness 1748) in paragraph at lines 1108--1116 []\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 1108--1116 \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 1661) in paragraph at lines 1108--1116 \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 1108--1116 \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 1120--1122 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1911] Underfull \hbox (badness 10000) in paragraph at lines 1228--1231 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1912] [1913] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1311--1311 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1914] [1915] [1916] [1917] [1918] [1919] [1920] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1813--1813 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1921] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1848--1848 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1922] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1994--1994 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1923] Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 []\T1/pcr/m/n/10 charClass \T1/ptm/m/n/10 was added in \T1/phv/m/n/10 R \T1/ptm /m/n/10 4.1.0. A less di-rect way to ex-am-ine char- Underfull \hbox (badness 10000) in paragraph at lines 2063--2068 \T1/ptm/m/n/10 ac-ter classes which also worked in ear-lier ver-sions is to use some-thing like [1924] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2096--2096 []\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 2098--2098 []\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 2106--2106 []\T1/pcr/m/n/9 ## How many printable characters are there? (Around 280,000 in Unicode 13.)[] [1925] [1926] [1927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2254--2254 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1928] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2306--2306 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1929] [1930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2475--2475 [] \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")[] [1931] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2498--2498 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2618--2618 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1933] Underfull \hbox (badness 1082) in paragraph at lines 2692--2696 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2697 ... the Clipboard in MS Windows}{clipboard} [1934] Underfull \hbox (badness 1163) in paragraph at lines 2728--2730 []\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 . [1935] Underfull \hbox (badness 10000) in paragraph at lines 2816--2818 []\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 [1936] [1937] [1938] [1939] Underfull \hbox (badness 10000) in paragraph at lines 3034--3036 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1940] [1941] [1942] [1943] Underfull \hbox (badness 1762) in paragraph at lines 3327--3330 []\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 = [1944] Overfull \hbox (63.78036pt too wide) in paragraph at lines 3419--3419 []\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 3420--3420 []\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 '[] [1945] Underfull \hbox (badness 2452) in paragraph at lines 3496--3499 []\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 [1946] [1947] [1948] [1949] [1950] [1951] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3905--3905 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1952] [1953] Underfull \hbox (badness 10000) in paragraph at lines 3993--3996 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 4062--4070 []\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 [1954] Underfull \hbox (badness 1231) in paragraph at lines 4139--4151 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 4152--4157 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 4152--4157 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1955] [1956] Underfull \hbox (badness 4660) in paragraph at lines 4272--4275 \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 Underfull \hbox (badness 10000) in paragraph at lines 4296--4298 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1957] [1958] [1959] Underfull \hbox (badness 1565) in paragraph at lines 4481--4485 []\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 [1960] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4564--4564 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1961] Underfull \hbox (badness 1931) in paragraph at lines 4599--4606 []\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) [1962] [1963] [1964] [1965] [1966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4923--4923 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1967]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4994 ...mat Unordered and Ordered Lists}{format} [1968] [1969] [1970] [1971] [1972] [1973] [1974] [1975] Underfull \hbox (badness 1622) in paragraph at lines 5513--5517 []\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 [1976] [1977] [1978] [1979] [1980] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5835--5835 []\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 5847--5847 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1981] [1982] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5980--5980 [] \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 5981--5981 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1983] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6191--6191 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1986] Underfull \hbox (badness 10000) in paragraph at lines 6275--6277 []\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 [1987] Underfull \hbox (badness 1502) in paragraph at lines 6324--6329 []\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 6324--6329 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 6497--6506 []\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 6497--6506 \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 [1990] Underfull \hbox (badness 2150) in paragraph at lines 6561--6564 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6577--6580 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1991] [1992] Underfull \hbox (badness 3118) in paragraph at lines 6700--6702 []\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 [1993] [1994] Underfull \hbox (badness 5091) in paragraph at lines 6875--6877 []\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 [1995] Underfull \hbox (badness 5331) in paragraph at lines 6891--6897 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6891--6897 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6891--6897 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6905--6912 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") Underfull \hbox (badness 1270) in paragraph at lines 6920--6930 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If [1996] Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6963--6966 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., Underfull \hbox (badness 1424) in paragraph at lines 6971--6974 []\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 [1997] Underfull \hbox (badness 2376) in paragraph at lines 7042--7049 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7042--7049 \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 7042--7049 \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 7050--7053 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1998] Underfull \hbox (badness 1314) in paragraph at lines 7129--7136 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 7176--7179 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing \T1/pcr/m/n/10 available.pac kages(filters = Underfull \hbox (badness 1314) in paragraph at lines 7176--7179 \T1/pcr/m/n/10 "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 ,] \T1/ptm/m/n/ 10 will show if the pack-age is avail-able for any \T1/phv/m/n/10 R \T1/ptm/m/n /10 ver-sion (for Underfull \hbox (badness 10000) in paragraph at lines 7209--7214 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , [1999] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7232--7232 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7268--7272 []\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 7282--7285 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along [2000] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7329--7329 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [2001] [2002] Underfull \hbox (badness 4132) in paragraph at lines 7453--7455 []\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 [2003] [2004] [2005] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7620--7620 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [2006] [2007] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7763--7763 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [2008] Underfull \hbox (badness 10000) in paragraph at lines 7803--7805 []\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 [2009] [2010] Underfull \hbox (badness 10000) in paragraph at lines 7991--7993 []\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 7996--7998 []\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 [2011] [2012] [2013] [2014] Underfull \hbox (badness 1859) in paragraph at lines 8224--8227 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [2015] Underfull \hbox (badness 1655) in paragraph at lines 8318--8321 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \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 8329--8329 []\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 8337--8337 []\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):[] [2016] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8345--8345 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2017] Underfull \hbox (badness 1917) in paragraph at lines 8432--8434 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [2018] [2019] [2020] [2021] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8704--8704 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8705--8705 [] \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 8706--8706 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2022] Underfull \hbox (badness 10000) in paragraph at lines 8734--8736 []\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 8748--8750 []\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 8756--8761 []\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, [2023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8802--8802 [] \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 8803--8803 [] \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[] [2024] [2025] Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8932--8937 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8932--8937 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8939--8942 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [2026] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9055--9055 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9056--9056 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2027] [2028] [2029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9229--9229 [] \T1/pcr/m/n/9 "S original, "),[] [2030] Underfull \hbox (badness 1789) in paragraph at lines 9362--9364 []\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 [2031] [2032] [2033] [2034] [2035] [2036] [2037] [2038] [2039] Underfull \hbox (badness 5203) in paragraph at lines 9935--9938 []\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 [2040] [2041] Underfull \hbox (badness 1394) in paragraph at lines 10161--10168 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [2042] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10185--10185 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2043] [2044] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10346--10346 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2045] [2046] [2047] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10527--10527 []\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[] [2048] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10613--10613 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10616--10616 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10621--10621 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2049] Underfull \hbox (badness 2027) in paragraph at lines 10693--10696 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2050] [2051] [2052] [2053] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10972--10972 []\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 10973--10973 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10980--10985 []\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 10980--10985 \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 10980--10985 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2054] [2055] [2056] [2057] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11213--11213 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2058] [2059] [2060] [2061] Underfull \hbox (badness 10000) in paragraph at lines 11474--11478 \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 11492--11492 []\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 11497--11497 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2062] [2063] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11630--11630 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11631--11631 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2064] [2065] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11766--11766 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2066] Underfull \hbox (badness 1917) in paragraph at lines 11890--11893 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11890--11893 \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 [2067] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11913--11913 []\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 '[] [2068] Underfull \hbox (badness 10000) in paragraph at lines 11976--11978 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 type = "txt"\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 file.show[][][] \T1/ptm/m/n/10 is used. [][]\T1/pcr/m/n/10 vignette[][][]\ T1/ptm/m/n/10 s are nicely viewed via [2069] Underfull \hbox (badness 6725) in paragraph at lines 12026--12035 \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 6428) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 12026--12035 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 12026--12035 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2070] Underfull \hbox (badness 1377) in paragraph at lines 12126--12129 []\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 [2071] Underfull \hbox (badness 3646) in paragraph at lines 12161--12163 [][][]$\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 12199--12199 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 12380--12384 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12411--12417 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2075] [2076] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12587--12587 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2077] Underfull \hbox (badness 1009) in paragraph at lines 12605--12617 []\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 12645--12647 []\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 [2078] Underfull \hbox (badness 1043) in paragraph at lines 12688--12693 []\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 [2079] [2080] [2081] [2082] Underfull \hbox (badness 1888) in paragraph at lines 12981--12984 []\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 12998--13001 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2083] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13044--13044 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2084] Underfull \hbox (badness 2158) in paragraph at lines 13099--13102 []\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 13147--13147 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2085] [2086] [2087] Underfull \hbox (badness 2302) in paragraph at lines 13304--13306 []\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 [2088] Underfull \hbox (badness 3333) in paragraph at lines 13411--13413 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2089] [2090] [2091] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13578--13578 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13602--13607 []\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 have Underfull \hbox (badness 5970) in paragraph at lines 13611--13614 []\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 13611--13614 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2092] Underfull \hbox (badness 1442) in paragraph at lines 13638--13642 []\T1/ptm/m/n/10 numeric or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, 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 13684--13684 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2093] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13715--13715 []\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 13722--13722 []\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 13724--13724 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] Underfull \vbox (badness 10000) has occurred while \output is active [2094] [2095] [2096] Underfull \hbox (badness 10000) in paragraph at lines 13892--13894 []\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 [2097] [2098] Underfull \hbox (badness 6300) in paragraph at lines 14049--14056 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 14049--14056 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 14049--14056 \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$"\T1/ptm/m/n/10 ) and [2099] [2100] Underfull \hbox (badness 2020) in paragraph at lines 14218--14234 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 14218--14234 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2101] [2102] Underfull \hbox (badness 5022) in paragraph at lines 14357--14361 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 14364--14367 [][][]$\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 14364--14367 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2103] [2104] [2105] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14528--14528 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2106] [2107] [2108] [2109] [2110] [2111] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14969--14969 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14975--14975 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14996--14998 []\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 15011--15015 \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 Underfull \hbox (badness 1694) in paragraph at lines 15025--15029 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 15031--15036 \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 15031--15036 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 15037--15039 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2112] Underfull \hbox (badness 10000) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 15067--15072 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault 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 15088--15093 []\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 Underfull \hbox (badness 10000) in paragraph at lines 15096--15099 [][][]\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.packages[] [][]\T1/ptm/m/n/10 , [2113] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15150--15150 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2114] [2115] [2116] Underfull \hbox (badness 10000) in paragraph at lines 15357--15360 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 15357--15360 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2117] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15373--15373 []\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:[] [2118] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15440--15440 [] \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 15462--15462 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2119] [2120] Underfull \hbox (badness 1297) in paragraph at lines 15593--15595 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2121] Underfull \hbox (badness 4036) in paragraph at lines 15640--15642 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2122] [2123] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2124] Underfull \hbox (badness 1715) in paragraph at lines 15829--15832 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/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 15874--15876 []\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 = [2125] [2126] [2127]) [2128] [2129] [2130] (./KernSmooth-pkg.tex Chapter 15. [2131] 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) [2132] [2133] [2134] [2135] [2136] 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, [2137] [2138] [2139] [2140]) (./MASS-pkg.tex Chapter 16. [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2152] [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2419--2419 []\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 2423--2423 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2175] [2176] [2177] [2178] Underfull \hbox (badness 6559) in paragraph at lines 2703--2706 []\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 [2179] [2180] [2181] Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2873--2878 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "negative binomial"\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 , [2182] [2183] Underfull \hbox (badness 4686) in paragraph at lines 3041--3043 []\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 [2184] [2185] [2186] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3236--3236 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] [2187] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3366--3366 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] Underfull \hbox (badness 1845) in paragraph at lines 4154--4156 []\T1/ptm/m/n/10 The va-ri-ety of bar-ley (\T1/pcr/m/n/10 "manchuria"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "velvet"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "trebi" \T1/ptm/m/n/10 and [2200] [2201] [2202] [2203] [2204] [2205] [2206] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4650--4650 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2207] [2208] [2209] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4872--4872 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, [2210] [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5924--5924 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2224] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5985--5985 []\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") [2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica te ignored \relax l.6146 ...sical N, P, K Factorial Experiment}{npk} [2227] [2228] Underfull \hbox (badness 1783) in paragraph at lines 6266--6270 []\T1/ptm/m/n/10 Given a ma-trix, \T1/pcr/m/n/10 M\T1/ptm/m/n/10 , find a ma-tr ix \T1/pcr/m/n/10 N \T1/ptm/m/n/10 giv-ing a ba-sis for the (left) null space. That is [2229] [2230] [2231] [2232] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6566--6566 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6654--6654 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2234] [2235] [2236] [2237] [2238] [2239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7093--7093 []\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 7110--7110 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] [2240] Underfull \hbox (badness 10000) in paragraph at lines 7133--7135 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7188--7194 []\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 ) = [2241] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7258--7258 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2242] [2243] Underfull \hbox (badness 5091) in paragraph at lines 7367--7370 \T1/ptm/m/n/10 only the first \T1/pcr/m/n/10 dimen \T1/ptm/m/n/10 dis-crim-i-na nt com-po-nents are used (ex-cept for [2244] [2245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2246] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7562--7562 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2247] [2248] [2249] [2250] [2251] [2252] Underfull \hbox (badness 4686) in paragraph at lines 8000--8002 []\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 [2253] [2254] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8119--8119 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8143--8147 []\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 [2255] [2256] [2257] [2258] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271] [2272] [2273] [2274] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9527--9527 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2275] Underfull \hbox (badness 2035) in paragraph at lines 9639--9641 []\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 9654--9657 []\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-larly), [2276] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9736--9736 []\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 9738--9738 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9741--9741 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2277] [2278] [2279] [2280] [2281] [2282] [2283] [2284] [2285] [2286] [2287] [2288] [2289]) (./Matrix-pkg.tex [2290] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\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 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2291] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\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 [2292] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\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 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2293] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\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 [2294] [2295] Overfull \hbox (15.18042pt too wide) in paragraph at lines 471--471 [] \T1/pcr/m/n/9 band(sm5, -1, 1)# "dsyMatrix": symmetric band preserves sym metry property[] [2296] Underfull \hbox (badness 5147) in paragraph at lines 501--504 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in Underfull \hbox (badness 5119) in paragraph at lines 514--518 []\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 518--523 [][][]\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/pcr/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 548--548 []\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 550--550 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 559--559 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2297] [2298] Overfull \hbox (52.98038pt too wide) in paragraph at lines 673--673 []\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 674--674 []\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 675--675 []\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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 688--688 [] \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 689--689 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 694--694 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 763--767 \T1/pcr/m/n/10 lapack / double / dsytrf . f$[][] \T1/ptm/m/n/10 and [][]$\T1/pc r/m/n/10 https : / / www . netlib . org / lapack / double / [2300] [2301] Underfull \hbox (badness 3536) in paragraph at lines 882--887 []\T1/ptm/m/n/10 option [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 in-di-c at-ing if the re-sult should be sparse, i.e., for- Underfull \hbox (badness 7777) in paragraph at lines 882--887 \T1/ptm/m/n/10 mally in-her-it-ing from \T1/pcr/m/n/10 "[][]sparseMatrix[][][]" \T1/ptm/m/n/10 . The de-fault, [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , de- Underfull \hbox (badness 6188) in paragraph at lines 882--887 \T1/ptm/m/n/10 cides from the ``spar-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 [2302] Underfull \hbox (badness 10000) in paragraph at lines 925--930 []\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 meth-ods: [2303] Overfull \hbox (72.78088pt too wide) in paragraph at lines 986--986 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2304] [2305]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) has been already used, duplicate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic ate ignored \relax l.1173 ...- 'Matrix' S4 Generic and Methods}{chol} [2306] Underfull \hbox (badness 2285) in paragraph at lines 1259--1264 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2307] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1305--1305 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2308] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1400--1400 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1428--1431 []\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 [2309] Underfull \hbox (badness 1609) in paragraph at lines 1475--1479 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra Overfull \hbox (4.38043pt too wide) in paragraph at lines 1502--1502 []\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 1516--1516 []\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[] [2310] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1524--1524 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] Underfull \hbox (badness 10000) in paragraph at lines 1571--1578 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1571--1578 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or [2311] Underfull \hbox (badness 1783) in paragraph at lines 1606--1610 []\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 Underfull \hbox (badness 1221) in paragraph at lines 1622--1628 \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 . Hen ce, 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.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup licate ignored \relax l.1663 ... Row and Column Sums and Means}{colSums} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl icate ignored \relax l.1664 \aliasA{colMeans}{colSums}{colMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i gnored \relax l.1685 \aliasA{rowMeans}{colSums}{rowMeans} pdfTeX warning (ext4): destination w ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig nored \relax l.1696 \aliasA{rowSums}{colSums}{rowSums} [2312] 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 from 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/10 , since [2313] [2314] [2315] 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 [2316] [2317] [2318] [2319] Underfull \hbox (badness 1484) in paragraph at lines 2277--2279 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2320] Underfull \hbox (badness 7379) in paragraph at lines 2373--2375 []\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 [2321] [2322] [2323] Underfull \hbox (badness 4846) in paragraph at lines 2649--2653 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2717) in paragraph at lines 2654--2658 []\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 2661--2664 []\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 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2324] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2708--2708 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2717--2719 []\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 2721--2726 []\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 2721--2726 [][]\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 [2325] Underfull \hbox (badness 1097) in paragraph at lines 2744--2747 []\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 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2757--2762 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2326] Underfull \hbox (badness 3646) in paragraph at lines 2996--2999 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 3028--3030 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 3031--3035 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 3040--3046 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2327] Underfull \hbox (badness 10000) in paragraph at lines 3047--3051 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3057--3061 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these 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 [2328] [2329] Underfull \hbox (badness 10000) in paragraph at lines 3241--3243 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3288--3290 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2330] Underfull \hbox (badness 2469) in paragraph at lines 3408--3411 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 3573--3577 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3573--3577 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2333] Underfull \hbox (badness 2285) in paragraph at lines 3623--3626 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2334] [2335] Underfull \hbox (badness 10000) in paragraph at lines 3770--3775 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3770--3775 \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 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3782--3785 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2336] Underfull \hbox (badness 10000) in paragraph at lines 3858--3860 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3945--3945 []\T1/pcr/m/n/9 stopifnot(all(S1 == S2)) # equal "seen as matrix", but differ internally :[] [2338] [2339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4078--4078 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] [2340] Underfull \hbox (badness 3635) in paragraph at lines 4146--4150 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class Underfull \hbox (badness 10000) in paragraph at lines 4155--4158 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4155--4158 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4160--4164 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2341] [2342] Underfull \hbox (badness 3158) in paragraph at lines 4343--4347 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2343] [2344] [2345] [2346] Overfull \hbox (112.38031pt too wide) in paragraph at lines 4593--4593 []\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 4600--4600 [] \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 4604--4604 []\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 4607--4607 []\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 4617--4617 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2347] [2348] [2349] [2350] Underfull \hbox (badness 10000) in paragraph at lines 4919--4924 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2351] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5000--5000 []\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 5002--5002 [] \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 5006--5006 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2352] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5013--5013 [] \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 '[] [2353] [2354] Underfull \hbox (badness 4120) in paragraph at lines 5157--5160 []\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 (15.18042pt too wide) in paragraph at lines 5194--5194 []\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 5200--5200 [] \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 5201--5201 [] \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 5205--5205 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5207--5207 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2355] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5214--5214 []\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 5217--5217 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2356] Underfull \hbox (badness 1817) in paragraph at lines 5306--5315 []\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 within the Underfull \hbox (badness 10000) in paragraph at lines 5348--5350 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5350--5353 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5363--5366 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2357] Underfull \hbox (badness 4765) in paragraph at lines 5381--5384 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2358] [2359] [2360] [2361] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5699--5699 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2362] Underfull \hbox (badness 10000) in paragraph at lines 5782--5785 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5793--5793 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2363] Underfull \hbox (badness 1622) in paragraph at lines 5830--5835 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5830--5835 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2364] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5891--5891 []\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 5892--5892 [] \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 5899--5899 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2365] [2366] Underfull \hbox (badness 1062) in paragraph at lines 6028--6031 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 6057--6060 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2367] Underfull \hbox (badness 2635) in paragraph at lines 6169--6174 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6169--6174 \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 "Matrix"\T1/ptm/ m/n/10 , by class [2368] Underfull \hbox (badness 10000) in paragraph at lines 6177--6180 []\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 ); us e, e.g., Underfull \hbox (badness 10000) in paragraph at lines 6287--6297 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6287--6297 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2369] Underfull \hbox (badness 3179) in paragraph at lines 6369--6372 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2370] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\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., [2371] Underfull \hbox (badness 10000) in paragraph at lines 6542--6545 []\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., [2372] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6558--6558 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Underfull \hbox (badness 2443) in paragraph at lines 6597--6603 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6597--6603 [][]\T1/pcr/m/n/10 stop[][][]\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, Underfull \hbox (badness 1675) in paragraph at lines 6618--6621 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2373] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6688--6688 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2374] [2375] Underfull \hbox (badness 10000) in paragraph at lines 6829--6832 []\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 [2376] Underfull \hbox (badness 1490) in paragraph at lines 6851--6853 []\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[][][] \T 1/ptm/m/n/10 and (one case of) [2377] Underfull \hbox (badness 5036) in paragraph at lines 6931--6935 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6931--6935 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2378]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.7030 \aliasA{det}{Matrix-class}{det} [2379] Underfull \hbox (badness 10000) in paragraph at lines 7133--7136 Underfull \hbox (badness 10000) in paragraph at lines 7143--7145 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2380]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7206 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.crossprod}) has been already used, dup licate ignored \relax l.7314 ...A{crossprod}{matrix-products}{crossprod} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du plicate ignored \relax l.7413 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7510--7516 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2381] Underfull \hbox (badness 10000) in paragraph at lines 7583--7586 []\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 1199) in paragraph at lines 7583--7586 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7586--7591 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7586--7591 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7591--7595 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7591--7595 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7601--7602 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2382] [2383] Underfull \hbox (badness 1009) in paragraph at lines 7737--7739 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see [2384] Underfull \hbox (badness 1062) in paragraph at lines 7782--7785 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \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 7816--7819 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2385] Underfull \hbox (badness 10000) in paragraph at lines 7872--7874 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7974--7974 [] \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 8014--8014 []\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 [2388] Underfull \hbox (badness 2635) in paragraph at lines 8079--8084 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 8079--8084 \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 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 8087--8090 []\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 ); us e, e.g., [2389] Underfull \hbox (badness 3482) in paragraph at lines 8161--8167 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2390] Underfull \hbox (badness 1867) in paragraph at lines 8281--8283 []\T1/ptm/m/n/10 fast sim- [2391]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8321 \HeaderA{norm}{Matrix Norms}{norm} [2392] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8408--8408 []\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 8409--8409 []\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 8410--8410 []\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 8523--8533 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2393] Underfull \hbox (badness 3179) in paragraph at lines 8594--8597 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally 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 8684--8687 []\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 8760--8763 []\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] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8776--8776 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2397] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8888--8891 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8894--8901 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2398] [2399] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8987--8987 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8990--8990 []\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 8992--8992 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8996--8996 []\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 8997--8997 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 9022--9032 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 9022--9032 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2400] [2401]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9123 \aliasA{qr}{qr-methods}{qr} [2402] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9196--9196 []\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 9207--9207 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9227--9227 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9235--9235 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2403] Underfull \hbox (badness 10000) in paragraph at lines 9292--9298 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9309--9312 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2404] [2405] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9408--9408 []\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 9424--9424 []\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 9430--9430 []\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 9431--9431 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9449 ... the Reciprocal Condition Number}{rcond} [2406] [2407] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9562--9562 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2408] [2409] [2410] Underfull \hbox (badness 2351) in paragraph at lines 9753--9761 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9753--9761 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2411] [2412] Underfull \hbox (badness 1558) in paragraph at lines 9900--9903 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2413] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9962--9962 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9966--9966 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2414]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.10028 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10125--10125 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 10132--10132 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2415] Underfull \hbox (badness 1616) in paragraph at lines 10167--10179 []\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 10184--10187 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 10193--10200 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10206--10216 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10206--10216 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, Underfull \hbox (badness 6032) in paragraph at lines 10233--10237 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's [2416] Underfull \hbox (badness 10000) in paragraph at lines 10240--10242 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10263--10264 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10269--10271 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10273--10274 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10281--10284 [][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10299--10299 []\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 10303--10303 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2417] Underfull \hbox (badness 10000) in paragraph at lines 10324--10327 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10352--10354 []\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 10360--10363 []\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 10360--10363 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10371--10375 []\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 10371--10375 \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 [2418] Underfull \hbox (badness 1668) in paragraph at lines 10386--10391 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse Underfull \hbox (badness 1158) in paragraph at lines 10407--10413 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2419] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10466--10466 [] \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 10467--10467 [] \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 10468--10468 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2420] [2421] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10652--10652 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2422] Underfull \hbox (badness 1668) in paragraph at lines 10694--10699 [][][]\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/pcr/m/n/10 "R" \T1/ptm/m/n/10 , spec-i-fy-ing the sparse [2423] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10791--10791 []\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 10795--10795 []\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 10796--10796 []\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 10801--10801 []\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 10804--10804 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2424] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10827--10827 []\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 10828--10828 []\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)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10854--10854 []\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 10856--10856 [] \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 10858--10858 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] Underfull \vbox (badness 10000) has occurred while \output is active [2425] [2426] Underfull \hbox (badness 10000) in paragraph at lines 10999--11003 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.11039 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2427] [2428] Underfull \hbox (badness 10000) in paragraph at lines 11169--11171 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 11197--11197 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2429] Underfull \hbox (badness 5036) in paragraph at lines 11225--11227 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a Underfull \hbox (badness 2970) in paragraph at lines 11359--11365 []\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 11359--11365 \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 "lsparseVec tor"\T1/ptm/m/n/10 , [2430] Underfull \hbox (badness 10000) in paragraph at lines 11432--11435 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2431] Underfull \hbox (badness 10000) in paragraph at lines 11450--11455 []\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 11465--11467 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2432] [2433] Underfull \hbox (badness 2698) in paragraph at lines 11590--11596 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2434] Underfull \hbox (badness 10000) in paragraph at lines 11683--11685 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11701--11706 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11701--11706 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other [2435] Underfull \hbox (badness 2591) in paragraph at lines 11709--11714 \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-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or Underfull \hbox (badness 2057) in paragraph at lines 11781--11783 []\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., [2436] [2437] Underfull \hbox (badness 6641) in paragraph at lines 11867--11870 []\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 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11907--11911 []\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 11907--11911 \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 [2438] [2439] Underfull \hbox (badness 7649) in paragraph at lines 12014--12016 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2440] [2441] [2442] Underfull \hbox (badness 7362) in paragraph at lines 12215--12217 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 12253--12253 []\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 12254--12254 []\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)[] [2443] [2444] [2445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12396--12396 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12409--12409 [] \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 12414--12414 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2446] Underfull \hbox (badness 6910) in paragraph at lines 12590--12592 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2447] Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. Package hyperref Warning: Glyph not defined in PU encoding, (hyperref) removing `\Rpercent' on input line 12637. [2448] [2449]) (./boot-pkg.tex [2450] Chapter 18. [2451] [2452] [2453] [2454] [2455] [2456] [2457] 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"), [2458] 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- [2459] [2460] [2461] 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 boot.c i[][][]\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 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2462] 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 [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1068--1072 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2465] 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 [2466] [2467] [2468] [2469] 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- [2470] [2471] [2472] [2473] [2474] 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), [2475] [2476] [2477] Underfull \vbox (badness 10000) has occurred while \output is active [2478] 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),[] [2479] 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. [2480] [2481] [2482] 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 [2483] 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$statis tic \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 , [2484] [2485] 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/10 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/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2486] [2487] [2488] [2489] [2490] 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,[] [2491] [2492] [2493] 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.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/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 , [2494] 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)) [2495] [2496] [2497] 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 [2498] [2499] [2500] [2501] [2502] [2503] [2504] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2505] [2506] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2507] [2508] [2509] Underfull \hbox (badness 10000) in paragraph at lines 4190--4192 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2510] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2511] [2512] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2522] [2523] [2524] [2525] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2526] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2527] [2528] [2529] [2530] [2531] [2532] [2533] [2534] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2535] 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 t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2536] 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 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2537] [2538] [2539] [2540] 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). [2541] [2542] 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[] [2543] [2544] [2545] 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 [2546] [2547] 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),[] [2548] [2549] [2550] [2551] [2552] [2553] [2554] [2555]) (./class-pkg.tex [2556] Chapter 19. [2557] [2558] [2559] [2560] [2561] [2562] [2563] [2564] [2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]) (./cluster-pkg.tex Chapter 20. [2573] Underfull \hbox (badness 1655) in paragraph at lines 134--143 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 134--143 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 134--143 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 134--143 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2574] [2575] 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]))[] [2576] [2577] Underfull \vbox (badness 10000) has occurred while \output is active [2578] [2579] 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, ...)[] [2580] [2581] 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)[] [2582] 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 [2583] [2584] 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-ence s; [][]\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 , [2585] 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 [2586] 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), ...)[] [2587] 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, [2588] [2589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1120--1120 [] \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 1137--1137 []\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 [2590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1175--1175 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] Underfull \hbox (badness 4144) in paragraph at lines 1207--1211 []\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 [2591] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1283--1283 [] \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 1289--1289 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2592] [2593] Underfull \hbox (badness 10000) in paragraph at lines 1428--1433 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or [2594] Underfull \hbox (badness 10000) in paragraph at lines 1476--1479 Underfull \hbox (badness 10000) in paragraph at lines 1493--1497 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\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/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/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 1517--1517 []\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 1527--1527 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2595] Underfull \hbox (badness 5741) in paragraph at lines 1567--1570 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2597] [2598] Underfull \hbox (badness 1540) in paragraph at lines 1753--1761 \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 = [2599] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1844--1844 []\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 1863--1863 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2600] [2601] [2602] [2603] [2604] Underfull \hbox (badness 10000) in paragraph at lines 2182--2185 Underfull \hbox (badness 3179) in paragraph at lines 2196--2202 [][][]\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/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2605] [2606] Underfull \hbox (badness 10000) in paragraph at lines 2354--2357 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2607] Underfull \hbox (badness 1292) in paragraph at lines 2422--2425 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and [2608] Underfull \hbox (badness 6675) in paragraph at lines 2431--2433 []\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 2454--2457 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\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 , [2609] [2610] [2611] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2670--2670 []\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 ):[] [2612] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2749--2749 [] \T1/pcr/m/n/10 variant = c("original", "o_1", "o_2", "f_3", "f_4", "f_5" , "faster"),[] [2613] [2614] [2615] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2978--2978 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2616] [2617] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3081--3081 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2618] [2619] [2620] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2621] Underfull \hbox (badness 10000) in paragraph at lines 3345--3348 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2622] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3396--3396 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2623] [2624] [2625] Underfull \hbox (badness 10000) in paragraph at lines 3581--3584 []\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 [2626] Underfull \hbox (badness 10000) in paragraph at lines 3644--3649 [][][]\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.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2627] Underfull \hbox (badness 3884) in paragraph at lines 3706--3711 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/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 3718--3721 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\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/10 hclust[][][]\T 1/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 , [2628] [2629] [2630] Underfull \hbox (badness 10000) in paragraph at lines 3903--3906 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3934--3937 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3987--3987 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3998--4000 []\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 [2632] [2633] [2634] [2635] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4191--4191 [] \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 4193--4193 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2636] [2637] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4336--4336 []\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 4345--4345 [] \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 4347--4347 [] \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 4350--4350 []\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 4352--4352 [] \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 4359--4359 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2638] [2639] [2640] [2641] [2642] [2643] [2644] Underfull \hbox (badness 10000) in paragraph at lines 4732--4738 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4748--4750 []\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 4761--4761 []\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 4763--4763 []\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)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4773--4773 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2645] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4777--4777 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2646]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2647] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2648] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2649] [2650] [2651]) (./foreign-pkg.tex [2652] Chapter 22. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][]$\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 . [2653] 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 [2654] [2655] 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 , [2656] 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, [2657] [2658] [2659] 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,[] [2660] 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 10000) 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- Underfull \hbox (badness 6001) in paragraph at lines 505--514 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 505--514 \T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 , 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 "_dupli cated_"\T1/ptm/m/n/10 ) if [2661] Underfull \hbox (badness 10000) in paragraph at lines 550--558 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 https : / / docs . microsoft . com / e n-[]us / windows / win32 / intl / Underfull \hbox (badness 7613) in paragraph at lines 568--574 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2662] Overfull \hbox (20.58041pt too wide) in paragraph at lines 623--623 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2663] Overfull \hbox (9.78043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ ate variables[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 cat.long.string <- function(x, w=70) cat(paste(strwrap(x, widt h=w), "\n"))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 668--668 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, collapse="")[] [2664] [2665] Underfull \hbox (badness 10000) in paragraph at lines 812--813 Overfull \hbox (4.38043pt too wide) in paragraph at lines 822--822 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2666] Underfull \hbox (badness 10000) in paragraph at lines 869--873 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of a Data Underfull \hbox (badness 10000) in paragraph at lines 869--873 \T1/ptm/m/n/10 Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][]$\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 . [2667] 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) [2668] 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))) [2669] [2670] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2671] [2672] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2673] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2674]) (./lattice-pkg.tex Chapter 23. [2675] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\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 / [2676] [2677] 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"),[] [2678] 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"),[] [2679] [2680] [2681] [2682] 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 [2683] [2684] [2685] [2686] 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. [2687] 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 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2688] [2689] 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 [2690] [2691] [2692] 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 , [2693] 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/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2694] Underfull \vbox (badness 10000) has occurred while \output is active [2695] 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 [2696] 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\T1/pt m/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 [2697] [2698] [2699] [2700] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2701] 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-fied, t he 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 first ch ecked. If [2702] [2703] [2704] 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"),[] [2705] [2706] [2707] [2708] [2709] 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"),[] [2710] [2711] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2712] 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.rast er[][][]\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[][][] \T 1/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 [2713] 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 [2714] 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),[] [2715] 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"),[] [2716] 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/pc r/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/p tm/m/n/10 must have the same lengths as [2717] [2718] [2719]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} [2720] 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"),[] [2721] [2722] [2723] [2724] [2725] 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))) [2726] [2727] 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 [2728] 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 [2729] 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-rent se t-tings (ob-tained by [2730] 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 trellis .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 [2731] [2732] 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 i s 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 "superpose.p olygon"\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 f or \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 c ol.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 plot .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 pl ot.polygon \T1/ptm/m/n/10 and [2733] [2734] [2735] [2736] [2737] 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")[] [2738] [2739] Underfull \vbox (badness 1092) has occurred while \output is active [2740] 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 . [2741] [2742] 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-gles via rect-an-gles. \T1/pcr/m/n/10 print.shingle \T1/ptm/m/n/10 and [2743] [2744] [2745] [2746] [2747] 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-cally the en-try f or 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],[] [2748] 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 lef t of pan-els us-ing [2749] 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, wh ich is to draw a strip ap-pro-pri-ate for [2750] [2751] 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",[] [2752] 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 [2753] 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-fault 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 , ex-tr a 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 , these are used (in com-bi-na-tion with [2754] [2755] 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 Lattice[ ][][]\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 , [2756] Underfull \vbox (badness 10000) has occurred while \output is active [2757] [2758] 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- [2759] [2760] 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/1 0 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-fault, the ac-tual box-plot statis-tics are cal-cu-lated us-ing [2761] 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,[] [2762] [2763] 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/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2764] 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 v alid color. The [2765] [2766] [2767] [2768] [2769] 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 pan el 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 [2770] [2771] 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 this fu nc-tion is passed [2772] [2773] 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 [2774] [2775] 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 [2776] 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))[] [2777] [2778] 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 on 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 be a list of ar-gu-ments to be sup-plied to [2779] 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),[] [2780] 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)[] [2781] [2782] [2783] 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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] 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.superpo se 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 [2792] [2793] 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, ...)[] [2794] 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 [2795] 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 [2796] [2797] 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 [2798] 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)[] [2799] [2800] 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)),[] [2801] Overfull \hbox (46.28876pt too wide) in paragraph at lines 9228--9232 []\T1/ptm/m/n/10 Returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9228--9232 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2802] [2803] [2804] [2805] [2806] [2807] [2808] 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/10 , \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/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2809] [2810] [2811]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} [2812] [2813] [2814] 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 Heart 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),[] [2815] [2816]) (./mgcv-pkg.tex Chapter 24. [2817] [2818] 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,[] [2819] 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. [2820] [2821] [2822] [2823] Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 378--385 [][]\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 378--385 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2824] Overfull \hbox (4.38043pt too wide) in paragraph at lines 421--421 []\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)+[] [2825] [2826] [2827] Underfull \hbox (badness 2922) in paragraph at lines 633--634 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2828] [2829] Underfull \hbox (badness 1406) in paragraph at lines 703--704 []\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 [2830] [2831] Underfull \hbox (badness 1158) in paragraph at lines 813--815 []\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 [2832] Underfull \hbox (badness 1259) in paragraph at lines 876--877 []\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). [2833] Underfull \vbox (badness 10000) has occurred while \output is active [2834] [2835] [2836] [2837] [2838] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1225--1225 []\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 1226--1226 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2839] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1243--1243 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1255--1255 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1264--1264 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1266--1266 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2840] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1297--1297 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2841] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1380--1380 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2842] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1391--1391 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1425--1425 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1931--1931 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2852] [2853] [2854] [2855] [2856] [2857] Underfull \hbox (badness 1052) in paragraph at lines 2319--2327 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2336--2336 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2348--2351 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2361--2365 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2858] Underfull \hbox (badness 1043) in paragraph at lines 2387--2392 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2859] [2860] [2861] Underfull \hbox (badness 1043) in paragraph at lines 2552--2558 \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 [2862] Underfull \hbox (badness 10000) in paragraph at lines 2688--2694 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\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 2688--2694 [][]\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 2688--2694 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2863] [2864] Underfull \vbox (badness 10000) has occurred while \output is active [2865] Underfull \vbox (badness 10000) has occurred while \output is active [2866] [2867] [2868] [2869] [2870] [2871] [2872] [2873] [2874] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3344--3344 [] \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 3347--3347 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] Underfull \hbox (badness 5189) in paragraph at lines 3822--3826 []\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 [2883] [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3939--3939 []\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 [2885] [2886] [2887] Underfull \hbox (badness 1184) in paragraph at lines 4108--4112 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2888] [2889] [2890] [2891] [2892] [2893] [2894] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4554--4554 [] \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)+[] [2895] [2896] [2897] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4704--4704 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2898] [2899] Underfull \hbox (badness 1142) in paragraph at lines 4829--4833 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2900] Underfull \hbox (badness 10000) in paragraph at lines 4901--4910 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2901] [2902] Underfull \hbox (badness 5970) in paragraph at lines 5018--5024 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-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 5018--5024 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/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 . [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] [2905] [2906] [2907] Underfull \hbox (badness 1577) in paragraph at lines 5370--5373 []\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 5377--5378 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2908] [2909] [2910] [2911] [2912] [2913] [2914] Underfull \hbox (badness 6708) in paragraph at lines 5766--5767 []\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 [2915] [2916] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5815--5815 [] \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 5840--5840 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2917] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5869--5869 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2918] [2919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5991--5991 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2920] [2921] [2922] [2923] [2924] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6328--6328 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2925] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6330--6330 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6351--6355 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2926] [2927] [2928] Underfull \vbox (badness 10000) has occurred while \output is active [2929] [2930] [2931] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6670--6670 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2932] [2933] [2934] [2935] Underfull \vbox (badness 10000) has occurred while \output is active [2936] Underfull \vbox (badness 10000) has occurred while \output is active [2937] [2938] [2939] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7102--7102 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7129--7129 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] Underfull \hbox (badness 1242) in paragraph at lines 7672--7673 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2949] [2950] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7759--7759 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2951] [2952] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7822--7822 []\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 7841--7841 [] \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 [2953] [2954] [2955] [2956] [2957] [2958] [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] [2967] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] [2972] Underfull \hbox (badness 10000) in paragraph at lines 9061--9064 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\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 9061--9064 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ 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 9061--9064 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2973] Underfull \hbox (badness 10000) in paragraph at lines 9117--9120 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 9117--9120 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2974] [2975] [2976] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9337--9337 []\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 9338--9338 [] \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 9341--9341 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2977] [2978] [2979] Underfull \hbox (badness 1629) in paragraph at lines 9499--9504 \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 [2980] [2981] [2982] [2983] Overfull \hbox (84.78088pt too wide) in paragraph at lines 9710--9710 [] \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 9747--9751 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 type=="terms" \T1/ptm/m/n/10 or \T1/pcr/m/n/ 10 type="iterms" \T1/ptm/m/n/10 then terms (smooth or para- Underfull \hbox (badness 1292) in paragraph at lines 9747--9751 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2984] [2985] [2986] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9880--9880 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2987] [2988] [2989] Underfull \vbox (badness 10000) has occurred while \output is active [2990] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10153--10153 [] \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[] [2991] Underfull \hbox (badness 1205) in paragraph at lines 10191--10193 []\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 10191--10193 \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 10197--10202 []\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 [2992] Underfull \hbox (badness 1205) in paragraph at lines 10281--10283 []\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 10281--10283 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2993] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\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 10350--10353 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh 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, [2994] [2995] Underfull \hbox (badness 1253) in paragraph at lines 10480--10482 []\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, [2996] [2997] [2998] [2999] [3000] Underfull \hbox (badness 1946) in paragraph at lines 10733--10740 []\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 10733--10740 \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 10733--10740 \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: s ee [3001] Underfull \hbox (badness 2846) in paragraph at lines 10741--10744 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 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 10741--10744 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3002] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10807--10807 []\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 10817--10817 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] Underfull \hbox (badness 10000) in paragraph at lines 10848--10851 []\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 , [3003] [3004] [3005] [3006] [3007] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11150--11150 []\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) [3008] [3009] [3010] [3011] [3012] [3013] [3014] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11521--11521 [] \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 11535--11535 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~s(times, k = 1 0), ~1, ~1),[] [3015] Underfull \vbox (badness 10000) has occurred while \output is active [3016] Underfull \hbox (badness 3861) in paragraph at lines 11637--11640 []\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 11646--11646 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] Underfull \hbox (badness 10000) in paragraph at lines 11663--11667 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3017] Underfull \hbox (badness 10000) in paragraph at lines 11703--11707 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [3018] [3019] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11847--11847 [] \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 11858--11863 []\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 [3020] [3021] Underfull \hbox (badness 1803) in paragraph at lines 11935--11939 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11947--11959 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11964--11968 \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 11964--11968 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [3022] [3023] [3024] [3025] Underfull \hbox (badness 6876) in paragraph at lines 12159--12165 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 12200--12201 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3026] [3027] Underfull \hbox (badness 10000) in paragraph at lines 12318--12319 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3028] [3029] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12372--12372 [] \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 12384--12384 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12396--12396 [] \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 12401--12401 [] \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 12407--12407 [] \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 12408--12408 [] \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:[] [3030] Underfull \hbox (badness 10000) in paragraph at lines 12477--12479 []\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 12477--12479 \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 [3031] [3032] [3033] Underfull \hbox (badness 10000) in paragraph at lines 12607--12608 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12688--12688 []\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 12689--12689 []\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[] [3035] [3036] [3037] Underfull \hbox (badness 10000) in paragraph at lines 12840--12841 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3038] [3039] [3040] [3041] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13090--13090 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3042] Underfull \hbox (badness 10000) in paragraph at lines 13151--13153 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 13310--13313 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 13310--13313 \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 13310--13313 \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" [3046] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13396--13396 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3047] Underfull \hbox (badness 10000) in paragraph at lines 13441--13447 []\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 13441--13447 \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- [3048] [3049] [3050] Underfull \vbox (badness 10000) has occurred while \output is active [3051] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13655--13655 []\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 [3052] Underfull \hbox (badness 10000) in paragraph at lines 13758--13766 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [3053] Underfull \hbox (badness 10000) in paragraph at lines 13784--13785 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3054] [3055] [3056] [3057] Underfull \hbox (badness 3396) in paragraph at lines 14044--14047 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [3058] Underfull \hbox (badness 10000) in paragraph at lines 14089--14091 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 14370--14373 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 14370--14373 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3064] Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][][]\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 14403--14407 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14403--14407 [][]\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 , [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2158) in paragraph at lines 14693--14693 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3070] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14772--14772 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3071] [3072] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14906--14906 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3073] [3074] Underfull \hbox (badness 4846) in paragraph at lines 15037--15040 []\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 [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16231--16231 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3095] [3096] [3097] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16441--16441 []\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, [3098] Overfull \hbox (48.78088pt too wide) in paragraph at lines 16443--16443 []\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 16445--16445 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] Underfull \hbox (badness 10000) in paragraph at lines 16465--16466 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16465--16466 \T1/pcr/m/n/10 (ar.stop[i-1]+1):ar.stop[i] \T1/ptm/m/n/10 of the rows se-lected by \T1/pcr/m/n/10 ar.row [3099] [3100] [3101] [3102] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16653--16653 []\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 16654--16654 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16666--16666 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3103] [3104] [3105]) (./nlme-pkg.tex [3106] Chapter 25. [3107] 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 - fi t-ted) are used; else, if [3108] 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 - fi t-ted) are used; else, if [3109] [3110] [3111] [3112] [3113] 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,[] [3114] [3115] 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 --------------------------- ---------------[] [3116] [3117] [3118] [3119] [3120] [3121] [3122] [3123] 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"),[] [3124] 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.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3125] [3126] [3127] [3128] [3129] [3130] [3131] 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.effe cts.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 , [3132] 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 [3133] [3134] [3135] [3136] [3137] 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 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3138] 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")[] [3139] 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 [3140] [3141] 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 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3142] 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,[] [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] 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 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3151] [3152] [3153] [3154] [3155] [3156pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored ...shipout:D \box_use:N \l_shipout_box l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3157] [3158] [3159] [3160] [3161] [3162] 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 corGaus[][ ][]\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 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3163] [3164] [3165] [3166] [3167] [3168] [3169] [3170] [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] Underfull \hbox (badness 10000) in paragraph at lines 5165--5169 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3187] [3188] [3189] [3190] [3191] [3192] [3193] 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 , [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] 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 [3203] 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 , [3204] Underfull \hbox (badness 2057) in paragraph at lines 6248--6259 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\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 , [3205] Underfull \hbox (badness 10000) in paragraph at lines 6312--6314 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6344--6344 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3206] [3207] [3208] [3209] Underfull \hbox (badness 7133) in paragraph at lines 6562--6566 []\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 , [3210] Underfull \hbox (badness 10000) in paragraph at lines 6661--6667 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6688--6688 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3211] Underfull \hbox (badness 10000) in paragraph at lines 6726--6728 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3212] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6756--6756 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3213] [3214] [3215] Underfull \hbox (badness 10000) in paragraph at lines 6999--7006 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3216] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7017--7017 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7022--7022 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7044--7046 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3217] [3218] [3219] Underfull \hbox (badness 10000) in paragraph at lines 7259--7264 [][][]\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 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3220] [3221] [3222] Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7411--7419 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7411--7419 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7434--7437 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3223] [3224] [3225] Underfull \hbox (badness 3354) in paragraph at lines 7650--7652 []\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 [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8162--8179 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\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 8205--8205 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8214--8236 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3234] [3235] [3236] [3237] [3238] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8479--8479 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8527--8529 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3239] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8571--8571 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8578 \aliasA{sigma}{lmeObject}{sigma} [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] [3248] [3249] [3250] [3251] Underfull \hbox (badness 10000) in paragraph at lines 9330--9337 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9341--9341 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3252] Underfull \hbox (badness 6300) in paragraph at lines 9423--9426 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3253] [3254] [3255] [3256]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9692 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3257] Underfull \hbox (badness 10000) in paragraph at lines 9712--9715 []\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 9756--9759 []\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 9756--9759 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3258] [3259] [3260] [3261] [3262] [3263] [3264] [3265] Underfull \hbox (badness 7291) in paragraph at lines 10220--10222 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3266] [3267] [3268] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10436--10436 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3269] Underfull \hbox (badness 1596) in paragraph at lines 10465--10491 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3270] [3271] [3272] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10641--10641 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3273] [3274] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10792--10792 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10803--10808 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3275] Underfull \hbox (badness 8075) in paragraph at lines 10825--10829 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10844--10846 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10880--10880 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3276] [3277] [3278] [3279] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11136--11136 []\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 11137--11137 []\T1/pcr/m/n/9 mat.class <- class(matrix(1)) # ("matrix", "array") for R >= 4 .0.0; ("matrix" in older R)[] [3280] [3281] [3282] [3283] [3284] [3285] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3286] [3287] [3288] [3289] [3290] [3291] Underfull \hbox (badness 6268) in paragraph at lines 11914--11924 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] Underfull \hbox (badness 10000) in paragraph at lines 12175--12181 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3296] [3297] [3298] [3299] [3300] Underfull \hbox (badness 6876) in paragraph at lines 12497--12499 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-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 [3301] [3302] Underfull \hbox (badness 2452) in paragraph at lines 12653--12660 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\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 , [3303] Underfull \hbox (badness 10000) in paragraph at lines 12718--12724 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3304] [3305] [3306] [3307] [3308] [3309] [3310] [3311] [3312] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13307--13307 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3313] [3314] [3315] [3316] [3317] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13672--13672 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3318] Underfull \hbox (badness 10000) in paragraph at lines 13699--13702 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3319] Underfull \hbox (badness 1838) in paragraph at lines 13742--13749 []\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 13742--13749 \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 13799--13799 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3320] Underfull \hbox (badness 10000) in paragraph at lines 13806--13809 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13806--13809 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13834--13837 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13834--13837 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3321] Underfull \hbox (badness 10000) in paragraph at lines 13914--13917 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3322] Underfull \hbox (badness 1472) in paragraph at lines 13939--13946 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3323] Underfull \hbox (badness 10000) in paragraph at lines 14008--14010 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] Underfull \hbox (badness 1215) in paragraph at lines 14288--14290 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3328] [3329] [3330] [3331] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14532--14532 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3332] [3333] [3334] [3335] [3336] [3337] [3338] [3339] [3340]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15185 ...Extract Random Effects}{random.effects} [3341] [3342] [3343] [3344] [3345] [3346] [3347] [3348] [3349] [3350] Underfull \hbox (badness 2126) in paragraph at lines 15825--15829 []\T1/ptm/m/n/10 Charles F. Minto, Thomas W. Schnider and Steven L. Shafer (199 7). Phar-ma-coki-net- [3351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15833--15833 []\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 15852--15852 [] \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 15853--15853 [] \T1/pcr/m/n/9 all.equal(LBM, LBMfn(Wt, Ht, Sex), tol = 7e-7)[] [3352] Underfull \hbox (badness 1009) in paragraph at lines 15883--15892 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3353] [3354] Overfull \hbox (66.78088pt too wide) in paragraph at lines 16030--16030 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 10000) in paragraph at lines 16365--16371 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\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.reStruc t[][][]\T1/ptm/m/n/10 , [3360] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16396--16396 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3361] [3362] [3363] [3364] [3365] [3366] [3367] Underfull \hbox (badness 1728) in paragraph at lines 16885--16888 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3368] [3369] [3370] [3371] [3372] Underfull \hbox (badness 1867) in paragraph at lines 17220--17229 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple 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 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17220--17229 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3373] Underfull \hbox (badness 10000) in paragraph at lines 17291--17292 []\T1/pcr/m/n/10 "Constant plus power of variance Underfull \hbox (badness 10000) in paragraph at lines 17292--17293 []\T1/pcr/m/n/10 "Constant plus proportion of variance [3374] [3375] [3376] [3377] Underfull \hbox (badness 10000) in paragraph at lines 17542--17550 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstProp[][][]\T1/ptm/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 , [3378] [3379] [3380] [3381] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17814--17814 []\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 17816--17816 []\T1/pcr/m/n/9 # overparameterisation in the case of a constant term in the v ariance function[] [3382] [3383] [3384] [3385] [3386] [3387] Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][][]\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.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18252--18262 [][]\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 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3388] Underfull \hbox (badness 3579) in paragraph at lines 18290--18295 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3389] Underfull \hbox (badness 3579) in paragraph at lines 18354--18359 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3390] Underfull \hbox (badness 3579) in paragraph at lines 18417--18422 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3391] Underfull \hbox (badness 1577) in paragraph at lines 18478--18480 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18480--18485 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3392] Underfull \hbox (badness 3579) in paragraph at lines 18543--18548 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18576--18585 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\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 18576--18585 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3393] Underfull \hbox (badness 3579) in paragraph at lines 18615--18620 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3394] [3395] Underfull \hbox (badness 1009) in paragraph at lines 18761--18770 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3396] [3397] Underfull \hbox (badness 1009) in paragraph at lines 18893--18902 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406]) (./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): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3407] 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,[] [3408] [3409] [3410] 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,[] [3411] 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)[] [3412] [3413] 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,[] [3414]) (./rpart-pkg.tex Chapter 27. [3415] [3416] [3417] [3418] 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, ...)[] [3419] [3420] [3421] [3422] 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 will be at the hor-i-zon-tal plot co-or-di-nates of [3423] [3424] Overfull \hbox (0.78088pt too wide) in paragraph at lines 738--738 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3425] [3426] [3427] Overfull \hbox (25.98041pt too wide) in paragraph at lines 914--914 []\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 933--933 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"),[] [3428] [3429] [3430] [3431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1179--1179 []\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 1180--1180 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2846) in paragraph at lines 1242--1244 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3432] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1286--1286 []\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 1302--1302 []\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 1303--1303 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3433] [3434] [3435] [3436] [3437] [3438] [3439] Underfull \hbox (badness 1565) in paragraph at lines 1759--1762 []\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 ', [3440] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1853--1853 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3441] [3442] [3443]) (./spatial-pkg.tex [3444] Chapter 28. [3445] [3446] [3447] [3448] [3449] [3450] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463]) (./survival-pkg.tex [3464] Chapter 29. [3465] [3466] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\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 190--190 []\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 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3467] [3468] Underfull \hbox (badness 6412) in paragraph at lines 282--284 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3469] [3470]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica te ignored \relax l.382 ... Myelogenous Leukemia survival data}{aml} [3471] Overfull \hbox (9.78043pt too wide) in paragraph at lines 483--483 []\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 485--485 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3472] Overfull \hbox (6.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3473] [3474] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3475] [3476] 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 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"),[] [3477] [3478] 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,[] [3479] [3480] [3481] 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[] [3482] [3483] 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) [3484] 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} [3485] Underfull \hbox (badness 10000) in paragraph at lines 1356--1360 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by 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, ...)[] [3486] [3487] [3488] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1575--1575 [] \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 1624--1624 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3489] [3490] [3491] [3492] [3493] Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 []\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 1940--1955 \T1/ptm/m/n/10 some cod-ing guides and prepend \T1/pcr/m/n/10 survival:: \T1/pt m/m/n/10 onto ev-er-thing, in-clud-ing the spe- Underfull \hbox (badness 10000) in paragraph at lines 1940--1955 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3494] Underfull \hbox (badness 1337) in paragraph at lines 2024--2028 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.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 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3495] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2079--2079 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2651--2651 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2678--2678 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3504] [3505] [3506] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2910--2910 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3507] [3508] [3509] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3510] [3511] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3251--3251 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3512] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3286--3286 [] \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 3300--3302 []\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 3311--3311 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3513] [3514] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3445--3445 [] \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 )))[] [3515] [3516] Overfull \hbox (467.89665pt too wide) in alignment at lines 3586--3586 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3517] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3518] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3708--3708 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3519] [3520] [3521] [3522] [3523] [3524] [3525] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4144--4144 [] \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 )))[] [3526] [3527] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4290--4290 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] [3528] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4295--4295 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4299--4299 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3529] [3530] [3531] Overfull \vbox (11.01616pt too high) has occurred while \output is active [3532] [3533] [3534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4716--4716 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3535] [3536] [3537] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4946--4946 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3538] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5072--5072 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3539] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5080--5080 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3540] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5166--5166 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5244--5244 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3542] Underfull \hbox (badness 1852) in paragraph at lines 5316--5318 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3543] [3544] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5441--5441 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3545] [3546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5543--5543 []\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 5544--5544 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3547] [3548] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5810--5810 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5831--5831 []\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 5833--5833 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3551] [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6348--6348 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3557] [3558] [3559] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6528--6528 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6540--6543 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3560] [3561] [3562] [3563] [3564] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6848--6848 []\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 6849--6849 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3565] [3566] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7014--7014 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3567] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7088--7088 []\T1/pcr/m/n/9 cdf <- cdf[!duplicated(aml$time[index], fromLast=TRUE)] # rem ove duplicates[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7092 ...ata from a soldering experiment}{solder} [3568] [3569] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7198--7198 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3570] [3571] [3572] [3573] [3574] [3575] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7562--7562 []\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 7563--7563 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3576] [3577] [3578] [3579] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7881--7881 [] \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 ),[] [3580] [3581] [3582] [3583] Underfull \hbox (badness 1253) in paragraph at lines 8170--8173 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8300--8300 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3586] Underfull \hbox (badness 10000) in paragraph at lines 8422--8431 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 8422--8431 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3587] [3588] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8518--8518 [] \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 8536--8536 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8578--8584 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3589] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8630--8630 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3590] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8716--8716 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 8941--8946 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3594] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8960--8960 [] \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 8961--8961 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3595] [3596] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9171--9171 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3597] [3598] Underfull \hbox (badness 3058) in paragraph at lines 9304--9309 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 9304--9309 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3599] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9434--9434 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3601] [3602] [3603] [3604] [3605] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9819--9819 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, Underfull \hbox (badness 1354) in paragraph at lines 9860--9864 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3606] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9906--9906 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3607] [3608] Underfull \hbox (badness 2035) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10070--10077 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 10070--10077 \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, it is [3609] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10150--10150 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3610] [3611] [3612] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10307--10307 [] \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 )[] [3613] [3614] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10439--10439 [] \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 10442--10442 [] \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 )[] [3615] [3616] [3617] [3618] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10751--10751 []\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 10752--10752 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10758--10758 [] \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 10760--10760 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3620] [3621] [3622] [3623] [3624] [3625] [3626] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11201--11201 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3627] [3628] [3629]) [3630] (./fullrefman.ind [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640] [3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] [3652] [3653] [3654] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2583--2585 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , [3655] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2585--2587 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2587--2589 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2589--2591 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2591--2593 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2593--2595 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2595--2597 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2597--2599 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2599--2601 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 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paragraph at lines 3236--3238 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 3238--3240 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3240--3242 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 3242--3244 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3244--3246 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3662] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3399--3401 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3663] [3664] [3665] [3666] [3667] [3668] [3669] [3670] [3671] Overfull \hbox (62.8567pt too wide) in paragraph at lines 4506--4508 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox 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paragraph at lines 4766--4768 []\T1/pcr/m/n/10 [<-,diagonalMatrix,missing,missing,ANY-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 4768--4770 []\T1/pcr/m/n/10 [<-,indMatrix,index,ANY,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4770--4772 []\T1/pcr/m/n/10 [<-,indMatrix,missing,index,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 4772--4774 []\T1/pcr/m/n/10 [<-,indMatrix,missing,missing,ANY-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 4774--4776 []\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,ANY,sparseMatrix-method Overfull \hbox (98.8567pt too wide) in paragraph at lines 4776--4778 []\T1/pcr/m/n/10 [<-,sparseMatrix,ANY,missing,sparseMatrix-method Overfull \hbox (98.8567pt too wide) in paragraph at lines 4778--4780 []\T1/pcr/m/n/10 [<-,sparseMatrix,missing,ANY,sparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 4780--4782 []\T1/pcr/m/n/10 [<-,sparseMatrix,missing,missing,ANY-method [3674] Overfull \hbox (104.8567pt too wide) in paragraph at lines 4782--4784 []\T1/pcr/m/n/10 [<-,sparseVector,index,missing,replValueSp-method Overfull \hbox (146.8567pt too wide) in paragraph at lines 4784--4786 []\T1/pcr/m/n/10 [<-,sparseVector,sparseVector,missing,replValueSp-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4866--4868 []\T1/pcr/m/n/10 %*%,CsparseMatrix,CsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4868--4870 []\T1/pcr/m/n/10 %*%,CsparseMatrix,ddenseMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 4870--4872 []\T1/pcr/m/n/10 %*%,CsparseMatrix,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 4874--4876 []\T1/pcr/m/n/10 %*%,CsparseMatrix,numLike-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 4892--4894 []\T1/pcr/m/n/10 %*%,TsparseMatrix,TsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 4900--4902 []\T1/pcr/m/n/10 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cbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7276--7278 []\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7278--7280 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3690] [3691] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7534--7536 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3692] [3693] Overfull \hbox (50.8567pt too wide) in paragraph at lines 8035--8037 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8037--8039 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8039--8041 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method [3694] Overfull \hbox (26.8567pt too wide) in paragraph at lines 8045--8047 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox 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in paragraph at lines 11633--11635 \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 , [3719] [3720] Overfull \hbox (56.8567pt too wide) in paragraph at lines 11975--11977 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11977--11979 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11979--11981 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11981--11983 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11983--11985 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 11985--11987 []\T1/pcr/m/n/10 forceSymmetric,dpoMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11987--11989 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[]\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14533--14535 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14535--14537 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 14537--14539 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14539--14541 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14541--14543 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method [3733] Overfull \hbox (26.8567pt too wide) in paragraph at lines 14543--14545 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14545--14547 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 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in paragraph at lines 17473--17475 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17477--17479 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17479--17481 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 17481--17483 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17501--17503 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method [3748] Overfull \hbox (38.8567pt too wide) in paragraph at lines 17503--17505 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17505--17507 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 17507--17509 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17511--17513 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17515--17517 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17519--17521 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method Overfull \hbox (46.01662pt too wide) in paragraph at lines 17727--17729 \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 , [3749] Overfull \hbox (77.3567pt too wide) in paragraph at lines 17755--17757 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3750] [3751] [3752] [3753] [3754] Overfull \hbox (46.01662pt too wide) in paragraph at lines 19060--19062 \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 19063--19065 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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(\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 19077--19079 \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 19079--19081 \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 19083--19085 \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 19085--19087 \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 (4.01662pt too wide) in paragraph at lines 19087--19089 \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 19089--19091 \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 19091--19093 \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 19093--19095 \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 , [3756] [3757] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19445--19447 \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 19519--19521 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3758] [3759] [3760] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19990--19992 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19999--20001 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20001--20003 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20003--20005 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20005--20007 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20017--20019 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20027--20029 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20042--20044 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20048--20050 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3761] Overfull \hbox (62.8567pt too wide) in paragraph at lines 20169--20171 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3762] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20383--20385 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20385--20387 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20387--20389 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20389--20391 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 20393--20395 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20395--20397 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20397--20399 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20399--20401 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20401--20403 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20403--20405 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20405--20407 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20411--20413 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20415--20417 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20425--20427 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method [3763] Overfull \hbox (8.8567pt too wide) in paragraph at lines 20429--20431 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20431--20433 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20433--20435 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20435--20437 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20437--20439 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20439--20441 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 20441--20443 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20470--20472 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20472--20474 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20474--20476 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20476--20478 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20480--20482 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20484--20486 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20488--20490 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20492--20494 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20496--20498 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20500--20502 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20504--20506 []\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method 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Schur,symmetricMatrix,missing-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21512--21514 []\T1/pcr/m/n/10 Schur,triangularMatrix,logical-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21514--21516 []\T1/pcr/m/n/10 Schur,triangularMatrix,missing-method [3769] [3770] Overfull \hbox (26.8567pt too wide) in paragraph at lines 21902--21904 []\T1/pcr/m/n/10 show,genericFunctionWithTrace-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 21906--21908 \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 21910--21912 []\T1/pcr/m/n/10 show,MethodDefinitionWithTrace-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 21914--21916 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21924--21926 []\T1/pcr/m/n/10 show,refClassRepresentation-method [3771] [3772] Overfull \hbox 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22196--22198 \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 22199--22203 []\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 22204--22206 \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 22252--22254 \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 (20.8567pt too wide) in paragraph at lines 22291--22293 []\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 22293--22295 []\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22295--22297 []\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method [3773] Overfull \hbox (2.8567pt too wide) in paragraph at lines 22305--22307 []\T1/pcr/m/n/10 solve,ddenseMatrix,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22307--22309 []\T1/pcr/m/n/10 solve,ddenseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 22309--22311 []\T1/pcr/m/n/10 solve,ddenseMatrix,missing-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 22311--22313 []\T1/pcr/m/n/10 solve,ddenseMatrix,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22315--22317 []\T1/pcr/m/n/10 solve,dgCMatrix,ddenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22317--22319 []\T1/pcr/m/n/10 solve,dgCMatrix,dsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22323--22325 []\T1/pcr/m/n/10 solve,dgeMatrix,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22329--22331 []\T1/pcr/m/n/10 solve,dgeMatrix,sparseMatrix-method Overfull \hbox (14.8567pt too wide) in 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22417--22419 []\T1/pcr/m/n/10 solve,Matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22419--22421 []\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22421--22423 []\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22423--22425 []\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22435--22437 []\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method Overfull \hbox (52.01662pt too wide) in paragraph at lines 22582--22584 \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 , [3775] [3776] Overfull \hbox (44.8567pt too wide) in paragraph at lines 23025--23027 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends Overfull \hbox (44.8567pt too wide) in paragraph at lines 23027--23029 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results Overfull \hbox (44.8567pt too wide) in paragraph at lines 23029--23031 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings [3777] [3778] [3779] [3780] [3781] Overfull \hbox (32.8567pt too wide) in paragraph at lines 23916--23918 []\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 23918--23920 []\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 23920--23922 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method [3782] Overfull \hbox (74.8567pt too wide) in paragraph at lines 23922--23924 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (86.8567pt too wide) in paragraph at lines 23924--23926 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 23926--23928 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,matrix-method Overfull 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tcrossprod,ddenseMatrix,lsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 23944--23946 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,matrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 23946--23948 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,missing-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 23948--23950 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,ndenseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 23950--23952 []\T1/pcr/m/n/10 tcrossprod,ddenseMatrix,nsCMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 23952--23954 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,dgeMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 23954--23956 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,diagonalMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 23956--23958 []\T1/pcr/m/n/10 tcrossprod,dgeMatrix,matrix-method Overfull \hbox (20.8567pt 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-4.1.3/src/library' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/src' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' installing R manuals in PDF format ... make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/doc/manual' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/doc/manual' make: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3' + 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-4.1 /usr/lib64/R/doc + ln -s ../../share/doc/R-4.1 /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/foreign/libs/foreign.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/KernSmooth/libs/KernSmooth.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/lattice/libs/lattice.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/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) Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.45652 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.1.3 + export TZ= + TZ= + make check make: Entering directory '/usr/src/RPM/BUILD/R-4.1.3' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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' ... OK 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-4.1.3/tests/Examples' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' running strict specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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 '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-4.1.3/tests' running sloppy specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' checking Sys.timezone ... make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' running code in 'timezone.R' ...make[4]: *** [Makefile.common:111: timezone.Rout] Error 1 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' Sys.timezone() appears unknown make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' running regression tests ... make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/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-4.1.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' running tests of Internet functions make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.1.3/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < 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, test http and ftp. > > > > 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 > > read.table("ftp://ftp.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-4.1.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3/tests' make: Leaving directory '/usr/src/RPM/BUILD/R-4.1.3' + exit 0 Processing files: R-base-4.1.3-alt1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.36930 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.1.3 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.1.3 + exit 0 warning: File listed twice: /usr/lib64/R/library/KernSmooth/html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html 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/usr/lib64/R/library/utils/html/maintainer.html warning: File listed twice: /usr/lib64/R/library/utils/html/make.packages.html.html warning: File listed twice: /usr/lib64/R/library/utils/html/make.socket.html warning: 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.M895dW find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,python3,shell,tcl,typelib) lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1295 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2022-05-13 01:11:30.956872333 +0000 +++ filter-provides-deps 2022-05-13 01:11:30.957872345 +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.HXMXhg find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,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 fgrep: warning: fgrep is obsolescent; using grep -F find-requires: FINDPACKAGE-COMMANDS: cat grep sh Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set:odjvQNYfHFGF6Xo9rSYpedZEKSBIIjA5am5Aozs2zTPMtECSL8v82ZxZ1wSiUTrcy7nNqGiflliOlRYkEVx3WbfE9EMjzuK8DfBqYQcAGSCUjhEWgFy7bjqYrcIhpemd39JgsUAEWlyvigzGsYEDY7RU0BduV21HBnLVs166Agm0wqBaOZ7QMXrtCqjPpLZlVF5MyudrnpP6spQVgufJGBNYBKgdNBT6oZAsw9aaqOHEnB223TLF9SD7vFOvsFy2WSgly51YPRTia82U8m3T8UVVsicquR30lOBHSdZbK0oOr42ikaNO8qMDqrMqi0uEqjGkcECmkbLpzWU07KcMFZshih0Y6E9D7Q3sUVyIXGSKHZnsn2MWmyvL1UwIIEdwUgMkJEJZzbrO0Gf6mSh3Gp4chaB6ZBSNxEBzQfo88MQNemMl5Vt7KTCYyY9GpkEApkZ0Sz5BY7sZtggK1s9I2O5fbrxZD2N1MmwiZEPvpCC4E6hVwPPNKtk5Z54WqF8IIn6OpFgx9iGMhuOZ9pYbIddk4Y0aLn19nimTu0LddCZCycnoIBi1r9TC7h8ZmccJLISk6aCoFpqQJ3iFKgSntpZk034k2flyTmfYyYLy30mTX4t1ZAsmGC2rkqqxsA7IWLCDDDcu0FCg1AaW4kq0KP0U91sLtX4mNCj89TSDWo5lC5t2rcS2qunxQqytYaTyPiUPSgdUvaWcQrIfWakfXYef4Iw40nPKHzryyBdOtTAwzgqgskhonz60wMdtMRy1PP1Ud2ZuGXGZHZb9HIuB0g7zQojkh0nT44gke8dPq84aawne4PvcZCksRBipPGMBHAb9fZm6TAXkl29yP0rQOSnjijeePeqEsvdkAuMij9Z3gnAhxzzBZkkuRTUgjuHRjXrw8pyTG8ihTY1ggShVqV79meEJ4XzXCo3uAn63fxRxkUDXRXq3mlfCUhB0qAzX0TZwMMzHrX8OF90AlCtZ0ZEkgY5ZHo2h7RVr54iYtw8f8YYCxm270aLGupEiTDQf1VOxBBHx4c5Q33OTyFJLuw8epTGv9cIjnWTax6KrqqSle6flfZreOdGZ0EnwmSxv0RKgVeSYK6jSFAimnyr11EvEgpX2jBX3ytPIc7FiN8r44OoFjpja3gNiQQObZ68g453AU6RW8MyAwZqZ5JV793F9oQoi2VS3l6wvvWZkngZG4oO4mwooIzBjCyvicnaMsAMdgbh9288gZuZfZ64H05npa53dj0S5ydzjoaLEtW0UxADMGnh1BjZiNUtCgCZvhLy29aZcIjhPwKo75Z5g3ObTxx3NrhVUCxnDaPKZaTi638zOeZpi6h236FMiYQitYIZdiBNlWDv848tgYvP9ozYGMZjcejtGZvPFuWhEZG5XOCZceXmTzLsNw1FQh66H8Zh9M5P39eonFp9LpbBKXUL3g6w3d2tFja4jx4MJVBQpBUS6dkPH6ZemnpbvloyjFL2GDY5kiIHZtNB5gvtI4OM1ZzTGQXsCaUSR8gM0WOoRL9kJVOIsodv0YizyDi4e8gaPIbbm3GM9KYMk02FJOUtnFu1QT4763GOV9WuL34UZignmjOXBKaEDs6EV2gFN3TzWOJdZnnkUrY6L7frBHKPTdBckoIiH8csCt9KibguLiGia8VWQxsVaW8ajVgU0alYN7ys8hT32e21y1JTHx5xo4mjgUee3q8fKW7gwqZCEW99lEHcCJlr7QJh0kNwTSDYz1EUosdxRA32kMMcz4qVQ8Jb2Xz74Nj2h32oRoZiwKUH2KFg7lMPwu6vhtp7knaPgTpu5taTaZiCroA0Ka94U1WycQhZ2nL9aqclymCa9sBwWkeKr58Mafp4AwFvZedcxjtdVW7W2R6leEp1GPJxAz80ZkjsdtshhmoK3nAZDwIxteCCNvvasBscr8HsPvWrjBBf21kQw0xe61mmulBx4CKXByWoOx4kKcS9ZA7MUN0oZpqnqx2sV4vcBscXgInpx79dDHzpk2p7jMmJRNY7x3mM8gB3SjXJvkzLSguomVMRZi9aVN0nVhztCjiz3pawembJtAnybaMRchkLktLNKu2s6A7o6wVrkiSx6V4miEWrDTZhcNQkPu8QvPjSLcoPdf4KFu3CioZbt6DI5FOWm4zkrdhmMnf1Qv6e1VyM0aQr1dMOkNhGRYhO0PYZBBxIcPlfJy1wqNQmSZ3esm0qb8enWILVWmQDqTxSUf47Vs84xa40En0XhSh97W6eEhzF3OrBNnvvT0i8KdqzgxdnIcimTXt5CZ3dvQC2h1I85b0v0BSBZexfP0hLaiZpf9puNNt0yXLOVZ2usws4TlYqwtRqYIfpPFlTJZkb9ZrBF9S4J4TiTwJrZlruB9y5fwPVRqvVjJGKoGatTEfCLktajpyuC4QQN79ww0WMjuhTnjPtZLl86HhfcZ0PZI5ddVYumbCCz1uMJVI06W3cO6F9Jh0TZjkU1FCmwLVGcc9K9bztmC3r24ehtRf5Y9VxnJRyQGgiepzvZCAZ1aH6teSI0ZsFPZ6UKSmwQvCas26o93fiODiDwDVRFeVB5WuW7jblddf4Shj4a6w0ZJ3spLl2XoTdaiRVdddyqnjXSCHrFJf5PG0QWJzLj1b6KxRkpC6wcXfkQW0vft4TXu36M7fgN0 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_2.4)(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:mfatAp2k43cHoHyudAXK6A5F12upHNitAtSyj6bqmc5NZhw8di3ADFaa0WDvXke2GF9Ko5FZtiv406UMaswPMPapezOZ9VVAUf0aOlY6sB5wsWkcviWdq0OZle0zzA8T8iZ4ZnO5SGudBdEgBn7o7QA0ppQr8ZbSfBHsIYjmCwbO0dKIPFkZJzZtP, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, 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.71()(64bit) >= set:roCpJBMwdsu788poSGzU5Cmz3, libicuuc.so.71()(64bit) >= set:pmEZ8SeITDT3zrQK0, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITkXeYooZo0Vt8WFt6QYIOIZmWow6fzRMDwp9MGO0mKS7RhQ3GVqZb9tmpDVzoHaQByPHyhixGdIIpkSTvJQ1ifnZkTXQSQh1gp2EYbdIC9EweDuafV2FMlA13g1MukRM6QdwV1AkslhaI00W830w1g7el, 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), libopenblas.so.0()(64bit) >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQCfq9fPhNQgw41BExdcI9mdt, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre2-8.so.0()(64bit) >= set:kfq9tJAJZakapZcr8gHlRiHX2PuBva483hqVseVZw6HMZF1, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libreadline.so.7()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPRdDv8sK6EUfgoB1, 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.wa3tfQ Creating R-base-debuginfo package Processing files: R-full-4.1.3-alt1 Requires: R-devel = 4.1.3-alt1, R-tcltk = 4.1.3-alt1, R-doc-html = 4.1.3-alt1, gcc-c++, gcc-fortran, liblapack-devel, make Processing files: R-devel-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.fLOMNJ 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,maven,osgi-fc,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.rV2qRj find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,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) = 4.1.3 Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils Requires(pre): R-base = 4.1.3-alt1 Requires(postun): R-base = 4.1.3-alt1 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.UMIP4B Processing files: R-tcltk-4.1.3-alt1 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.xIfWLh find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,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.SfCqul find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,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 = 4.1.3-alt1, 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_2.4)(64bit), libc.so.6(GLIBC_2.7)(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.Jdv0Zr Creating R-tcltk-debuginfo package Processing files: R-doc-html-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.6Qs7cl find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,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.xxk2XV find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: R-base = 4.1.3-alt1, xdg-utils Processing files: R-doc-pdf-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.dyUxPC find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,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.YrcmBe find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: xdg-utils Conflicts: R-base > 4.1.3, R-base < 4.1.3 Processing files: R-doc-info-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.4rwy1m find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,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.5aJvWH find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 4.1.3, R-base < 4.1.3 Processing files: R-base-debuginfo-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.aADVoD 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.aEl0bO find-requires: running scripts (debuginfo) Provides: debug64(libR.so) Requires: R-base = 4.1.3-alt1, /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.71), debug64(libicuuc.so.71), 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.7), debug64(libtiff.so.5), debug64(libz.so.1) Processing files: R-tcltk-debuginfo-4.1.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.KhWspZ find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.mpq1qa find-requires: running scripts (debuginfo) Requires: R-tcltk = 4.1.3-alt1, 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-4.1.3/include/R_ext also prunning dir /usr/src/debug/R-4.1.3/src/include also prunning dir /usr/src/debug/R-4.1.3/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-4.1.3-alt1.x86_64.rpm (w2T16.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-full-4.1.3-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-4.1.3-alt1.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-4.1.3-alt1.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-4.1.3-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-4.1.3-alt1.noarch.rpm (w2T16.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-4.1.3-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-4.1.3-alt1.x86_64.rpm (w2T16.xzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-4.1.3-alt1.x86_64.rpm (w2.lzdio) 938.97user 151.82system 11:24.74elapsed 159%CPU (0avgtext+0avgdata 681676maxresident)k 0inputs+0outputs (0major+22344833minor)pagefaults 0swaps 1044.61user 186.14system 13:42.35elapsed 149%CPU (0avgtext+0avgdata 681676maxresident)k 1459600inputs+0outputs (30851major+27028591minor)pagefaults 0swaps --- R-base-4.1.3-alt1.x86_64.rpm.repo 2022-04-19 07:46:10.000000000 +0000 +++ R-base-4.1.3-alt1.x86_64.rpm.hasher 2022-05-13 01:12:31.711611842 +0000 @@ -13079,3 +13079,3 @@ File: /usr/lib64/R/library/KernSmooth 40755 root:root -File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root d3bd733a644c3f4d4806e5205aa8524e +File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root 5e2e6804659fc811d6fce2f2087baa20 File: /usr/lib64/R/library/KernSmooth/INDEX 100644 root:root 56080cdf3d21fa33a8cae73825b9ef9f @@ -13087,3 +13087,3 @@ File: /usr/lib64/R/library/KernSmooth/Meta/nsInfo.rds 100644 root:root dfa2fbeabc5045c8194ef7c5eb2c1089 -File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 7ce5c92769841d9a6fb4cf266ffa244c +File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 5f1fc6dbba3270abe31985a6012e3f19 File: /usr/lib64/R/library/KernSmooth/NAMESPACE 100644 root:root a93c919c53d25488f67acbe057fff7ed @@ -13095,4 +13095,4 @@ File: /usr/lib64/R/library/KernSmooth/help/AnIndex 100644 root:root 000e790525eb6d551fc2a2f3edd1f6d1 -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root 97e205f2fff8cccc7d02010186c97b0f -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root ce79d4941ac3dbb8612d25f27235f20b +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root c1ec7dd84e908e8a194267e5d77e42c3 +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root b5f3b8f1b97e965464629971495f8f27 File: /usr/lib64/R/library/KernSmooth/help/aliases.rds 100644 root:root ab44920ce8df2c6ef29bb0353e5261f0 @@ -13105,3 +13105,3 @@ File: /usr/lib64/R/library/KernSmooth/help/locpoly.html 100644 root:root c10703a022e65b781a7a6849a5cbb727 -File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root 73540d1a1968f039f2a858729d2a2146 +File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root 5835a108f7e78fedcb0a0633f161e845 File: /usr/lib64/R/library/KernSmooth/html 40755 root:root @@ -13117,3 +13117,3 @@ File: /usr/lib64/R/library/KernSmooth/libs 40755 root:root -File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root cdb33c2e64f56438899f84a43a67a426 +File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root 930688be1ade58ee773fd58163cab157 File: /usr/lib64/R/library/KernSmooth/po 40755 root:root @@ -13139,3 +13139,3 @@ File: /usr/lib64/R/library/MASS/CITATION 100644 root:root b712abcbf880df8140a6ba49b039db53 -File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 756126eb96b3f60cd80c37ccc5093054 +File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 9df1014c6f3b11b716603c9e4de6117f File: /usr/lib64/R/library/MASS/INDEX 100644 root:root 35aff05a505ecf7e81e0473767794ca9 @@ -13148,3 +13148,3 @@ File: /usr/lib64/R/library/MASS/Meta/nsInfo.rds 100644 root:root 7be8089565aee453bbdd981d3f58c748 -File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root f36a6c39e62acdae24288df3d47bac9d +File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root 5647b9182a92c31277756cb683923e3c File: /usr/lib64/R/library/MASS/NAMESPACE 100644 root:root 0ac7b30ad35a4c19ea69d76a6a366b02 @@ -13173,4 +13173,4 @@ File: /usr/lib64/R/library/MASS/help/MASS-internal.html 100644 root:root 688a8433a0ec233bc0f5d25e876e5a31 -File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root b5d7ca2bf6f482a006e66be9bca5e520 -File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root a1355733720509721fe2bfd575018430 +File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root e479f0856dafe2f71fd0046800cc7c33 +File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root 05011d79a00c9720bc7823d5c0c88fd0 File: /usr/lib64/R/library/MASS/help/Math.fractions.html 100644 root:root dfec13cc11c9dc49afbb5e2785371f6d @@ -13339,3 +13339,3 @@ File: /usr/lib64/R/library/MASS/help/parcoord.html 100644 root:root 04cd37ded90b52f0232b3b763c6b21f3 -File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root e41cf29fe8aa5ba3b05a9cfc7ea6037e +File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root 4e006a8167de5e3f78fccc912d1f4d84 File: /usr/lib64/R/library/MASS/help/petrol.html 100644 root:root 511f9185ce2d63254c488e36cbaba1b9 @@ -13578,3 +13578,3 @@ File: /usr/lib64/R/library/MASS/libs 40755 root:root -File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root 4f19368bbc1705774f0fbeeb0c988184 +File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root 1df436cdc15a85e69095b223bb55ab09 File: /usr/lib64/R/library/MASS/po 40755 root:root @@ -13617,3 +13617,3 @@ File: /usr/lib64/R/library/Matrix/Copyrights 100644 root:root 8734f0b040c6292983d273d4251d250a -File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root ce19fa96062fb6853e7ac5d633c37044 +File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root 87303f0e61c9ca216aba6e2d6b6f050e File: /usr/lib64/R/library/Matrix/Doxyfile 100644 root:root cb641eb46a4b4f459f4da4c67f99690a @@ -13628,3 +13628,3 @@ File: /usr/lib64/R/library/Matrix/Meta/nsInfo.rds 100644 root:root 40aa5d74ae068a1247958134bfbbbb22 -File: /usr/lib64/R/library/Matrix/Meta/package.rds 100644 root:root 10e9f132bf1599960dce5a142b2cfc16 +File: /usr/lib64/R/library/Matrix/Meta/package.rds 100644 root:root b20a7afa0ffe5e8fa26caeaa02d20633 File: /usr/lib64/R/library/Matrix/Meta/vignette.rds 100644 root:root 9baa97c36e41dcf59a5dd2c552de3ca7 @@ -14197,4 +14197,4 @@ File: /usr/lib64/R/library/Matrix/help/Matrix.html 100644 root:root 9c8c7c2944cc346c31e9594d81a4ed26 -File: /usr/lib64/R/library/Matrix/help/Matrix.rdb 100644 root:root 03d8540a60e33e39c3fbc80a09c1b3a2 -File: /usr/lib64/R/library/Matrix/help/Matrix.rdx 100644 root:root ede6cb91e29a0820d601fa9afcb27f80 +File: /usr/lib64/R/library/Matrix/help/Matrix.rdb 100644 root:root f11939c3503a1ea90b47c1829c0aa2d4 +File: /usr/lib64/R/library/Matrix/help/Matrix.rdx 100644 root:root 658295ad094d40a0d493f659f57cdf9f File: /usr/lib64/R/library/Matrix/help/MatrixClass.html 100644 root:root fc89f983620c1eb753e433b70beec6e2 @@ -15473,3 +15473,3 @@ File: /usr/lib64/R/library/Matrix/help/pack.html 100644 root:root b8e20439f64c1313096b4a4059cf1aa1 -File: /usr/lib64/R/library/Matrix/help/paths.rds 100644 root:root 28a465039a41435993a798eacb6c68eb +File: /usr/lib64/R/library/Matrix/help/paths.rds 100644 root:root 262ef3ee5704a4b93c47ef1e37f2ff93 File: /usr/lib64/R/library/Matrix/help/print+2CdiagonalMatrix-method.html 100644 root:root d46da5d3c8e3fcc4dba1786247143503 @@ -16090,3 +16090,3 @@ File: /usr/lib64/R/library/Matrix/libs 40755 root:root -File: /usr/lib64/R/library/Matrix/libs/Matrix.so 100644 root:root 08b37f36d6097d3deae079f33e9acb34 +File: /usr/lib64/R/library/Matrix/libs/Matrix.so 100644 root:root 95a9d7f1111c2cef65acb2637c6ea33e File: /usr/lib64/R/library/Matrix/po 40755 root:root @@ -16125,3 +16125,3 @@ File: /usr/lib64/R/library/base/CITATION 100644 root:root 16a31abf39268631f20e1478bf64d659 -File: /usr/lib64/R/library/base/DESCRIPTION 100644 root:root 8355817d28699a42a54c3c9decdbcd28 +File: /usr/lib64/R/library/base/DESCRIPTION 100644 root:root c429ea00e51309545cdb757dd2a38cea File: /usr/lib64/R/library/base/INDEX 100644 root:root 5f0e1788d064f11a593fd194133e8162 @@ -16133,3 +16133,3 @@ File: /usr/lib64/R/library/base/Meta/links.rds 100644 root:root bd1ba68973d15b7a0f81e78b32e2115e -File: /usr/lib64/R/library/base/Meta/package.rds 100644 root:root 7e375776fc196aef03e0977a2bd842ff +File: /usr/lib64/R/library/base/Meta/package.rds 100644 root:root 83e50c05307dfe807e71f803801fc650 File: /usr/lib64/R/library/base/R 40755 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