<86>Apr 30 10:51:36 userdel[4084824]: delete user 'rooter' <86>Apr 30 10:51:36 userdel[4084824]: removed group 'rooter' owned by 'rooter' <86>Apr 30 10:51:36 userdel[4084824]: removed shadow group 'rooter' owned by 'rooter' <86>Apr 30 10:51:36 groupadd[4084829]: group added to /etc/group: name=rooter, GID=615 <86>Apr 30 10:51:36 groupadd[4084829]: group added to /etc/gshadow: name=rooter <86>Apr 30 10:51:36 groupadd[4084829]: new group: name=rooter, GID=615 <86>Apr 30 10:51:36 useradd[4084833]: new user: name=rooter, UID=615, GID=615, home=/root, shell=/bin/bash <86>Apr 30 10:51:36 userdel[4084839]: delete user 'builder' <86>Apr 30 10:51:36 userdel[4084839]: removed group 'builder' owned by 'builder' <86>Apr 30 10:51:36 userdel[4084839]: removed shadow group 'builder' owned by 'builder' <86>Apr 30 10:51:36 groupadd[4084844]: group added to /etc/group: name=builder, GID=616 <86>Apr 30 10:51:36 groupadd[4084844]: group added to /etc/gshadow: name=builder <86>Apr 30 10:51:36 groupadd[4084844]: new group: name=builder, GID=616 <86>Apr 30 10:51:36 useradd[4084848]: new user: name=builder, UID=616, GID=616, home=/usr/src, shell=/bin/bash warning: Macro %add_tcl_lib_path not found <13>Apr 30 10:51:47 rpmi: libpng16-1.6.37-alt1 sisyphus+236677.100.2.1 1566917998 installed <13>Apr 30 10:51:47 rpmi: libjpeg-2:2.0.6-alt1 sisyphus+266888.100.1.1 1614172387 installed <13>Apr 30 10:51:47 rpmi: xorg-proto-devel-2020.1-alt1 sisyphus+250406.100.1.1 1587554810 installed <13>Apr 30 10:51:47 rpmi: libexpat-2.2.10-alt1 sisyphus+259966.100.1.1 1602824518 installed <13>Apr 30 10:51:47 rpmi: libglvnd-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:47 rpmi: perl-HTTP-Date-6.05-alt1 sisyphus+258981.100.1.1 1601542386 installed <13>Apr 30 10:51:47 rpmi: libICE-1.0.10-alt1 sisyphus+247690.100.1.1 1584000387 installed <13>Apr 30 10:51:47 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586158 installed <13>Apr 30 10:51:47 rpmi: tex-common-0.2-alt4 1244804096 installed <13>Apr 30 10:51:47 rpmi: perl-Unicode-Normalize-1:5.30.3-alt1 sisyphus+259030.200.1.1 1601554162 installed <13>Apr 30 10:51:47 rpmi: perl-Term-ANSIColor-5.01-alt1 sisyphus+244783.100.1.2 1579747505 installed <13>Apr 30 10:51:47 rpmi: libpaper-1.1.28-alt1 sisyphus+259176.100.1.1 1601738993 installed <13>Apr 30 10:51:47 rpmi: libidn2-2.3.0-alt1 sisyphus+240846.100.1.2 1573870475 installed <13>Apr 30 10:51:48 rpmi: libicu67-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796126 installed <13>Apr 30 10:51:48 rpmi: libgraphite2-1.3.14-alt2 sisyphus+250009.100.1.1 1586943065 installed <13>Apr 30 10:51:48 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520843 installed <13>Apr 30 10:51:48 rpmi: rpm-macros-info-install-6.7-alt1 sisyphus+262609.100.1.1 1606438100 installed <13>Apr 30 10:51:49 rpmi: libopenblas-0.3.9-alt1 sisyphus+238855.200.5.1 1593950422 installed <13>Apr 30 10:51:49 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550601058 installed <13>Apr 30 10:51:49 rpmi: liblksctp-1.0.17-alt2 1523113261 installed <13>Apr 30 10:51:49 rpmi: javapackages-filesystem-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed <13>Apr 30 10:51:49 rpmi: javapackages-tools-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed <13>Apr 30 10:51:49 rpmi: libnspr-1:4.30-alt1 sisyphus+268304.100.1.1 1616591582 installed <13>Apr 30 10:51:49 rpmi: libpixman-3:0.40.0-alt1 sisyphus+250700.100.1.1 1587971055 installed <13>Apr 30 10:51:49 rpmi: libwayland-server-1.19.0-alt1 sisyphus+265427.100.1.1 1611852858 installed <13>Apr 30 10:51:49 rpmi: libtcl-8.6.11-alt1 sisyphus+264361.140.8.1 1610711374 installed <13>Apr 30 10:51:49 rpmi: tcl-8.6.11-alt1 sisyphus+264361.140.8.1 1610711374 installed <13>Apr 30 10:51:49 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed <13>Apr 30 10:51:49 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed <13>Apr 30 10:51:49 rpmi: perl-Tie-RefHash-1.40-alt1 sisyphus+260329.100.1.1 1603548550 installed <13>Apr 30 10:51:49 rpmi: perl-IO-Socket-IP-0.41-alt1 sisyphus+259012.100.1.2 1601553446 installed <13>Apr 30 10:51:49 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed <13>Apr 30 10:51:49 rpmi: perl-Compress-Raw-Zlib-2.101-alt1 sisyphus+266765.100.1.2 1614138847 installed <13>Apr 30 10:51:49 rpmi: perl-libnet-1:3.13-alt1 sisyphus+266120.100.1.1 1612961310 installed <13>Apr 30 10:51:49 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed <13>Apr 30 10:51:49 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268152 installed <13>Apr 30 10:51:49 rpmi: libwebp7-1.2.0-alt1 sisyphus+265504.100.2.1 1612122046 installed <13>Apr 30 10:51:49 rpmi: libjbig-2.1-alt1 1401380926 installed <13>Apr 30 10:51:49 rpmi: libtiff5-4.2.0-alt1 sisyphus+266365.100.2.1 1613478695 installed <13>Apr 30 10:51:49 rpmi: libopenjpeg2.0-2.4.0-alt2 sisyphus+270166.100.1.1 1618663540 installed <13>Apr 30 10:51:49 rpmi: libnettle8-3.7.2-alt1 sisyphus+268184.100.1.1 1616430275 installed <13>Apr 30 10:51:49 rpmi: libquadmath0-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:49 rpmi: libgfortran5-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:49 rpmi: libgdbm-1.8.3-alt10 1454943334 installed <13>Apr 30 10:51:49 rpmi: libp11-kit-0.23.15-alt2 sisyphus+252784.100.2.2 1591274901 installed <13>Apr 30 10:51:49 rpmi: libtasn1-4.16.0-alt1 sisyphus+245480.100.1.1 1580825062 installed <13>Apr 30 10:51:49 rpmi: libgdbm-devel-1.8.3-alt10 1454943334 installed <13>Apr 30 10:51:50 rpmi: perl-devel-1:5.30.3-alt1 sisyphus+259030.200.1.1 1601554162 installed <13>Apr 30 10:51:50 rpmi: libquadmath10-devel-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:50 rpmi: libhogweed6-3.7.2-alt1 sisyphus+268184.100.1.1 1616430275 installed <13>Apr 30 10:51:50 rpmi: libgnutls30-3.6.15-alt2 sisyphus+268189.200.4.1 1616495163 installed <13>Apr 30 10:51:50 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268152 installed <13>Apr 30 10:51:50 rpmi: perl-autodie-2.34-alt1 sisyphus+265208.100.1.1 1611567479 installed <13>Apr 30 10:51:50 rpmi: perl-OLE-Storage_Lite-0.20-alt1 sisyphus+243912.100.1.1 1578493389 installed <13>Apr 30 10:51:50 rpmi: java-common-1.6.0-alt1 sisyphus+234020.100.1.1 1562437039 installed <13>Apr 30 10:51:50 rpmi: lksctp-tools-1.0.17-alt2 1523113261 installed <13>Apr 30 10:51:50 rpmi: libpng-devel-1.6.37-alt1 sisyphus+236677.100.2.1 1566917998 installed <13>Apr 30 10:51:50 rpmi: libopenblas-devel-0.3.9-alt1 sisyphus+238855.200.5.1 1593950422 installed <13>Apr 30 10:51:50 rpmi: libgraphite2-devel-1.3.14-alt2 sisyphus+250009.100.1.1 1586943065 installed <13>Apr 30 10:51:50 rpmi: icu-utils-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796126 installed <13>Apr 30 10:51:50 rpmi: libicu-devel-1:6.7.1-alt2 sisyphus+252432.100.2.2 1590796126 installed <13>Apr 30 10:51:50 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed <13>Apr 30 10:51:50 rpmi: perl-unicore-1:5.30.3-alt1 sisyphus+259030.200.1.1 1601554015 installed <13>Apr 30 10:51:50 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+258375.3200.14.3 1600987090 installed <13>Apr 30 10:51:50 rpmi: libICE-devel-1.0.10-alt1 sisyphus+247690.100.1.1 1584000387 installed <13>Apr 30 10:51:50 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586158 installed <13>Apr 30 10:51:50 rpmi: perl-File-Listing-6.14-alt1 sisyphus+262735.100.1.1 1606813544 installed <13>Apr 30 10:51:50 rpmi: libOpenGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:50 rpmi: libGLES-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:50 rpmi: libjasper-2.0.28-alt1 sisyphus+269002.100.1.1 1617642400 installed <13>Apr 30 10:51:50 rpmi: rpm-build-tcl-0.6.1-alt1 sisyphus+264761.20.4.1 1610806524 installed <13>Apr 30 10:51:50 rpmi: tcl-devel-8.6.11-alt1 sisyphus+264361.140.8.1 1610711374 installed <13>Apr 30 10:51:50 rpmi: rpm-macros-java-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed <13>Apr 30 10:51:50 rpmi: perl-Algorithm-Diff-1:1.201-alt1 sisyphus+263447.100.1.1 1607956595 installed <13>Apr 30 10:51:50 rpmi: perl-Unicode-EastAsianWidth-12.0-alt1 sisyphus+237401.100.1.1 1568197363 installed <13>Apr 30 10:51:50 rpmi: lua5.3-5.3.5-alt3 sisyphus+237725.540.7.3 1569407869 installed <13>Apr 30 10:51:50 rpmi: libtre5-0.8.0-alt2.2 sisyphus+249319.100.1.1 1585933008 installed <13>Apr 30 10:51:50 rpmi: libpcre2-10.36-alt1 sisyphus+262985.100.2.1 1607423140 installed <13>Apr 30 10:51:51 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388786 installed <13>Apr 30 10:51:51 rpmi: liblapack-1:3.8.0-alt4 sisyphus+264284.100.1.1 1609587717 installed <13>Apr 30 10:51:51 rpmi: libgomp1-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:51 rpmi: libpcsclite-1.9.0-alt1 sisyphus+253463.100.1.1 1592202070 installed <13>Apr 30 10:51:51 rpmi: javazi-2021a-alt1 sisyphus+265526.200.1.1 1612068684 installed <13>Apr 30 10:51:51 rpmi: libgif-4.1.6-alt3 1299634261 installed <13>Apr 30 10:51:51 rpmi: libgtk+2-locales-2.24.33-alt1 sisyphus+263711.100.20.1 1609407991 installed <13>Apr 30 10:51:51 rpmi: libdatrie-0.2.9-alt1_6 1511686676 installed <13>Apr 30 10:51:51 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed <13>Apr 30 10:51:51 rpmi: libfribidi-1.0.10-alt1 sisyphus+254557.100.1.1 1594020362 installed <13>Apr 30 10:51:51 rpmi: libatk-locales-2.36.0-alt1 sisyphus+249208.100.1.1 1585840405 installed <13>Apr 30 10:51:51 rpmi: libatk-2.36.0-alt1 sisyphus+249208.100.1.1 1585840406 installed <13>Apr 30 10:51:51 rpmi: icon-theme-hicolor-0.17-alt2 sisyphus+248343.100.1.1 1584979043 installed <13>Apr 30 10:51:51 rpmi: libkpathsea6-2019-alt2_7 sisyphus+266579.700.4.2 1614138684 installed <13>Apr 30 10:51:51 rpmi: libptexenc1-2019-alt2_7 sisyphus+266579.700.4.2 1614138684 installed <13>Apr 30 10:51:51 rpmi: libsynctex2-2019-alt2_7 sisyphus+266579.700.4.2 1614138684 installed <13>Apr 30 10:51:52 rpmi: libtexlua5-2019-alt2_7 sisyphus+266579.700.4.2 1614138684 installed <13>Apr 30 10:51:52 rpmi: zziplib-0.13.72-alt1 sisyphus+266579.140.4.2 1614137009 installed <13>Apr 30 10:51:52 rpmi: libsqlite3-3.35.5-alt1 sisyphus+270436.100.1.1 1619019903 installed <13>Apr 30 10:51:52 rpmi: liblcms2-2.12-alt1 sisyphus+265911.100.2.1 1613037796 installed <13>Apr 30 10:51:52 rpmi: publicsuffix-list-dafsa-20210419-alt1 sisyphus+270358.100.1.1 1618924010 installed <13>Apr 30 10:51:52 rpmi: libpsl-0.21.1-alt1 sisyphus+255206.100.1.1 1595348938 installed <13>Apr 30 10:51:52 rpmi: libnghttp2-1.41.0-alt1 sisyphus+253680.100.1.1 1592642271 installed <13>Apr 30 10:51:52 rpmi: openldap-common-2.4.57-alt1 sisyphus+266287.100.1.1 1613244218 installed <13>Apr 30 10:51:52 rpmi: libverto-0.3.2-alt1_1 sisyphus+268398.100.1.1 1616717462 installed <13>Apr 30 10:51:52 rpmi: liblmdb-0.9.23-alt1 sisyphus+225277.100.2.1 1553001679 installed <13>Apr 30 10:51:52 rpmi: libkeyutils-1.6.3-alt1 sisyphus+266061.100.1.1 1612919567 installed <13>Apr 30 10:51:52 rpmi: libcom_err-1.45.6.0.24.af1a-alt1 sisyphus+262279.100.1.1 1606088229 installed <13>Apr 30 10:51:52 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed <13>Apr 30 10:51:52 rpmi: libnuma-2.0.14-alt2 sisyphus+262152.100.1.1 1605821057 installed <13>Apr 30 10:51:52 rpmi: libx265-199-3.5-alt1 sisyphus+270617.300.3.1 1619587083 installed <13>Apr 30 10:51:52 rpmi: shared-mime-info-2.1-alt1 sisyphus+264261.100.1.1 1609507723 installed <13>Apr 30 10:51:52 rpmi: gsettings-desktop-schemas-data-40.0-alt1 sisyphus+268501.300.4.2 1617041783 installed <13>Apr 30 10:51:52 rpmi: libgio-2.68.1-alt1 sisyphus+269248.100.1.1 1617921065 installed <13>Apr 30 10:51:52 rpmi: gsettings-desktop-schemas-40.0-alt1 sisyphus+268501.300.4.2 1617041559 installed <13>Apr 30 10:51:52 rpmi: libgdk-pixbuf-locales-2.42.6-alt1 sisyphus+269312.100.1.1 1617990309 installed <13>Apr 30 10:51:52 rpmi: libgdk-pixbuf-2.42.6-alt1 sisyphus+269312.100.1.1 1617990316 installed <13>Apr 30 10:51:53 rpmi: gtk-update-icon-cache-3.24.29-alt1 sisyphus+270517.100.1.1 1619154827 installed <13>Apr 30 10:51:53 rpmi: libde265-1.0.7-alt1 sisyphus+258615.100.1.1 1600957231 installed <13>Apr 30 10:51:53 rpmi: libaom2-2.0.2-alt1 sisyphus+267934.100.2.1 1615993478 installed <13>Apr 30 10:51:53 rpmi: libheif-1.11.0-alt1 sisyphus+270617.1000.4.1 1619590693 installed <13>Apr 30 10:51:53 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268571 installed <13>Apr 30 10:51:53 rpmi: libwayland-client-1.19.0-alt1 sisyphus+265427.100.1.1 1611852858 installed <13>Apr 30 10:51:53 rpmi: libpciaccess-1:0.16-alt1 sisyphus+234814.100.1.1 1563438291 installed <13>Apr 30 10:51:53 rpmi: libdrm-1:2.4.105-alt1 sisyphus+269183.100.1.1 1617867189 installed <13>Apr 30 10:51:53 rpmi: libgbm-4:21.0.2-alt1 sisyphus+269183.200.1.1 1617867532 installed <13>Apr 30 10:51:53 rpmi: t1utils-1.42-alt1 sisyphus+260603.100.1.1 1603963795 installed <13>Apr 30 10:51:53 rpmi: libqqwing-1.3.4-alt2 1436192940 installed <13>Apr 30 10:51:53 rpmi: qqwing-1.3.4-alt2 1436192940 installed <13>Apr 30 10:51:53 rpmi: perl-Unicode-Map-0.112-alt8 sisyphus+258728.100.1.1 1601155592 installed <13>Apr 30 10:51:53 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed <13>Apr 30 10:51:53 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed <13>Apr 30 10:51:53 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed <13>Apr 30 10:51:53 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed <13>Apr 30 10:51:53 rpmi: perl-IPC-System-Simple-1.30-alt1 sisyphus+248544.100.1.1 1585154078 installed <13>Apr 30 10:51:53 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>Apr 30 10:51:53 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>Apr 30 10:51:53 rpmi: perl-File-Which-1.24-alt1 sisyphus+268271.100.1.1 1616563376 installed <13>Apr 30 10:51:53 rpmi: perl-File-Copy-Recursive-0.45-alt1 sisyphus+235291.100.1.1 1564606222 installed <13>Apr 30 10:51:53 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+258375.4100.14.3 1600987517 installed <13>Apr 30 10:51:53 rpmi: perl-TimeDate-2.33-alt1 sisyphus+252901.100.1.1 1591387378 installed <13>Apr 30 10:51:53 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed <13>Apr 30 10:51:53 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed <13>Apr 30 10:51:53 rpmi: perl-Compress-Raw-Bzip2-2.101-alt1 sisyphus+266764.100.1.2 1614138565 installed <13>Apr 30 10:51:53 rpmi: hd2u-1.0.3-alt2 1400842666 installed <13>Apr 30 10:51:53 rpmi: libpython-2.7.18-alt5 sisyphus+270920.100.1.1 1619657728 installed <13>Apr 30 10:51:53 rpmi: python2-base-2.7.18-alt5 sisyphus+270920.100.1.1 1619657728 installed <13>Apr 30 10:51:53 rpmi: perl-Filter-1.60-alt1 sisyphus+258375.300.14.2 1600904226 installed <13>Apr 30 10:51:53 rpmi: perl-Encode-3.08-alt1 sisyphus+263440.100.1.1 1607955886 installed <13>Apr 30 10:51:53 rpmi: perl-URI-5.09-alt1 sisyphus+267398.100.1.1 1614944505 installed <13>Apr 30 10:51:53 rpmi: perl-HTML-Parser-3.76-alt1 sisyphus+267397.100.1.3 1614945689 installed <13>Apr 30 10:51:53 rpmi: perl-IO-Compress-2.102-alt1 sisyphus+267295.100.1.1 1614764488 installed <13>Apr 30 10:51:53 rpmi: perl-Net-HTTP-6.21-alt1 sisyphus+268278.100.1.1 1616563972 installed <13>Apr 30 10:51:53 rpmi: perl-Pod-Simple-3.42-alt1 sisyphus+261979.100.1.1 1605684633 installed <13>Apr 30 10:51:53 rpmi: perl-Pod-Usage-2.01-alt1 sisyphus+260315.100.1.3 1603550551 installed <13>Apr 30 10:51:53 rpmi: perl-podlators-4.14-alt1 sisyphus+243914.100.1.1 1578493399 installed <13>Apr 30 10:51:53 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>Apr 30 10:51:53 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>Apr 30 10:51:53 rpmi: perl-IO-HTML-1.004-alt1 sisyphus+258983.100.1.1 1601542619 installed <13>Apr 30 10:51:53 rpmi: perl-HTTP-Message-6.29-alt1 sisyphus+267426.100.1.1 1615033749 installed <13>Apr 30 10:51:53 rpmi: perl-HTTP-Cookies-6.10-alt1 sisyphus+264349.100.1.1 1609891183 installed <13>Apr 30 10:51:53 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>Apr 30 10:51:53 rpmi: perl-libwww-6.53-alt1 sisyphus+267863.100.1.1 1615828994 installed <13>Apr 30 10:51:53 rpmi: perl-XML-Parser-2.46-alt1 sisyphus+263451.100.1.1 1607958574 installed <13>Apr 30 10:51:53 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed <13>Apr 30 10:51:53 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed <13>Apr 30 10:51:53 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed <13>Apr 30 10:51:53 rpmi: perl-HTML-Form-6.07-alt1 sisyphus+246847.100.1.1 1582555741 installed <13>Apr 30 10:51:53 rpmi: perl-WWW-Mechanize-2.03-alt1 sisyphus+261983.100.1.3 1605688412 installed <13>Apr 30 10:51:53 rpmi: perl-XML-Writer-0.900-alt1 sisyphus+260334.100.1.2 1603554641 installed <13>Apr 30 10:51:53 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+248432.200.2.1 1585065505 installed <13>Apr 30 10:51:53 rpmi: perl-Text-CSV_XS-1.46-alt1 sisyphus+268759.100.1.1 1617219119 installed <13>Apr 30 10:51:53 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed <13>Apr 30 10:51:53 rpmi: perl-libintl-1.32-alt1 sisyphus+260753.100.1.1 1604233943 installed <13>Apr 30 10:51:53 rpmi: libteckit-2.5.1-alt2.1 1319227325 installed <13>Apr 30 10:51:53 rpmi: libteckit-utils-2.5.1-alt2.1 1319227325 installed <13>Apr 30 10:51:53 rpmi: rgb-1.0.6-alt3 sisyphus+229441.100.1.2 1557940338 installed <13>Apr 30 10:51:53 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672199 installed <13>Apr 30 10:51:54 rpmi: sharutils-4.15.2-alt1 sisyphus+266638.600.6.1 1614140863 installed <13>Apr 30 10:51:54 rpmi: ncompress-4.2.4.4-alt1 1366160442 installed <13>Apr 30 10:51:54 rpmi: libX11-locales-3:1.7.0-alt1 sisyphus+264667.100.1.2 1610655150 installed <13>Apr 30 10:51:54 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949353 installed <13>Apr 30 10:51:54 rpmi: libxcb-1.14-alt1 sisyphus+247358.200.1.3 1583854228 installed <13>Apr 30 10:51:54 rpmi: libX11-3:1.7.0-alt1 sisyphus+264667.100.1.2 1610655170 installed <13>Apr 30 10:51:54 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949429 installed <13>Apr 30 10:51:54 rpmi: libXrender-0.9.10-alt1 sisyphus+261890.100.1.1 1605595177 installed <13>Apr 30 10:51:54 rpmi: libXt-1.2.1-alt1 sisyphus+265202.200.1.1 1611565459 installed <13>Apr 30 10:51:54 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949641 installed <13>Apr 30 10:51:54 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614841 installed <13>Apr 30 10:51:54 rpmi: libXpm-3.5.13-alt1 sisyphus+247690.300.1.1 1584000526 installed <13>Apr 30 10:51:54 rpmi: libXi-1.7.10-alt1 sisyphus+232786.300.1.1 1561106978 installed <13>Apr 30 10:51:54 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949137 installed <13>Apr 30 10:51:56 rpmi: libxcb-devel-1.14-alt1 sisyphus+247358.200.1.3 1583854228 installed <13>Apr 30 10:51:56 rpmi: libX11-devel-3:1.7.0-alt1 sisyphus+264667.100.1.2 1610655170 installed <13>Apr 30 10:51:56 rpmi: libXt-devel-1.2.1-alt1 sisyphus+265202.200.1.1 1611565459 installed <13>Apr 30 10:51:56 rpmi: libXrender-devel-0.9.10-alt1 sisyphus+261890.100.1.1 1605595177 installed <13>Apr 30 10:51:56 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949429 installed <13>Apr 30 10:51:56 rpmi: libXaw-1.0.12-alt1 1391072624 installed <13>Apr 30 10:51:56 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949218 installed <13>Apr 30 10:51:56 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438594 installed <13>Apr 30 10:51:56 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949710 installed <13>Apr 30 10:51:56 rpmi: libXxf86vm-1.1.4-alt2 1527672187 installed <13>Apr 30 10:51:56 rpmi: libGLX-mesa-4:21.0.2-alt1 sisyphus+269183.200.1.1 1617867532 installed <13>Apr 30 10:51:56 rpmi: libEGL-mesa-4:21.0.2-alt1 sisyphus+269183.200.1.1 1617867532 installed <13>Apr 30 10:51:56 rpmi: libEGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:56 rpmi: libGLX-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:56 rpmi: libGL-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:56 rpmi: libglvnd-devel-7:1.3.2-alt1 sisyphus+254610.100.1.1 1594124268 installed <13>Apr 30 10:51:56 rpmi: libEGL-devel-4:21.0.2-alt1 sisyphus+269183.200.1.1 1617867532 installed <13>Apr 30 10:51:56 rpmi: libGL-devel-4:21.0.2-alt1 sisyphus+269183.200.1.1 1617867532 installed <13>Apr 30 10:51:56 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268216 installed <13>Apr 30 10:51:56 rpmi: libXtst-1.2.3-alt1 sisyphus+261890.200.1.1 1605595243 installed <13>Apr 30 10:51:57 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672199 installed <13>Apr 30 10:51:57 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949286 installed <13>Apr 30 10:51:57 rpmi: xprop-1.2.5-alt1 sisyphus+265434.100.1.1 1611856896 installed <13>Apr 30 10:51:57 rpmi: xdg-utils-1.1.3-alt7 sisyphus+259358.100.1.1 1602057656 installed <13>Apr 30 10:51:57 rpmi: liblz4-1:1.9.3-alt1 sisyphus+262305.100.1.1 1606099167 installed <13>Apr 30 10:51:57 rpmi: libgpg-error-1.41-alt4 sisyphus+264254.200.1.1 1609440111 installed <13>Apr 30 10:51:57 rpmi: libgcrypt20-1.9.2-alt1 sisyphus+266496.100.1.1 1613559234 installed <13>Apr 30 10:51:57 rpmi: libsystemd-1:247.3-alt2 sisyphus+266129.100.1.3 1613012672 installed <13>Apr 30 10:51:57 rpmi: libdbus-1.12.18-alt1 sisyphus+252758.100.1.1 1591203693 installed <13>Apr 30 10:51:57 rpmi: libavahi-0.8-alt2 sisyphus+270871.100.1.1 1619610383 installed <13>Apr 30 10:51:57 rpmi: libcups-2.3.3-alt3.op2 sisyphus+268789.100.1.1 1617267118 installed <13>Apr 30 10:51:57 rpmi: libxslt-1.1.34-alt2 sisyphus+248264.100.1.1 1584829770 installed <13>Apr 30 10:51:57 rpmi: gcc-fortran-common-1.4.27-alt1 sisyphus+262033.600.7.2 1607340230 installed <13>Apr 30 10:51:57 rpmi: libgfortran10-devel-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:58 rpmi: gcc10-fortran-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:51:58 rpmi: gcc-c++-common-1.4.27-alt1 sisyphus+262033.600.7.2 1607340230 installed <13>Apr 30 10:51:59 rpmi: libstdc++10-devel-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:52:00 rpmi: gcc10-c++-10.2.1-alt3 sisyphus+267829.100.1.1 1615808579 installed <13>Apr 30 10:52:00 rpmi: libbrotlicommon-1.0.9-alt2 sisyphus+257777.100.1.1 1599688017 installed <13>Apr 30 10:52:00 rpmi: libbrotlidec-1.0.9-alt2 sisyphus+257777.100.1.1 1599688017 installed <13>Apr 30 10:52:00 rpmi: libharfbuzz-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed <13>Apr 30 10:52:00 rpmi: libfreetype-2.10.4-alt2 sisyphus+260293.100.2.1 1604479496 installed <13>Apr 30 10:52:00 rpmi: fontconfig-2.13.1-alt1 sisyphus+257555.100.1.1 1599475160 installed Updating fonts cache: <29>Apr 30 10:52:01 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>Apr 30 10:52:01 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987708 installed <13>Apr 30 10:52:01 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515535 installed <13>Apr 30 10:52:01 rpmi: libpango-1.48.4-alt1 sisyphus+268501.500.4.2 1617042821 installed <13>Apr 30 10:52:02 rpmi: libgtk+2-2.24.33-alt1 sisyphus+263711.100.20.1 1609408077 installed <13>Apr 30 10:52:02 rpmi: libharfbuzz-icu-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed <13>Apr 30 10:52:02 rpmi: libgail-2.24.33-alt1 sisyphus+263711.100.20.1 1609408077 installed <13>Apr 30 10:52:02 rpmi: perl-Tk-804.036-alt1 sisyphus+266431.100.1.1 1613494702 installed <13>Apr 30 10:52:02 rpmi: libtk-8.6.11.1-alt1 sisyphus+269790.200.2.1 1618273804 installed <13>Apr 30 10:52:02 rpmi: tk-8.6.11.1-alt1 sisyphus+269790.200.2.1 1618273804 installed <13>Apr 30 10:52:02 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed <13>Apr 30 10:52:04 rpmi: libgs-9.53.3-alt1 sisyphus+260366.100.1.1 1603614538 installed <13>Apr 30 10:52:06 rpmi: ghostscript-common-9.53.3-alt1 sisyphus+260366.100.1.1 1603614495 installed <13>Apr 30 10:52:06 rpmi: ghostscript-classic-9.53.3-alt1 sisyphus+260366.100.1.1 1603614538 installed <13>Apr 30 10:52:06 rpmi: ghostscript-module-X-9.53.3-alt1 sisyphus+260366.100.1.1 1603614538 installed <13>Apr 30 10:52:06 rpmi: libgd3-2.3.2-alt1 sisyphus+267489.100.1.1 1615277758 installed <13>Apr 30 10:52:06 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed <13>Apr 30 10:52:06 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267507 installed <13>Apr 30 10:52:06 rpmi: libharfbuzz-gobject-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed <13>Apr 30 10:52:06 rpmi: xml-utils-1:2.9.10-alt6 sisyphus+265234.30740.49.1 1613765060 installed <13>Apr 30 10:52:06 rpmi: rpm-build-gir-0.7.3-alt3 sisyphus+242150.100.1.1 1575312005 installed <13>Apr 30 10:52:06 rpmi: ed-1:0.2-alt10 1449768440 installed <13>Apr 30 10:52:06 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed <13>Apr 30 10:52:06 rpmi: dialog-1.3.20171209-alt1 1529583087 installed <13>Apr 30 10:52:06 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587857 installed <13>Apr 30 10:52:06 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Apr 30 10:52:06 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Apr 30 10:52:06 rpmi: ca-certificates-2021.03.24-alt1 sisyphus+268304.300.1.1 1616591829 installed <13>Apr 30 10:52:06 rpmi: ca-trust-0.1.2-alt1 sisyphus+233348.100.1.1 1561653823 installed <13>Apr 30 10:52:06 rpmi: p11-kit-trust-0.23.15-alt2 sisyphus+252784.100.2.2 1591274901 installed <13>Apr 30 10:52:06 rpmi: libcrypto1.1-1.1.1k-alt1 sisyphus+268375.100.1.1 1616684255 installed <13>Apr 30 10:52:06 rpmi: libssl1.1-1.1.1k-alt1 sisyphus+268375.100.1.1 1616684255 installed <13>Apr 30 10:52:06 rpmi: libpython3-3.9.4-alt1 sisyphus+268966.100.1.1 1617609166 installed <13>Apr 30 10:52:06 rpmi: python3-3.9.4-alt1 sisyphus+268966.100.1.1 1617609166 installed <13>Apr 30 10:52:07 rpmi: python3-base-3.9.4-alt1 sisyphus+268966.100.1.1 1617609166 installed <13>Apr 30 10:52:07 rpmi: python3-module-six-1.15.0-alt2 sisyphus+270533.5100.6.1 1619685463 installed <13>Apr 30 10:52:08 rpmi: glib2-devel-2.68.1-alt1 sisyphus+269248.100.1.1 1617921065 installed <13>Apr 30 10:52:08 rpmi: libfreetype-devel-2.10.4-alt2 sisyphus+260293.100.2.1 1604479496 installed <13>Apr 30 10:52:08 rpmi: libharfbuzz-devel-2.6.8-alt1 sisyphus+254028.100.1.1 1593106819 installed <13>Apr 30 10:52:08 rpmi: fontconfig-devel-2.13.1-alt1 sisyphus+257555.100.1.1 1599475160 installed <86>Apr 30 10:52:08 groupadd[4087887]: group added to /etc/group: name=_keytab, GID=499 <86>Apr 30 10:52:08 groupadd[4087887]: group added to /etc/gshadow: name=_keytab <86>Apr 30 10:52:08 groupadd[4087887]: new group: name=_keytab, GID=499 <13>Apr 30 10:52:08 rpmi: libkrb5-1.19.1-alt2 sisyphus+267847.100.1.1 1615814853 installed <86>Apr 30 10:52:08 groupadd[4087899]: group added to /etc/group: name=sasl, GID=498 <86>Apr 30 10:52:08 groupadd[4087899]: group added to /etc/gshadow: name=sasl <86>Apr 30 10:52:08 groupadd[4087899]: new group: name=sasl, GID=498 <13>Apr 30 10:52:08 rpmi: libsasl2-3-2.1.27-alt2.1 sisyphus+255909.100.2.1 1597199456 installed <13>Apr 30 10:52:08 rpmi: libldap-2.4.57-alt1 sisyphus+266287.100.1.1 1613244306 installed <13>Apr 30 10:52:08 rpmi: libcurl-7.76.1-alt1 sisyphus+269986.100.1.1 1618487446 installed <13>Apr 30 10:52:08 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987708 installed <13>Apr 30 10:52:08 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515535 installed <13>Apr 30 10:52:08 rpmi: python3-module-genshi-0.7.4-alt2 sisyphus+261703.100.2.1 1605232240 installed <13>Apr 30 10:52:08 rpmi: python3-module-webencodings-0.5.1-alt2 sisyphus+245915.200.1.1 1581496105 installed <13>Apr 30 10:52:08 rpmi: python3-module-html5lib-1:1.0.1-alt1 sisyphus+238807.100.2.1 1570465973 installed <13>Apr 30 10:52:09 rpmi: python3-module-lxml-4.6.3-alt1 sisyphus+268152.100.1.1 1616388041 installed <13>Apr 30 10:52:09 rpmi: python3-module-cssselect-0.9.1-alt3 sisyphus+270533.2600.6.1 1619684675 installed <13>Apr 30 10:52:09 rpmi: python3-module-javapackages-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed <13>Apr 30 10:52:09 rpmi: rpm-build-java-1:5.3.0-alt1_4jpp8 sisyphus+234467.100.1.1 1563037789 installed <13>Apr 30 10:52:09 rpmi: perl-Net-SSLeay-1.90-alt1 sisyphus+265222.100.1.1 1611568851 installed <13>Apr 30 10:52:09 rpmi: perl-IO-Socket-SSL-2.070-alt1 sisyphus+267101.100.1.1 1614443766 installed <13>Apr 30 10:52:09 rpmi: perl-Net-HTTPS-6.21-alt1 sisyphus+268278.100.1.1 1616563972 installed <13>Apr 30 10:52:09 rpmi: perl-LWP-Protocol-https-6.10-alt1 sisyphus+263916.100.1.3 1608937434 installed <13>Apr 30 10:52:09 rpmi: ca-trust-java-0.1.2-alt1 sisyphus+233348.100.1.1 1561653823 installed <13>Apr 30 10:52:13 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.282.b08-alt1_0jpp8 sisyphus+265746.200.3.1 1612407392 installed <13>Apr 30 10:52:14 rpmi: gambit-4.9.3-alt2 sisyphus+241636.100.1.1 1574697266 installed <13>Apr 30 10:52:14 rpmi: foomatic-db-engine-4.0.12-alt1 1449527983 installed <13>Apr 30 10:52:14 rpmi: libnss-3.63.0-alt1 sisyphus+268304.200.1.1 1616591797 installed <13>Apr 30 10:52:14 rpmi: libpoppler97-0.86.1-alt2 sisyphus+262475.100.1.1 1606287192 installed <13>Apr 30 10:52:14 rpmi: ghostscript-utils-9.53.3-alt1 sisyphus+260366.100.1.1 1603614495 installed <13>Apr 30 10:52:16 rpmi: texlive-2019-alt2_7 sisyphus+266579.700.4.2 1614138684 installed <13>Apr 30 10:52:34 rpmi: texlive-collection-basic-2019-alt4_7 sisyphus+261965.100.1.1 1605675039 installed <13>Apr 30 10:52:34 rpmi: texlive-texmf-2019-alt4_7 sisyphus+261965.100.1.1 1605675039 installed <13>Apr 30 10:54:10 rpmi: texlive-dist-2019-alt4_7 sisyphus+261965.100.1.1 1605675039 installed <13>Apr 30 10:54:10 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed <13>Apr 30 10:54:10 rpmi: alsa-ucm-conf-1.2.4-alt1 sisyphus+260180.200.1.1 1603282405 installed <13>Apr 30 10:54:10 rpmi: alsa-topology-conf-1.2.4-alt1 sisyphus+260180.100.1.1 1603282384 installed <13>Apr 30 10:54:10 rpmi: libalsa-1:1.2.4-alt1 sisyphus+260180.300.1.1 1603282509 installed <13>Apr 30 10:54:10 rpmi: java-1.8.0-openjdk-0:1.8.0.282.b08-alt1_0jpp8 sisyphus+265746.200.3.1 1612407392 installed <13>Apr 30 10:54:12 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.282.b08-alt1_0jpp8 sisyphus+265746.200.3.1 1612407392 installed <13>Apr 30 10:54:12 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed <13>Apr 30 10:54:12 rpmi: libpango-devel-1.48.4-alt1 sisyphus+268501.500.4.2 1617042821 installed <13>Apr 30 10:54:12 rpmi: libcurl-devel-7.76.1-alt1 sisyphus+269986.100.1.1 1618487446 installed <13>Apr 30 10:54:12 rpmi: tk-devel-8.6.11.1-alt1 sisyphus+269790.200.2.1 1618273804 installed <13>Apr 30 10:54:12 rpmi: gcc-c++-10-alt1 sisyphus+263054.200.3.1 1607516810 installed <13>Apr 30 10:54:12 rpmi: gcc-fortran-10-alt1 sisyphus+263054.200.3.1 1607516810 installed <13>Apr 30 10:54:12 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949641 installed <13>Apr 30 10:54:12 rpmi: makeinfo-6.7-alt1 sisyphus+262609.100.1.1 1606438116 installed <13>Apr 30 10:54:12 rpmi: libgomp8-devel-8.4.1-alt1 sisyphus+247375.200.3.1 1583429415 installed <13>Apr 30 10:54:12 rpmi: liblapack-devel-1:3.8.0-alt4 sisyphus+264284.100.1.1 1609587717 installed <13>Apr 30 10:54:12 rpmi: libpcre2-devel-10.36-alt1 sisyphus+262985.100.2.1 1607423140 installed <13>Apr 30 10:54:12 rpmi: libtre-devel-0.8.0-alt2.2 sisyphus+249319.100.1.1 1585933008 installed <13>Apr 30 10:54:12 rpmi: libtiff-devel-4.2.0-alt1 sisyphus+266365.100.2.1 1613478695 installed <13>Apr 30 10:54:12 rpmi: texi2dvi-6.7-alt1 sisyphus+262609.100.1.1 1606438100 installed <13>Apr 30 10:54:12 rpmi: libjpeg-devel-2:2.0.6-alt1 sisyphus+266888.100.1.1 1614172387 installed <13>Apr 30 10:54:12 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686330 installed <13>Apr 30 10:54:12 rpmi: liblzma-devel-5.2.5-alt2 sisyphus+270022.200.3.1 1618664133 installed <13>Apr 30 10:54:12 rpmi: bzlib-devel-1:1.0.8-alt1 sisyphus+247226.100.1.1 1583187374 installed Building target platforms: i586 Building for target i586 Wrote: /usr/src/in/nosrpm/R-base-4.0.5-alt1.nosrc.rpm (w1.gzdio) Installing R-base-4.0.5-alt1.src.rpm Building target platforms: i586 Building for target i586 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.37002 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-4.0.5 + echo 'Source #0 (R-4.0.5.tar):' Source #0 (R-4.0.5.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-4.0.5.tar + cd R-4.0.5 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-4.0.5-alt1.patch):' Patch #0 (R-4.0.5-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/dbe24e8137437d3688e1d77cf1b67279d3099cea patching file .gear/tags/e6f3c8b737583c5e27038507647866d029bfb5e4 patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061 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/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.97600 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.0.5 + 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=firefox ac_cv_path_R_PDFVIEWER=evince '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=firefox + ac_cv_path_R_PDFVIEWER=evince + ac_cv_path_PAGER='less -isR' + ac_cv_prog_R_PRINTCMD=lpr + CFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing' + export CFLAGS + CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing' + export CXXFLAGS + FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing' + export FFLAGS + FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing' + export FCFLAGS + '[' -n '' ']' ++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing' ++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g' + ASFLAGS=' -march=i586 -mtune=generic' + 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=i586-alt-linux --host=i586-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --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/lib/tclConfig.sh --with-tk-config=/usr/lib/tkConfig.sh '--libdir=${prefix}/lib' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-4.0' configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules checking build system type... i586-alt-linux-gnu checking host system type... i586-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) firefox using default browser ... firefox checking for acroread... (cached) evince 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 i586-alt-linux-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking for i586-alt-linux-gcc... i586-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 we are using the GNU C compiler... yes checking whether i586-alt-linux-gcc accepts -g... yes checking for i586-alt-linux-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... i586-alt-linux-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether i586-alt-linux-gcc needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... i586-alt-linux-gcc -E looking for a modern Fortran compiler checking for i586-alt-linux-gfortran... i586-alt-linux-gfortran checking whether we are using the GNU Fortran compiler... yes checking whether i586-alt-linux-gfortran accepts -g... yes checking for i586-alt-linux-g++... i586-alt-linux-g++ checking whether we are using the GNU C++ compiler... yes checking whether i586-alt-linux-g++ accepts -g... yes checking whether i586-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing can compile C++ code... yes checking how to run the C++ preprocessor... i586-alt-linux-g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether i586-alt-linux-gcc accepts -fvisibility... yes checking whether i586-alt-linux-g++ accepts -fvisibility... yes checking whether i586-alt-linux-gfortran accepts -fvisibility... yes checking for i586-alt-linux-gcc... i586-alt-linux-gcc checking whether we are using the GNU Objective C compiler... no checking whether i586-alt-linux-gcc accepts -g... no checking whether i586-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 i586-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 i586-alt-linux-gnu file names to i586-alt-linux-gnu format... func_convert_file_noop checking how to convert i586-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 i586-alt-linux-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... (cached) pass_all checking for i586-alt-linux-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for i586-alt-linux-ar... (cached) ar checking for archiver @FILE support... @ checking for i586-alt-linux-strip... no checking for strip... strip checking for i586-alt-linux-ranlib... no checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from i586-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 i586-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 i586-alt-linux-gcc supports -fno-rtti -fno-exceptions... no checking for i586-alt-linux-gcc option to produce PIC... -fPIC -DPIC checking if i586-alt-linux-gcc PIC flag -fPIC -DPIC works... yes checking if i586-alt-linux-gcc static flag -static works... no checking if i586-alt-linux-gcc supports -c -o file.o... yes checking if i586-alt-linux-gcc supports -c -o file.o... (cached) yes checking whether the i586-alt-linux-gcc linker (/usr/bin/ld) 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... i586-alt-linux-g++ -E checking for ld used by i586-alt-linux-g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the i586-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes checking for i586-alt-linux-g++ option to produce PIC... -fPIC -DPIC checking if i586-alt-linux-g++ PIC flag -fPIC -DPIC works... yes checking if i586-alt-linux-g++ static flag -static works... no checking if i586-alt-linux-g++ supports -c -o file.o... yes checking if i586-alt-linux-g++ supports -c -o file.o... (cached) yes checking whether the i586-alt-linux-g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for i586-alt-linux-gfortran option to produce PIC... -fPIC checking if i586-alt-linux-gfortran PIC flag -fPIC works... yes checking if i586-alt-linux-gfortran static flag -static works... no checking if i586-alt-linux-gfortran supports -c -o file.o... yes checking if i586-alt-linux-gfortran supports -c -o file.o... (cached) yes checking whether the i586-alt-linux-gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for i586-alt-linux-gcc option to accept ISO C99... none needed checking for i586-alt-linux-gcc option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 4 checking size of long long... 8 checking size of double... 8 checking size of size_t... 4 checking for C stack direction... down checking size of long double... 12 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether i586-alt-linux-gcc supports -c -o FILE.lo... yes checking for i586-alt-linux-gcc option to support OpenMP... unsupported checking how to get verbose linking output from i586-alt-linux-gfortran... -v checking for Fortran libraries of i586-alt-linux-gfortran... -L/usr/local/lib -L/usr/lib/gcc/i586-alt-linux/10 -L/usr/lib/gcc/i586-alt-linux/10/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from i586-alt-linux-gcc... -v checking for C libraries of i586-alt-linux-gcc... -L/usr/local/lib -L/usr/lib/gcc/i586-alt-linux/10 -L/usr/lib/gcc/i586-alt-linux/10/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether i586-alt-linux-gfortran appends underscores to external names... yes checking whether i586-alt-linux-gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether i586-alt-linux-gfortran and i586-alt-linux-gcc agree on int and double... yes checking whether i586-alt-linux-gfortran and i586-alt-linux-gcc agree on double complex... yes checking for i586-alt-linux-gfortran option to support OpenMP... unsupported checking whether i586-alt-linux-g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking for ObjC runtime library... checking whether i586-alt-linux-gcc accepts -fobjc-exceptions... no checking if need -fno-optimize-sibling-calls for gfortran... yes checking for type of 'hidden' Fortran character lengths... size_t checking for xmkmf... no checking whether i586-alt-linux-g++ supports C++11 features with -std=gnu++11... yes checking whether i586-alt-linux-g++ supports C++14 features with -std=gnu++14... yes checking whether i586-alt-linux-g++ supports C++17 features with -std=gnu++17... yes checking whether i586-alt-linux-g++ supports C++20 features with -std=gnu++20... yes checking for i586-alt-linux-g++ -std=gnu++11 option to support OpenMP... unsupported checking for option providing pthread_kill... -pthread checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking thread.h usability... no checking thread.h presence... no checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... no checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... yes checking whether mktime works correctly outside 1902-2037... no checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_ in -lopenblas... yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking whether iconv accepts "CP1252"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking X11/Xmu/Atoms.h usability... yes checking X11/Xmu/Atoms.h presence... yes checking for X11/Xmu/Atoms.h... yes checking for XmuInternAtom in -lXmu... yes checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for /usr/lib/tclConfig.sh... /usr/lib/tclConfig.sh checking for /usr/lib/tkConfig.sh... /usr/lib/tkConfig.sh checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes checking tk.h usability... yes checking tk.h presence... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking rpc/types.h usability... no checking rpc/types.h presence... no checking for rpc/types.h... no checking tirpc/rpc/types.h usability... no checking tirpc/rpc/types.h presence... no checking for tirpc/rpc/types.h... no checking for XDR support... no checking for inflateInit2_ in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking for BZ2_bzlibVersion in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking pcre2.h usability... yes checking pcre2.h presence... yes checking for pcre2.h... yes checking for pcre2_compile_8 in -lpcre2-8... yes checking if PCRE2 has Unicode support... yes checking whether PCRE support suffices... yes checking for tre_regncompb in -ltre... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.76.1 checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.28.0... yes checking if libcurl supports https... yes checking if pkg-config knows about libjpeg... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if pkg-config knows about libpng... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking if pkg-config knows about libtiff... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for sys/time.h... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for struct stat.st_atim.tv_nsec... yes checking whether struct stat.st_atim is of type struct timespec... yes checking for setitimer... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether KERN_USRSTACK sysctl is supported... no checking for visible __lib_stack_end... yes checking for lpr... (cached) lpr checking for paperconf... /usr/bin/paperconf checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .f95 files... none checking for i586-alt-linux-gfortran option to support OpenMP... (cached) unsupported checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for i586-alt-linux-ranlib... ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by i586-alt-linux-gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.7.6, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... no 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 i586-alt-linux-gnu Source directory: . Installation directory: /usr C compiler: i586-alt-linux-gcc -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing Fortran fixed-form compiler: i586-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing Default C++ compiler: i586-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing C++14 compiler: i586-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing C++17 compiler: i586-alt-linux-g++ -std=gnu++17 -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing C++20 compiler: i586-alt-linux-g++ -std=gnu++20 -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing Fortran free-form compiler: i586-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing Obj-C compiler: i586-alt-linux-gcc Interfaces supported: X11, tcltk External libraries: pcre2, readline, BLAS(OpenBLAS), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, static HTML Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally + make -j8 make[1]: Nothing to be done for 'R'. make[1]: Nothing to be done for 'R'. make[2]: Nothing to be done for 'R'. make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/scripts' creating src/scripts/R.fe make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/scripts' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/scripts' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/include' mkdir -p -- ../../include make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/include' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/include/R_ext' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' making xdr_float.d from xdr_float.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' making xdr_mem.d from xdr_mem.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' making xdr.d from xdr.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' making xdr_stdio.d from xdr_stdio.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making regerror.d from regerror.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making regexec.d from regexec.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making regcomp.d from regcomp.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-ast.d from tre-ast.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-compile.d from tre-compile.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-match-approx.d from tre-match-approx.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-match-backtrack.d from tre-match-backtrack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-match-parallel.d from tre-match-parallel.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-mem.d from tre-mem.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-parse.d from tre-parse.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making tre-stack.d from tre-stack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c xdr_float.c -o xdr_float.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' making xmalloc.d from xmalloc.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c xdr.c -o xdr.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/extra/xdr' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' i586-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/extra/tre' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making interv.d from interv.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making integrate.d from integrate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making maxcol.d from maxcol.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making pretty.d from pretty.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making uncmin.d from uncmin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' making optim.d from optim.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpbfa.f -o dpbfa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpbsl.f -o dpbsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c maxcol.c -o maxcol.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c interv.c -o interv.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dchdc.f -o dchdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpodi.f -o dpodi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpofa.f -o dpofa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pretty.c -o pretty.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpoco.f -o dpoco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dposl.f -o dposl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dqrls.f -o dqrls.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dqrdc.f -o dqrdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dqrutl.f -o dqrutl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dqrsl.f -o dqrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtrsl.f -o dtrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtrco.f -o dtrco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c integrate.c -o integrate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dsvdc.f -o dsvdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c uncmin.c -o uncmin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c optim.c -o optim.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/appl' #@make install-Linpack make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making i1mach.d from i1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making fmax2.d from fmax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making mlutils.d from mlutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making fmin2.d from fmin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making fprec.d from fprec.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making d1mach.d from d1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making fround.d from fround.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making ftrunc.d from ftrunc.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making sign.d from sign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making fsign.d from fsign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making imax2.d from imax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making chebyshev.d from chebyshev.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making log1p.d from log1p.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making imin2.d from imin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making lgammacor.d from lgammacor.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making gammalims.d from gammalims.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making bd0.d from bd0.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making stirlerr.d from stirlerr.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making lgamma.d from lgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making gamma.d from gamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making gamma_cody.d from gamma_cody.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making beta.d from beta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making lbeta.d from lbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making polygamma.d from polygamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making cospi.d from cospi.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making bessel_i.d from bessel_i.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making bessel_j.d from bessel_j.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making bessel_k.d from bessel_k.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making bessel_y.d from bessel_y.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making choose.d from choose.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making sexp.d from sexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making snorm.d from snorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pgamma.d from pgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dgamma.d from dgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qgamma.d from qgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rgamma.d from rgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dbeta.d from dbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pbeta.d from pbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qbeta.d from qbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rbeta.d from rbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dunif.d from dunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making punif.d from punif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qunif.d from qunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making runif.d from runif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnorm.d from dnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnorm.d from pnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnorm.d from qnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rnorm.d from rnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making plnorm.d from plnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dlnorm.d from dlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qlnorm.d from qlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rlnorm.d from rlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making df.d from df.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pf.d from pf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qf.d from qf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rf.d from rf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnf.d from dnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dt.d from dt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pt.d from pt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qt.d from qt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rt.d from rt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnt.d from dnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dchisq.d from dchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pchisq.d from pchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qchisq.d from qchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rchisq.d from rchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dbinom.d from dbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rnchisq.d from rnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pbinom.d from pbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qbinom.d from qbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rbinom.d from rbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dcauchy.d from dcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rmultinom.d from rmultinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pcauchy.d from pcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qcauchy.d from qcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rcauchy.d from rcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dexp.d from dexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pexp.d from pexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qexp.d from qexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rexp.d from rexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dgeom.d from dgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pgeom.d from pgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qgeom.d from qgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rgeom.d from rgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dhyper.d from dhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making phyper.d from phyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qhyper.d from qhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rhyper.d from rhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnbinom.d from dnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnbinom.d from pnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnbinom.d from qnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rnbinom.d from rnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dpois.d from dpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making ppois.d from ppois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qpois.d from qpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dweibull.d from dweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rpois.d from rpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pweibull.d from pweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qweibull.d from qweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rweibull.d from rweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dlogis.d from dlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making plogis.d from plogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qlogis.d from qlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making rlogis.d from rlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnchisq.d from dnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnchisq.d from pnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnchisq.d from qnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnbeta.d from pnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making dnbeta.d from dnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnbeta.d from qnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnf.d from pnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making pnt.d from pnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnf.d from qnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qnt.d from qnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making qtukey.d from qtukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making ptukey.d from ptukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making toms708.d from toms708.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making wilcox.d from wilcox.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' making signrank.d from signrank.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mlutils.c -o mlutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fmax2.c -o fmax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c d1mach.c -o d1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fmin2.c -o fmin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c i1mach.c -o i1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c ftrunc.c -o ftrunc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fprec.c -o fprec.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fround.c -o fround.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sign.c -o sign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c imax2.c -o imax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fsign.c -o fsign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c imin2.c -o imin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c log1p.c -o log1p.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chebyshev.c -o chebyshev.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gammalims.c -o gammalims.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lgammacor.c -o lgammacor.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c stirlerr.c -o stirlerr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bd0.c -o bd0.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c beta.c -o beta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lgamma.c -o lgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gamma.c -o gamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lbeta.c -o lbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cospi.c -o cospi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sexp.c -o sexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c choose.c -o choose.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c polygamma.c -o polygamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bessel_i.c -o bessel_i.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c snorm.c -o snorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bessel_y.c -o bessel_y.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgamma.c -o dgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bessel_k.c -o bessel_k.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bessel_j.c -o bessel_j.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dbeta.c -o dbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rgamma.c -o rgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pbeta.c -o pbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qgamma.c -o qgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dunif.c -o dunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rbeta.c -o rbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pgamma.c -o pgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c punif.c -o punif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qunif.c -o qunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing 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-DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnorm.c -o pnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c plnorm.c -o plnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qlnorm.c -o qlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c df.c -o df.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qf.c -o qf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pf.c -o pf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rf.c -o rf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dnf.c -o dnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qbeta.c -o qbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dt.c -o dt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pt.c -o pt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dchisq.c -o dchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rt.c -o rt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dnt.c -o dnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pchisq.c -o pchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qchisq.c -o qchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rchisq.c -o rchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rnchisq.c -o rnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pbinom.c -o pbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dbinom.c -o dbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dcauchy.c -o dcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qt.c -o qt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rmultinom.c -o rmultinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pcauchy.c -o pcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qbinom.c -o qbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rcauchy.c -o rcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qcauchy.c -o qcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dexp.c -o dexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic 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-I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pgeom.c -o pgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qgeom.c -o qgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dhyper.c -o dhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c phyper.c -o phyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qhyper.c -o qhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rnbinom.c -o rnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnbinom.c -o pnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c ppois.c -o ppois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpois.c -o dpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qnbinom.c -o qnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dnbinom.c -o dnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic 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-frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pweibull.c -o pweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rweibull.c -o rweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpois.c -o rpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qweibull.c -o qweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dlogis.c -o dlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c plogis.c -o plogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dnchisq.c -o dnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rlogis.c -o rlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dnbeta.c -o dnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qlogis.c -o qlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qnbeta.c -o qnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qnchisq.c -o qnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnbeta.c -o pnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnf.c -o pnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnchisq.c -o pnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qnf.c -o qnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qnt.c -o qnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pnt.c -o pnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qtukey.c -o qtukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c ptukey.c -o ptukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c signrank.c -o signrank.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c wilcox.c -o wilcox.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c toms708.c -o toms708.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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 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-4.0.5/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making Rembedded.d from Rembedded.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making dynload.d from dynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making X11.d from X11.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making system.d from system.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making sys-unix.d from sys-unix.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' making sys-std.d from sys-std.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Rembedded.c -o Rembedded.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dynload.c -o dynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c X11.c -o X11.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c system.c -o system.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sys-unix.c -o sys-unix.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sys-std.c -o sys-std.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' i586-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -L/usr/local/lib -DR_HOME='"/usr/src/RPM/BUILD/R-4.0.5"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making CommandLineArgs.d from CommandLineArgs.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making RNG.d from RNG.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making agrep.d from agrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making Renviron.d from Renviron.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making altrep.d from altrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making Rdynload.d from Rdynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making apply.d from apply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making altclasses.d from altclasses.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making arithmetic.d from arithmetic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making bind.d from bind.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making attrib.d from attrib.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making character.d from character.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making builtin.d from builtin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making array.d from array.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making colors.d from colors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making coerce.d from coerce.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making complex.d from complex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making cum.d from cum.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making context.d from context.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making debug.d from debug.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making datetime.d from datetime.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making dcf.d from dcf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making deparse.d from deparse.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making connections.d from connections.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making devices.d from devices.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making dstruct.d from dstruct.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making duplicate.d from duplicate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making dotcode.d from dotcode.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making dounzip.d from dounzip.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making edit.d from edit.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making engine.d from engine.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making envir.d from envir.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making errors.d from errors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making format.d from format.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making gevents.d from gevents.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making gram-ex.d from gram-ex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making eval.d from eval.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making graphics.d from graphics.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making gram.d from gram.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making grep.d from grep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making identical.d from identical.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making inlined.d from inlined.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making localecharset.d from localecharset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making inspect.d from inspect.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making internet.d from internet.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making iosupport.d from iosupport.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making lapack.d from lapack.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making list.d from list.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making logic.d from logic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making mapply.d from mapply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making match.d from match.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making main.d from main.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making objects.d from objects.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making names.d from names.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making options.d from options.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making memory.d from memory.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making paste.d from paste.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making plot.d from plot.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making plot3d.d from plot3d.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making printvector.d from printvector.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making printarray.d from printarray.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making plotmath.d from plotmath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making print.d from print.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making platform.d from platform.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making printutils.d from printutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making qsort.d from qsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making radixsort.d from radixsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making raw.d from raw.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making random.d from random.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making registration.d from registration.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making rlocale.d from rlocale.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making relop.d from relop.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making seq.d from seq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making saveload.d from saveload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making scan.d from scan.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making sort.d from sort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making split.d from split.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making source.d from source.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making sprintf.d from sprintf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making serialize.d from serialize.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making startup.d from startup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making subscript.d from subscript.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making subassign.d from subassign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making subset.d from subset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making summary.d from summary.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making times.d from times.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making unique.d from unique.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making sysutils.d from sysutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making Rmain.d from Rmain.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making alloca.d from alloca.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making version.d from version.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making g_alab_her.d from g_alab_her.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making g_cntrlify.d from g_cntrlify.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making g_fontdb.d from g_fontdb.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making strdup.d from strdup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making strncasecmp.d from strncasecmp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making g_her_glyph.d from g_her_glyph.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making util.d from util.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' making mkdtemp.d from mkdtemp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Renviron.c -o Renviron.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c RNG.c -o RNG.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c altrep.c -o altrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c apply.c -o apply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Rdynload.c -o Rdynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c altclasses.c -o altclasses.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agrep.c -o agrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c colors.c -o colors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c builtin.c -o builtin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c attrib.c -o attrib.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c complex.c -o complex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c character.c -o character.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cum.c -o cum.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bind.c -o bind.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dcf.c -o dcf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c context.c -o context.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c array.c -o array.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c debug.c -o debug.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c devices.c -o devices.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dstruct.c -o dstruct.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c arithmetic.c -o arithmetic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dounzip.c -o dounzip.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coerce.c -o coerce.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c edit.c -o edit.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c duplicate.c -o duplicate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c deparse.c -o deparse.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dotcode.c -o dotcode.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c datetime.c -o datetime.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gram-ex.c -o gram-ex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gevents.c -o gevents.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall 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'/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c inlined.c -o inlined.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c engine.c -o engine.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c iosupport.c -o iosupport.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c connections.c -o connections.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c internet.c -o internet.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lapack.c -o lapack.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c inspect.c -o inspect.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c localecharset.c -o localecharset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c list.c -o list.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mapply.c -o mapply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c match.c -o match.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c main.c -o main.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c logic.c -o logic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c envir.c -o envir.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c names.c -o names.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c options.c -o options.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c paste.c -o paste.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c plot.c -o plot.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gram.c -o gram.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c objects.c -o objects.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c grep.c -o grep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c plot3d.c -o plot3d.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c printvector.c -o printvector.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c printarray.c -o printarray.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c printutils.c -o printutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c print.c -o print.o print.c: In function 'PrintGenericVector': print.c:484:27: warning: '%s' directive output may be truncated writing between 100 and 2147483645 bytes into a region of size 100 [-Wformat-truncation=] 484 | snprintf(pbuf, 101, "\"%s\"", ctmp); | ^~ In file included from /usr/include/stdio.h:866, from ../../src/include/Rinternals.h:39, from ../../src/include/Defn.h:81, from print.c:65: /usr/include/bits/stdio2.h:70:10: note: '__builtin___snprintf_chk' output between 103 and 2147483648 bytes into a destination of size 101 70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c platform.c -o platform.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qsort.c -o qsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c registration.c -o registration.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rlocale.c -o rlocale.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c raw.c -o raw.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c random.c -o random.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c memory.c -o memory.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c plotmath.c -o plotmath.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c radixsort.c -o radixsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c source.c -o source.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c scan.c -o scan.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c split.c -o split.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c relop.c -o relop.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c saveload.c -o saveload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c startup.c -o startup.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sprintf.c -o sprintf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sort.c -o sort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c seq.c -o seq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c subscript.c -o subscript.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c serialize.c -o serialize.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c times.c -o times.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c version.c -o version.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sysutils.c -o sysutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c summary.c -o summary.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c xxxpr.f -o xxxpr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c subset.c -o subset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c unique.c -o unique.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c subassign.c -o subassign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c util.c -o util.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c eval.c -o eval.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-alt-linux-gcc -shared -pthread -L/usr/local/lib -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 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-4.0.5/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.0.5/bin/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-4.0.5/lib make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Rmain.c -o Rmain.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' i586-alt-linux-gcc -Wl,--export-dynamic -pthread -L"../../lib" -L/usr/local/lib -o R.bin Rmain.o -lR make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' making rbitmap.d from rbitmap.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' making Lapack.d from Lapack.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making internet.d from internet.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making Rhttpd.d from Rhttpd.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making libcurl.d from libcurl.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making Rsock.d from Rsock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making nanoftp.d from nanoftp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' making rotated.d from rotated.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making sock.d from sock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making nanohttp.d from nanohttp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' making sockconn.d from sockconn.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' making devX11.d from devX11.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-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/lib/glib-2.0/include -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rbitmap.c -o rbitmap.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' i586-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib -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-4.0.5/src/modules/internet' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' mkdir -p -- /usr/src/RPM/BUILD/R-4.0.5/modules make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-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/lib/glib-2.0/include -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rotated.c -o rotated.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' i586-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Lapack.c -o Lapack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' i586-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-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/lib/glib-2.0/include -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c devX11.c -o devX11.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib -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-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-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/lib/glib-2.0/include -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dataentry.c -o dataentry.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/modules/X11' i586-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib -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-4.0.5/src/modules/X11' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' mkdir -p -- ../../library make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/profile' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/translations' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' building package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making md5.d from md5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making text.d from text.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making http.d from http.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making signals.d from signals.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making Rmd5.d from Rmd5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making install.d from install.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making getfmts.d from getfmts.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making gramLatex.d from gramLatex.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' making gramRd.d from gramRd.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c http.c -o http.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c signals.c -o signals.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c Rmd5.c -o Rmd5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c install.c -o install.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c getfmts.c -o getfmts.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c text.c -o text.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c md5.c -o md5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c gramLatex.c -o gramLatex.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c gramRd.c -o gramRd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/compiler' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' mkdir -p -- ../../../library/utils/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making sock.d from sock.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making size.d from size.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making io.d from io.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c sock.c -o sock.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c size.c -o size.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c io.c -o io.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -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-4.0.5/src/library/utils/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/utils' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/grDevices' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making axis_scales.d from axis_scales.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making chull.d from chull.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making devices.d from devices.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making devCairo.d from devCairo.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making devPicTeX.d from devPicTeX.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making colors.d from colors.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making devQuartz.d from devQuartz.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' making devPS.d from devPS.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c axis_scales.c -o axis_scales.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c devCairo.c -o devCairo.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c devQuartz.c -o devQuartz.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c devices.c -o devices.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c chull.c -o chull.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c colors.c -o colors.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c devPS.c -o devPS.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src' make[7]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[7]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src/cairo' i586-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/lib/glib-2.0/include -I/usr/include/libpng16 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cairoBM.c -o cairoBM.o make[9]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices/src/cairo' i586-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib -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-4.0.5/src/library/grDevices/src/cairo' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grDevices' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making stem.d from stem.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making base.d from base.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making par.d from par.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making graphics.d from graphics.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making plot.d from plot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' making plot3d.d from plot3d.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c stem.c -o stem.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c base.c -o base.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c graphics.c -o graphics.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c plot3d.c -o plot3d.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c par.c -o par.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c plot.c -o plot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -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-4.0.5/src/library/graphics/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/graphics' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making kmeans.d from kmeans.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making ansari.d from ansari.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making d2x2xk.d from d2x2xk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making chisqsim.d from chisqsim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making kendall.d from kendall.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making fexact.d from fexact.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making bandwidths.d from bandwidths.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making line.d from line.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making prho.d from prho.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making ks.d from ks.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making swilk.d from swilk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making smooth.d from smooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making ksmooth.d from ksmooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making monoSpl.d from monoSpl.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making loessc.d from loessc.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making dblcen.d from dblcen.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making isoreg.d from isoreg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making Srunmed.d from Srunmed.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making hclust-utils.d from hclust-utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making nls.d from nls.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making distance.d from distance.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making HoltWinters.d from HoltWinters.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making rWishart.d from rWishart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making PPsum.d from PPsum.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making burg.d from burg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making arima.d from arima.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making filter.d from filter.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making mAR.d from mAR.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making pacf.d from pacf.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making starma.d from starma.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making port.d from port.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making family.d from family.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making sbart.d from sbart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making approx.d from approx.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making massdist.d from massdist.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making lowess.d from lowess.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making loglin.d from loglin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making lm.d from lm.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making complete_cases.d from complete_cases.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making fft.d from fft.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making cov.d from cov.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making deriv.d from deriv.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making fourier.d from fourier.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making model.d from model.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making zeroin.d from zeroin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making integrate.d from integrate.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making optim.d from optim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making rcont.d from rcont.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making optimize.d from optimize.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making random.d from random.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making distn.d from distn.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' making influence.d from influence.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c kendall.c -o kendall.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c ansari.c -o ansari.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c chisqsim.c -o chisqsim.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c bandwidths.c -o bandwidths.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 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i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c swilk.c -o swilk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c monoSpl.c -o monoSpl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include 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'/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c distance.c -o distance.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c rWishart.c -o rWishart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c PPsum.c -o PPsum.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c loessc.c -o loessc.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 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i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c lm.c -o lm.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c loglin.c -o loglin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include 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-I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rcont.c -o rcont.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bvalue.f -o bvalue.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bsplvd.f -o bsplvd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qsbart.f -o qsbart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sgram.f -o sgram.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sinerp.f -o sinerp.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c stxwx.f -o stxwx.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sslvrg.f -o sslvrg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c distn.c -o distn.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c eureka.f -o eureka.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c hclust.f -o hclust.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c deriv.c -o deriv.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lminfl.f -o lminfl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c kmns.f -o kmns.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c stl.f -o stl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c mAR.c -o mAR.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c ppr.f -o ppr.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c loessf.f -o loessf.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c model.c -o model.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gfortran -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o portsrc.f:2:34: 2 | LOGICAL FUNCTION STOPX(DUMMY) | 1 Warning: Unused dummy argument 'dummy' at (1) [-Wunused-dummy-argument] portsrc.f:6664:72: 6664 | NCOMP = NCOMP + 1 | ^ Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:6684:72: 6684 | JPU = JPNTR(JCOL+1) - 1 | ^ Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5522:51: 5522 | IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) | ^ Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5659:18: 5659 | IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310 | ^ Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10330:55: 10330 | IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) | ^ Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10413:72: 10413 | V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA) | ^ Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10325:72: 10325 | LK = DMAX1(LK, PHI*W(PHIPIN)) | ^ Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10467:10: 10467 | IF (KA .GE. KAMIN) GO TO 340 | ^ Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12244:72: 12244 | V(NREDUC) = NRED | ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12247:72: 12247 | V(DST0) = DNWTST | ^ Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2516:72: 2516 | V(NREDUC) = NRED | ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2515:72: 2515 | 60 V(DST0) = DS0 | ^ Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8175:72: 8175 | V(NREDUC) = NRED | ^ Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8174:72: 8174 | 90 V(DST0) = DS0 | ^ Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8653:72: 8653 | 210 IV(FDH) = HES | ^ Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:3588:10: 3588 | IF (LIV .LT. MIV2) GO TO 300 | ^ Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12080:72: 12080 | 270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) | ^ Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:459:72: 459 | 300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) | ^ Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:367:72: 367 | CALL DL7VML(P, V(G1), V(RMAT1), V(QTR1)) | ^ Warning: 'rmat1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:367:72: Warning: 'qtr1' may be used uninitialized in this function [-Wmaybe-uninitialized] make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -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 -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/stats' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making slot.d from slot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making class_support.d from class_support.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making tests.d from tests.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making methods_list_dispatch.d from methods_list_dispatch.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c slot.c -o slot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c class_support.c -o class_support.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c tests.c -o tests.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-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 -march=i586 -mtune=generic -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' i586-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib -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-4.0.5/src/library/methods/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/methods' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid' make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid/src' making gpar.d from gpar.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/grid/src' making just.d from just.c make[5]: Leaving directory 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'/usr/src/tmp/Rjavareconf.aupyTV' JAVA_HOME : /usr/lib/jvm/java Java library path: $(JAVA_HOME)/jre/lib/i386/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/i386/server -ljvm Updating Java configuration in /usr/src/RPM/BUILD/R-4.0.5 Done. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc' creating doc/NEWS.pdf make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' creating doc/manual/version.texi make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' creating doc/manual/R-data.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' creating doc/manual/R-FAQ.html make[2]: Leaving directory 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make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' building/updating package metadata ... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' writing package indices make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library' building all R object docs converting help for package 'base' Arithmetic html AsIs html Bessel html CallExternal html Colon html Comparison html Constants html Control html Cstack_info html DateTimeClasses html Dates html Defunct html Deprecated html Encoding html EnvVar html Extract html Extract.data.frame html Extract.factor html Extremes html Foreign-internal html Foreign html Hyperbolic html ISOdatetime html Internal html InternalMethods html La_library html La_version html Last.value html Log html Logic html LongVectors html MathFun html Memory-limits html Memory html NA html NULL html NumericConstants html Ops.Date html Paren html Platform html Primitive html Quotes html Random-user html Random html RdUtils html Recall html Reserved html Rhome html Round html S3method html Special html Startup html Syntax html Sys.getenv html Sys.getpid html Sys.glob html Sys.info html Sys.localeconv html Sys.readlink html Sys.setFileTime html Sys.setenv html Sys.sleep html Sys.time html Sys.which html Trig html UTF8filepaths html UseMethod html Vectorize html Version html abbreviate html agrep html all html all.equal html allnames html any html aperm html append html apply html args html array html as.Date html as.POSIXlt html as.data.frame html as.environment html as.function html asplit html assign html assignOps html attach html attr html attributes html autoload html backsolve html base-defunct html base-deprecated html base-internal html base-package html basename html bincode html bindenv html bitwise html body html bquote html browser html browserText html builtins html by html c html call html callCC html capabilities html cat html cbind html char.expand html character html charmatch html chartr html chkDots html chol html chol2inv html class html col html colSums html colnames html commandArgs html comment html complex html conditions html conflicts html connections html contributors html copyright html crossprod html cumsum html curlGetHeaders html cut.POSIXt html cut html data.class html data.frame html data.matrix html dataframeHelpers html date html dcf html debug html delayedAssign html deparse html deparseOpts html det html detach html dev html diag html diff html difftime html dim html dimnames html do.call html dontCheck html dots html double html dput html drop html droplevels html dump html duplicated html dynload html eapply html eigen html encodeString html environment html eval html exists html expand.grid html expression html extSoftVersion html factor html file.access html file.choose html file.info html file.path html file.show html files html files2 html find.package html findInterval html force html forceAndCall html formals html format html format.info html format.pval html formatDL html formatc html function html funprog html gc html gc.time html gctorture html get html getCallingDLL html getDLLRegisteredRoutines html getLoadedDLLs html getNativeSymbolInfo html gettext html getwd html gl html grep html grepRaw html groupGeneric html grouping html gzcon html hexmode html iconv html icuSetCollate html identical html identity html ifelse html integer html interaction html interactive html invisible html is.finite html is.function html is.language html is.object html is.recursive html is.single html is.unsorted html isR html isS4 html isSymmetric html jitter html kappa html kronecker html l10n_info html labels html lapply html lazyload html length html lengths html levels html libPaths html libcurlVersion html library html library.dynam html license html list html list.files html list2DF html list2env html load html locales html logical html lower.tri html ls html make.names html make.unique html mapply html marginSums html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memlimits html memory.profile html merge html message html missing html mode html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pcre_config html plot html pmatch html polyroot html pos.to.env html pretty html print html print.dataframe html print.default html prmatrix html proc.time html prod html proportions html pushBack html qr html qraux html quit html range html rank html rapply html raw html rawConnection html rawConversion html readBin html readChar html readLines html readRDS html readRenviron html readline html reg.finalizer html regex html regmatches html rep html replace html rev html rle html rm html round.POSIXt html row html row.names html rowsum html sQuote html sample html save html scale html scan html search html seek html seq.Date html seq.POSIXt html seq html sequence html serialize html setTimeLimit html sets html shQuote html showConnections html sign html sink html slice.index html slotOp html socketSelect html solve html sort html source html split html sprintf html srcfile html standardGeneric html startsWith html stop html stopifnot html strptime html strrep html strsplit html strtoi html strtrim html structure html strwrap html subset html substitute html substr html sum html summary html svd html sweep html switch html sys.parent html sys.source html system html system.file html system.time html system2 html t html table html tabulate html tapply html taskCallback html taskCallbackManager html taskCallbackNames html tempfile html textconnections html tilde html timezones html toString html trace html traceback html tracemem html transform html trimws html try html typeof html unique html unlink html unlist html unname html userhooks html utf8Conversion html validUTF8 html vector html warning html warnings html weekday.POSIXt html which html which.min html with html withVisible html write html writeLines html xtfrm html zMachine html zScript html zapsmall html zpackages html zutils html Signals html converting help for package 'tools' CRANtools html HTMLheader html HTMLlinks html QC html Rcmd html Rd2HTML html Rd2txt_options html RdTextFilter html Rdiff html Rdindex html Rdutils html SweaveTeXFilter html add_datalist html assertCondition html bibstyle html buildVignette html buildVignettes html charsets html checkFF html checkMD5sums html checkPoFiles html checkRd html checkRdaFiles html checkTnF html checkVignettes html check_packages_in_dir html codoc html compactPDF html delimMatch html dependsOnPkgs html encoded html fileutils html find_gs_cmd html getVignetteInfo html loadRdMacros html makeLazyLoading html make_translations_pkg html makevars html md5sum html package_dependencies html package_native_routine_registration_skeleton html parseLatex html parse_Rd html print.via.format html pskill html psnice html read.00Index html showNonASCII html startDynamicHelp html testInstalledPackage html texi2dvi html toHTML html toRd html toTitleCase html tools-defunct html tools-deprecated html tools-package html undoc html updatePACKAGES html update_pkg_po html userdir html vignetteEngine html vignetteInfo html writePACKAGES html xgettext html converting help for package 'utils' BATCH html COMPILE html DLL.version html INSTALL html LINK html PkgUtils html Question html REMOVE html RHOME html RShowDoc html RSiteSearch html Rconsole html Rprof html Rprofmem html Rscript html Rtangle html RweaveLatex html SHLIB html Sweave html SweaveSyntConv html SweaveUtils html URLencode html View html adist html alarm html apropos html aregexec html arrangeWindows html askYesNo html aspell-utils html aspell html available.packages html bibentry html browseEnv html browseURL html browseVignettes html bug.report html capture.output html changedFiles 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 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 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-4.0.5/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package MASS make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package lattice make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package codetools make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package foreign make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package KernSmooth make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package rpart make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package nnet make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package spatial make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpJaVwvt/R.INSTALL182f25df60d3f/nnet/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c nnet.c -o nnet.o make[3]: Leaving directory '/usr/src/tmp/RtmpJaVwvt/R.INSTALL182f25df60d3f/nnet/src' make[3]: Entering directory '/usr/src/tmp/RtmpJaVwvt/R.INSTALL182f25df60d3f/nnet/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpJaVwvt/R.INSTALL182f25df60d3f/nnet/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c krc.c -o krc.o make[3]: Leaving directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pps.c -o pps.o make[3]: Leaving directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpLBdg22/R.INSTALL1830676470ea3/spatial/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c blkest.f -o blkest.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cp.f -o cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgedi.f -o dgedi.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgefa.f -o dgefa.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgesl.f -o dgesl.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c linbin.f -o linbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c linbin2D.f -o linbin2D.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c locpoly.f -o locpoly.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rlbin.f -o rlbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sdiag.f -o sdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sstdiag.f -o sstdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpN5SPAd/R.INSTALL182ee69c3be09/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c R_systat.c -o R_systat.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c SASxport.c -o SASxport.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c avl.c -o avl.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dbfopen.c -o dbfopen.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c file-handle.c -o file-handle.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c minitab.c -o minitab.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pfm-read.c -o pfm-read.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c spss.c -o spss.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sfm-read.c -o sfm-read.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c stataread.c -o stataread.o make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpKpSrnr/R.INSTALL182f1356c990d/foreign/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c anova.c -o anova.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c anovapred.c -o anovapred.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c branch.c -o branch.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c bsplit.c -o bsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c choose_surg.c -o choose_surg.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fix_cp.c -o fix_cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c free_tree.c -o free_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gini.c -o gini.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c graycode.c -o graycode.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c insert_split.c -o insert_split.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mysort.c -o mysort.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c nodesplit.c -o nodesplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c partition.c -o partition.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c poisson.c -o poisson.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c print_tree.c -o print_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpartexp.c -o rpartexp.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpart.c -o rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpcountup.c -o rpcountup.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rundown.c -o rundown.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rundown2.c -o rundown2.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c surrogate.c -o surrogate.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c usersplit.c -o usersplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c xval.c -o xval.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c xpred.c -o xpred.o make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpLN1CL2/R.INSTALL182ec79beabab/rpart/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c MASS.c -o MASS.o make[3]: Leaving directory '/usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' make[3]: Entering directory '/usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lqs.c -o lqs.o make[3]: Leaving directory '/usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' make[3]: Entering directory '/usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 Rd warning: /usr/src/tmp/Rtmp1yxuFW/R.INSTALL182dd735db7f6/MASS/man/pairs.lda.Rd:42: missing file link 'splom' 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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package cluster make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package class make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpNgZ6Of/R.INSTALL1893cc99aee9/class/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c class.c -o class.o make[3]: Leaving directory '/usr/src/tmp/RtmpNgZ6Of/R.INSTALL1893cc99aee9/class/src' make[3]: Entering directory '/usr/src/tmp/RtmpNgZ6Of/R.INSTALL1893cc99aee9/class/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -o class.so class.o -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpNgZ6Of/R.INSTALL1893cc99aee9/class/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c threeDplot.c -o threeDplot.o make[3]: Leaving directory '/usr/src/tmp/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpFw84dk/R.INSTALL182e2424afd3c/lattice/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package Matrix make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package nlme make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dysta.f -o dysta.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c daisy.f -o daisy.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sildist.c -o sildist.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mona.c -o mona.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c spannel.c -o spannel.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c fanny.c -o fanny.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c twins.c -o twins.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c clara.c -o clara.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pam.c -o pam.o make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 Rd warning: /usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html Rd warning: /usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic Rd warning: /usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic 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 Rd warning: /usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic 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 Rd warning: /usr/src/tmp/RtmpOeswZ3/R.INSTALL1893a6e16c72d/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic 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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chol.f -o chol.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gnls.c -o gnls.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pythag.c -o pythag.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pdMat.c -o pdMat.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c nlme.c -o nlme.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c rs.f -o rs.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c corStruct.c -o corStruct.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c nlmefit.c -o nlmefit.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmp3XKduE/R.INSTALL18a086762d4e0/nlme/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 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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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Tsparse.c -o Tsparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cs_utils.c -o cs_utils.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dense.c -o dense.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chm_common.c -o chm_common.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgCMatrix.c -o dgCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dppMatrix.c -o dppMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Mutils.c -o Mutils.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dsCMatrix.c -o dsCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c Csparse.c -o Csparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c factorizations.c -o factorizations.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' ( cd Lib ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c ldense.c -o ldense.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' ( cd Source ; make clean ) ( cd Source ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-4.0.5/etc/Makeconf" -f Makefile ) make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c abIndex.c -o abIndex.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cs.c -o cs.o cs.c: In function 'cs_qr': cs.c:1409:18: warning: variable 'm' set but not used [-Wunused-but-set-variable] 1409 | csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai, | ^ make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sparseQR.c -o sparseQR.o make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:30:10: 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:238:10: 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:30:10: 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:238:10: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:1497:2: 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:1495:9: 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, | ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1496:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] 1496 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, | ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:562:7: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:50:46: 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:50:46: 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:50:46: 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:50:46: 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:50:46: 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:50:46: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o ../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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:1497:2: 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:1495:9: 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, | ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1496:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] 1496 | jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, | ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:50:46: 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:50:46: 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:50:46: 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:50:46: 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:50:46: 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:50:46: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:30:10: 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:238:10: 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:30:10: 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:238:10: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:562:7: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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; | ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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 ; | ^~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:433:33: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/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 -march=i586 -mtune=generic -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:433:33: 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/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/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 make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/CHOLMOD/Lib' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.0.5/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c colamd.c -o colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' ar -rucs ../../COLAMD.a colamd.o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/COLAMD/Source' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-4.0.5/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/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 make[5]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/AMD/Source' make[4]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/SuiteSparse_config' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/SuiteSparse_config' ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src/SuiteSparse_config' make[3]: Entering directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 Rd warning: /usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic 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 Rd warning: /usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/man/image-methods.Rd:81: file link 'get.gpar' in package 'grid' does not exist and so has been treated as a topic 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 Rd warning: /usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic 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 Rd warning: /usr/src/tmp/RtmpxpKq2u/R.INSTALL18a062d6d3144/Matrix/man/rankMatrix.Rd:87: file link 'qr' in package 'Matrix' does not exist and so has been treated as a topic 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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package survival make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package mgcv make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agexact.c -o agexact.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agfit4.c -o agfit4.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agmart.c -o agmart.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agmart3.c -o agmart3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agscore2.c -o agscore2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agsurv4.c -o agsurv4.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agsurv3.c -o agsurv3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agsurv5.c -o agsurv5.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c agfit5.c -o agfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cdecomp.c -o cdecomp.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chinv2.c -o chinv2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cholesky2.c -o cholesky2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chinv3.c -o chinv3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chsolve2.c -o chsolve2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cholesky3.c -o cholesky3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cholesky5.c -o cholesky5.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chsolve5.c -o chsolve5.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c chsolve3.c -o chsolve3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c collapse.c -o collapse.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c concordance1.c -o concordance1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxdetail.c -o coxdetail.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxcount1.c -o coxcount1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxmart.c -o coxmart.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxmart2.c -o coxmart2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxsafe.c -o coxsafe.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxexact.c -o coxexact.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxscho.c -o coxscho.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c concordance3.c -o concordance3.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxscore2.c -o coxscore2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxfit6.c -o coxfit6.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c dmatrix.c -o dmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c doloop.c -o doloop.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gchol.c -o gchol.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c finegray.c -o finegray.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxsurv2.c -o coxsurv2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxfit5.c -o coxfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxsurv1.c -o coxsurv1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c multicheck.c -o multicheck.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c norisk.c -o norisk.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pystep.c -o pystep.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survConcordance.c -o survConcordance.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survfit4.c -o survfit4.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pyears2.c -o pyears2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pyears3b.c -o pyears3b.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survdiff2.c -o survdiff2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c pyears1.c -o pyears1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survpenal.c -o survpenal.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survfitci.c -o survfitci.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survregc1.c -o survregc1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survreg6.c -o survreg6.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survfitresid.c -o survfitresid.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survsplit.c -o survsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survregc2.c -o survregc2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c tmerge.c -o tmerge.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survreg7.c -o survreg7.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c survfitkm.c -o survfitkm.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c zph1.c -o zph1.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c zph2.c -o zph2.o make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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 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-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpjD0z9y/R.INSTALL25411b1840a8/survival/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' begin installing recommended package boot make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c davies.c -o davies.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c coxph.c -o coxph.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mgcv.c -o mgcv.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c misc.c -o misc.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c magic.c -o magic.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mvn.c -o mvn.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c soap.c -o soap.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c qp.c -o qp.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c tprs.c -o tprs.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c discrete.c -o discrete.o discrete.c: In function 'Xbd0': discrete.c:366: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 366 | #pragma omp critical 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sparse-smooth.c -o sparse-smooth.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c mat.c -o mat.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c gdi.c -o gdi.o make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-4.0.5/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -march=i586 -mtune=generic -fno-strict-aliasing -c sparse.c -o sparse.o sparse.c: In function 'sprealloc': sparse.c:116: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas] 116 | #pragma omp critical | make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' i586-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-4.0.5/lib -L/usr/local/lib -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 -L/usr/src/RPM/BUILD/R-4.0.5/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpGWeGuX/R.INSTALL2541669f71818/mgcv/src' installing to /usr/src/RPM/BUILD/R-4.0.5/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 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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-4.0.5/src/library/Recommended' make[1]: Entering directory 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Converting parsed Rd's to LaTeX ........................................... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi @setfilename R-FAQ.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3285--3293 @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, 357484 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3285--3293 @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, 373468 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] 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] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3285--3293 @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, 373471 bytes). Transcript written on R-FAQ.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi @setfilename R-data.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/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] 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] ) Output written on R-data.pdf (33 pages, 267310 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.aux) Chapter 1 [1] Writing index file R-data.cp [2] [3] [4] 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] [29] (Concept index) [30] [31] ) Output written on R-data.pdf (35 pages, 306499 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-data.aux) Chapter 1 [1] Writing index file R-data.cp [2] [3] [4] 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] [29] (Concept index) [30] [31] ) Output written on R-data.pdf (35 pages, 306501 bytes). Transcript written on R-data.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi @setfilename R-admin.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/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 [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 1483--1487 []@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 2060--2060 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] [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 3223--3223 []@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 (37.99364pt too wide) in paragraph at lines 4968--4968 []@texttt curl -OL https://mac.r-project.org/libs-4/pcre2-10.34-darwin.17-x86_ 64.tar.gz[] Overfull \hbox (20.74757pt too wide) in paragraph at lines 4970--4970 []@texttt curl -OL https://mac.r-project.org/libs-4/xz-5.2.4-darwin.17-x86_64. tar.gz[] Overfull \hbox (106.97789pt too wide) in paragraph at lines 5024--5024 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [60] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5062--5062 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [61] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5173--5173 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [62] [63] [64] Overfull \hbox (16.31242pt too wide) in paragraph at lines 5392--5392 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Cont ents/Home[] [65] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5513--5513 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5515--5521 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5544--5544 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [66] [67] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5746--5746 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [68] [69] (Function and variable index) [70] No file R-admin.vrs. (Concept index) [71] No file R-admin.cps. (Environment variable index) [72] No file R-admin.ens. [73] ) (see the transcript file for additional information) Output written on R-admin.pdf (76 pages, 467932 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [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 1483--1487 []@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 2060--2060 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] [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 3223--3223 []@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 (37.99364pt too wide) in paragraph at lines 4968--4968 []@texttt curl -OL https://mac.r-project.org/libs-4/pcre2-10.34-darwin.17-x86_ 64.tar.gz[] Overfull \hbox (20.74757pt too wide) in paragraph at lines 4970--4970 []@texttt curl -OL https://mac.r-project.org/libs-4/xz-5.2.4-darwin.17-x86_64. tar.gz[] Overfull \hbox (106.97789pt too wide) in paragraph at lines 5024--5024 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [60] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5062--5062 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [61] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5173--5173 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [62] [63] [64] Overfull \hbox (16.31242pt too wide) in paragraph at lines 5392--5392 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Cont ents/Home[] [65] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5513--5513 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5515--5521 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5544--5544 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [66] [67] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5746--5746 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [68] [69] (Function and variable index) [70] (Concept index) [71] (Environment variable index) [72] [73] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (78 pages, 511870 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [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 1483--1487 []@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 2060--2060 []@texttt Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))[] [24] [25] [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 3223--3223 []@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 (37.99364pt too wide) in paragraph at lines 4968--4968 []@texttt curl -OL https://mac.r-project.org/libs-4/pcre2-10.34-darwin.17-x86_ 64.tar.gz[] Overfull \hbox (20.74757pt too wide) in paragraph at lines 4970--4970 []@texttt curl -OL https://mac.r-project.org/libs-4/xz-5.2.4-darwin.17-x86_64. tar.gz[] Overfull \hbox (106.97789pt too wide) in paragraph at lines 5024--5024 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [60] Overfull \hbox (45.05586pt too wide) in paragraph at lines 5062--5062 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig[] [61] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5173--5173 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] [62] [63] [64] Overfull \hbox (16.31242pt too wide) in paragraph at lines 5392--5392 []@texttt JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Cont ents/Home[] [65] Overfull \hbox (14.99889pt too wide) in paragraph at lines 5513--5513 []@texttt PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++ abi.a[] Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5515--5521 @textrm tran run-time li-braries @texttt /usr/local/gfortran/lib/libgfortran.a [] @textrm and Underfull \hbox (badness 10000) in paragraph at lines 5515--5521 @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 5544--5544 []@texttt FC="/usr/local/gfortran/bin/gfortran -mtune=native -mmacosx-version- min=10.13"[] [66] [67] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5746--5746 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [68] [69] (Function and variable index) [70] (Concept index) [71] (Environment variable index) [72] [73] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (78 pages, 511892 bytes). Transcript written on R-admin.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' collecting LaTeX docs for package 'mgcv' ... Converting parsed Rd's to LaTeX ............... make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi @setfilename R-ints.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1468--1468 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1469--1469 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1470--1470 [] @texttt length(meth.Ops <- nM$`.__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 3653--3662 @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 3653--3662 @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 3653--3662 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3874--3879 @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, 402443 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/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 3653--3662 @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 3653--3662 @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 3653--3662 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3874--3879 @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] [63] (Concept index) [64] [65] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 453022 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/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 3653--3662 @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 3653--3662 @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 3653--3662 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3874--3879 @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] [63] (Concept index) [64] [65] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 453022 bytes). Transcript written on R-ints.log. tar: R-ints.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-ints.toc) 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$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1471--1471 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3653--3662 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3653--3662 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3653--3662 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3874--3879 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] [53] [54] [55] Chapter 9 [56] [57] Chapter 10 [58] Chapter 11 [59] Chapter 12 [60] [61] (Function and variable index) [62] [63] (Concept index) [64] [65] ) (see the transcript file for additional information) Output written on R-ints.pdf (69 pages, 453022 bytes). Transcript written on R-ints.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi @setfilename R-lang.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/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 4336--4338 []@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, 326171 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/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 4336--4338 []@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] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374575 bytes). Transcript written on R-lang.log. tar: R-lang.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) 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 4336--4338 []@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] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 383252 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-4.0.5/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 4336--4338 []@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] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374580 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi @setfilename R-intro.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/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, 571338 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc) (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] [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] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 629904 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-4.0.5/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] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb> Output written on R-intro.pdf (105 pages, 620868 bytes). Transcript written on R-intro.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi @setfilename R-exts.info This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/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] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2461--2461 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [28] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2463--2463 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2775--2775 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4434--4434 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4453--4453 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [51] [52] [53] [54] [55] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4856--4856 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4858--4858 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4859--4859 [] @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 4874--4874 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [56] Underfull \hbox (badness 7558) in paragraph at lines 4929--4933 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5548--5548 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [64] [65] [66] [67] [68] [69] Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 7138--7145 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7317--7323 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95] Chapter 4 [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 8611--8620 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [101] [102] [103] [104] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9028--9028 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [105] Underfull \hbox (badness 10000) in paragraph at lines 9056--9058 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [106] [107] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9202--9202 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [108] [109] [110] [111] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9604--9604 []@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 9623--9623 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [112] Overfull \hbox (119.7888pt too wide) in paragraph at lines 9634--9634 []@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 9664--9664 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10507--10507 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [123] [124] [125] [126] [127] [128] [129] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11084--11084 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [130] [131] [132] [133] [134] [135] [136] [137] [138] Underfull \hbox (badness 10000) in paragraph at lines 11927--11929 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12967--12967 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [152] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13067--13067 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [153] Chapter 6 [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 15002--15008 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [176] [177] Chapter 8 [178] [179] [180] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15413--15413 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [181] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15471--15471 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [182] [183] [184] [185] [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 15974--15981 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [188] [189] Underfull \hbox (badness 10000) in paragraph at lines 16097--16101 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [190] No file R-exts.vrs. (Concept index) [191] No file R-exts.cps. [192] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (195 pages, 922101 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.0.5/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] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2461--2461 []@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 2463--2463 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] [31] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2775--2775 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4434--4434 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] [50] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4453--4453 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [51] [52] [53] [54] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4856--4856 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4858--4858 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4859--4859 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [55] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4874--4874 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] Underfull \hbox (badness 7558) in paragraph at lines 4929--4933 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5548--5548 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [64] [65] [66] [67] [68] [69] Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 7138--7145 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7317--7323 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95] Chapter 4 [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 8611--8620 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [101] [102] [103] [104] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9028--9028 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [105] Underfull \hbox (badness 10000) in paragraph at lines 9056--9058 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [106] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9202--9202 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [107] [108] [109] [110] [111] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9604--9604 []@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 9623--9623 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [112] Overfull \hbox (119.7888pt too wide) in paragraph at lines 9634--9634 []@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 9664--9664 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10507--10507 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [123] [124] [125] [126] [127] [128] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11084--11084 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] Underfull \hbox (badness 10000) in paragraph at lines 11927--11929 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12967--12967 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [152] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13067--13067 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [153] Chapter 6 [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 15002--15008 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [176] [177] Chapter 8 [178] [179] [180] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15413--15413 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [181] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15471--15471 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [182] [183] [184] [185] [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 15974--15981 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [188] [189] Underfull \hbox (badness 10000) in paragraph at lines 16097--16101 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [190] [191] [192] [193] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [194] [195] [196] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (202 pages, 986130 bytes). Transcript written on R-exts.log. tar: R-exts.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 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] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2461--2461 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] [28] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2463--2463 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [29] [30] [31] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2775--2775 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4434--4434 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4453--4453 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [51] [52] [53] [54] [55] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4856--4856 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4858--4858 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4859--4859 [] @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 4874--4874 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [56] Underfull \hbox (badness 7558) in paragraph at lines 4929--4933 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5548--5548 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [64] [65] [66] [67] [68] [69] Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 7138--7145 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7317--7323 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95] Chapter 4 [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 8611--8620 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [101] [102] [103] [104] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9028--9028 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [105] Underfull \hbox (badness 10000) in paragraph at lines 9056--9058 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [106] [107] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9202--9202 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [108] [109] [110] [111] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9604--9604 []@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 9623--9623 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [112] Overfull \hbox (119.7888pt too wide) in paragraph at lines 9634--9634 []@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 9664--9664 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10507--10507 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [123] [124] [125] [126] [127] [128] [129] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11084--11084 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [130] [131] [132] [133] [134] [135] [136] [137] [138] Underfull \hbox (badness 10000) in paragraph at lines 11927--11929 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12967--12967 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [152] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13067--13067 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [153] Chapter 6 [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 15002--15008 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [176] [177] Chapter 8 [178] [179] [180] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15413--15413 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [181] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15471--15471 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [182] [183] [184] [185] [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 15974--15981 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [188] [189] Underfull \hbox (badness 10000) in paragraph at lines 16097--16101 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [190] [191] [192] [193] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [194] [195] [196] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (202 pages, 996700 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.0.5/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] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2461--2461 []@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 2463--2463 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] [31] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2775--2775 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4434--4434 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] [50] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4453--4453 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [51] [52] [53] [54] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4856--4856 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4858--4858 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4859--4859 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [55] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4874--4874 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] Underfull \hbox (badness 7558) in paragraph at lines 4929--4933 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5548--5548 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [64] [65] [66] [67] [68] [69] Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 7138--7145 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7317--7323 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95] Chapter 4 [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 8611--8620 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [101] [102] [103] [104] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9028--9028 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [105] Underfull \hbox (badness 10000) in paragraph at lines 9056--9058 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [106] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9202--9202 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [107] [108] [109] [110] [111] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9604--9604 []@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 9623--9623 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [112] Overfull \hbox (119.7888pt too wide) in paragraph at lines 9634--9634 []@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 9664--9664 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10507--10507 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [123] [124] [125] [126] [127] [128] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11084--11084 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] Underfull \hbox (badness 10000) in paragraph at lines 11927--11929 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12967--12967 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [152] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13067--13067 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [153] Chapter 6 [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 15002--15008 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [176] [177] Chapter 8 [178] [179] [180] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15413--15413 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [181] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15471--15471 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [182] [183] [184] [185] [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 15974--15981 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [188] [189] Underfull \hbox (badness 10000) in paragraph at lines 16097--16101 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [190] [191] [192] [193] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [194] [195] [196] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (202 pages, 986179 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2019-03-03.15]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-4.0.5/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-4.0.5/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] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2461--2461 []@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 2463--2463 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [28] [29] [30] [31] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2775--2775 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Overfull \hbox (59.67485pt too wide) in paragraph at lines 4434--4434 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] [50] Overfull \hbox (37.99364pt too wide) in paragraph at lines 4453--4453 []@texttt CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD config CXX PICFLAGS`[] [51] [52] [53] [54] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4856--4856 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4858--4858 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4859--4859 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [55] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4874--4874 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] Underfull \hbox (badness 7558) in paragraph at lines 4929--4933 @texttt /Applications/CMake.app/Contents/bin/cmake[] @textrm and that should b e looked for [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5548--5548 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [64] [65] [66] [67] [68] [69] Chapter 2 [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 7138--7145 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [82] [83] Underfull \hbox (badness 10000) in paragraph at lines 7317--7323 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [84] [85] [86] [87] Chapter 3 [88] [89] [90] [91] [92] [93] [94] [95] Chapter 4 [96] [97] [98] [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 8611--8620 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [101] [102] [103] [104] Overfull \hbox (56.55324pt too wide) in paragraph at lines 9028--9028 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] [105] Underfull \hbox (badness 10000) in paragraph at lines 9056--9058 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [106] Overfull \hbox (50.80455pt too wide) in paragraph at lines 9202--9202 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [107] [108] [109] [110] [111] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9604--9604 []@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 9623--9623 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [112] Overfull \hbox (119.7888pt too wide) in paragraph at lines 9634--9634 []@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 9664--9664 []@texttt Warning: Type mismatch in argument 'jpvt' at (1); passed REAL(8) to INTEGER(4)[] Chapter 5 [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10507--10507 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [123] [124] [125] [126] [127] [128] Overfull \hbox (16.31242pt too wide) in paragraph at lines 11084--11084 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] Underfull \hbox (badness 10000) in paragraph at lines 11927--11929 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12967--12967 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [152] Overfull \hbox (50.80455pt too wide) in paragraph at lines 13067--13067 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] [153] Chapter 6 [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Warning: unbalanced parentheses in @def... [170] [171] [172] [173] [174] [175] Underfull \hbox (badness 10000) in paragraph at lines 15002--15008 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [176] [177] Chapter 8 [178] [179] [180] Overfull \hbox (22.06111pt too wide) in paragraph at lines 15413--15413 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [181] Overfull \hbox (33.55849pt too wide) in paragraph at lines 15471--15471 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [182] [183] [184] [185] [186] [187] Underfull \hbox (badness 10000) in paragraph at lines 15974--15981 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [188] [189] Underfull \hbox (badness 10000) in paragraph at lines 16097--16101 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [190] [191] [192] [193] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [194] [195] [196] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (202 pages, 986082 bytes). Transcript written on R-exts.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-12-01> (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2018/09/03 v1.4i 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/ts1enc.def (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/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/oberdiek/hobsub-hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 377. 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(/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texmf-dist/tex/latex/oberdiek/grfext.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/generic/oberdiek/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 2435) in paragraph at lines 212--217 []\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/ ptm/m/n/10 is true, there are 10 such Underfull \hbox (badness 3009) in paragraph at lines 221--233 \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 363--366 [][][]\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 561--567 []\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] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 903--903 []\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 921--921 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1532--1538 Underfull \hbox (badness 10000) in paragraph at lines 1545--1547 []\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 1724--1724 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1752--1755 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1871--1873 []\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 [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2008--2008 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\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 2318--2318 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2446--2448 []\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 2449--2454 [][][]\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 2517--2519 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2684--2684 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3353--3353 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3384--3384 []\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 3385--3385 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3392--3392 []\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 3393--3393 [] \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 3396--3396 []\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 3836--3838 []\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] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] Underfull \hbox (badness 4927) in paragraph at lines 4335--4339 []\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 4335--4339 \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 [66] [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4419--4419 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4484--4487 []\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 4644--4644 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = TRUE)[] Underfull \hbox (badness 1199) in paragraph at lines 4675--4681 []\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 4686--4689 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [71] [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4862--4862 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 5115--5117 []\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 [77] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5528--5536 []\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 [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 1796) in paragraph at lines 6094--6102 []\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 : / / [92] [93] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6288--6288 []\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 6290--6290 []\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 6291--6291 []\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}[] [94] [95] Underfull \hbox (badness 1242) in paragraph at lines 6430--6434 \T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment. [96] Underfull \hbox (badness 1635) in paragraph at lines 6493--6496 []\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 6497--6500 []\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 [97] Underfull \hbox (badness 1308) in paragraph at lines 6540--6548 []\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 [98] [99] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6704--6704 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] Underfull \vbox (badness 10000) has occurred while \output is active [100] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6754--6756 []\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 : [101] Underfull \hbox (badness 1997) in paragraph at lines 6881--6886 []\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 , [102] Underfull \hbox (badness 10000) in paragraph at lines 6919--6922 []\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 6919--6922 \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 [103] [104] Underfull \hbox (badness 1406) in paragraph at lines 7101--7107 []\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 7101--7107 \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 7101--7107 \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 7101--7107 \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 7121--7123 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [105] Underfull \hbox (badness 3302) in paragraph at lines 7163--7170 []\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 7163--7170 \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 7163--7170 \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- [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [109] [110] Underfull \hbox (badness 1231) in paragraph at lines 7492--7498 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 7704--7706 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [114] [115] [116] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7849--7849 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [117] [118] [119] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 8209--8219 []\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 8209--8219 [][]\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 Overfull \hbox (4.63962pt too wide) in paragraph at lines 8241--8246 []\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") [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1629) in paragraph at lines 8730--8742 []\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 8730--8742 \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 = [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9178--9182 []\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 [135] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9269--9269 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9271--9271 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [136] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9297--9297 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9298--9298 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [137] [138] Underfull \hbox (badness 5403) in paragraph at lines 9435--9437 []\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 9454--9456 []\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 [139] [140] [141] Underfull \hbox (badness 1603) in paragraph at lines 9679--9682 []\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 [142] [143] [144] [145] [146] [147] [148] [149] [150] Underfull \hbox (badness 1917) in paragraph at lines 10292--10297 []\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 [151] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10347--10347 []\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 10348--10348 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [152] [153] Underfull \hbox (badness 1168) in paragraph at lines 10450--10455 \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 10489--10495 []\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 Underfull \hbox (badness 5403) in paragraph at lines 10496--10499 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [154] [155] Underfull \hbox (badness 2828) in paragraph at lines 10655--10660 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10655--10660 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10655--10660 \T1/pcr/m/n/10 754-[]2019$[][]\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 : [156] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10686--10686 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [157] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10759--10759 []\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, ..[] [158] [159] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10906--10906 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [160] [161] [162] Underfull \hbox (badness 6396) in paragraph at lines 11103--11111 []\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 11112--11114 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 11329--11332 []\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 [166] [167] [168] [169] [170] [171] [172] [173] [174] Underfull \hbox (badness 5288) in paragraph at lines 12029--12031 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [175] Underfull \hbox (badness 3039) in paragraph at lines 12039--12044 []\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 Underfull \hbox (badness 10000) in paragraph at lines 12099--12101 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 12221--12225 []\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 12221--12225 \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 [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 12336--12338 []\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 [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13181--13181 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [191] [192] [193] [194] [195] [196] Underfull \hbox (badness 2221) in paragraph at lines 13635--13644 \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 13635--13644 \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 [197] [198] [199] [200] Underfull \hbox (badness 2253) in paragraph at lines 13896--13898 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [201] [202] Underfull \hbox (badness 2573) in paragraph at lines 14013--14015 []\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 = [203] [204] Underfull \hbox (badness 10000) in paragraph at lines 14172--14174 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [205] [206] Underfull \hbox (badness 10000) in paragraph at lines 14289--14293 [][][]\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 14300--14303 [][][]$\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 14321--14321 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [207] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14346--14346 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [208] Underfull \hbox (badness 10000) in paragraph at lines 14440--14443 [][][]\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 14450--14450 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [209] Underfull \hbox (badness 10000) in paragraph at lines 14516--14519 []\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 14533--14533 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14562--14562 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14586--14593 []\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 14586--14593 \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 14594--14598 []\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, [211] [212] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14758--14758 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14759--14759 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [214] [215] [216] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14991--14991 []\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 14994--14994 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [217] Underfull \hbox (badness 1168) in paragraph at lines 15078--15082 []\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 15078--15082 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [218] Underfull \hbox (badness 6944) in paragraph at lines 15176--15179 [][][]\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 , [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15201--15201 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 15339--15341 []\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 15359--15359 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15365--15365 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [222] Underfull \hbox (badness 2790) in paragraph at lines 15372--15375 []\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 15403--15410 []\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 [223] Underfull \hbox (badness 10000) in paragraph at lines 15478--15480 []\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 15478--15480 \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 15500--15505 []\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 15506--15508 []\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 = [224] Underfull \hbox (badness 10000) in paragraph at lines 15512--15516 []\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 15512--15516 \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 15517--15525 []\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 [225] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15625--15625 []\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 [226] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15647--15647 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16468--16468 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [239] Underfull \hbox (badness 2418) in paragraph at lines 16577--16581 \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 16584--16587 []\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 [240] Underfull \hbox (badness 2326) in paragraph at lines 16619--16626 [][][]\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 , [241] [242] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16869--16869 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [244] Underfull \hbox (badness 1867) in paragraph at lines 16894--16901 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17189--17189 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17218--17218 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17269--17269 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [250] [251] [252] [253] [254] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17636--17636 []\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))) [255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17701--17701 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [256] [257] [258] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17891--17891 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [259] [260] [261] [262] Underfull \hbox (badness 2285) in paragraph at lines 18225--18227 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18233--18233 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] [263] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18263--18263 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [264] [265] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18397--18397 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18403--18403 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18406--18406 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18412--18412 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [266] [267] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18539--18539 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18547--18547 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [268] [269] [270] Underfull \hbox (badness 10000) in paragraph at lines 18752--18754 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [271] [272] [273] [274] [275] Underfull \hbox (badness 10000) in paragraph at lines 19090--19096 Underfull \hbox (badness 10000) in paragraph at lines 19103--19105 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [276] [277] [278] Underfull \hbox (badness 4699) in paragraph at lines 19335--19338 []\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 , [279] [280] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19463--19463 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [281] [282] [283] Underfull \hbox (badness 4739) in paragraph at lines 19598--19600 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19647--19647 []\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 19648--19648 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1975) in paragraph at lines 20224--20227 []\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 [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1077) in paragraph at lines 20622--20627 []\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 [299] Underfull \hbox (badness 10000) in paragraph at lines 20636--20643 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [300] Underfull \hbox (badness 10000) in paragraph at lines 20710--20714 []\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-tory [301] [302] Underfull \hbox (badness 10000) in paragraph at lines 20859--20863 []\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 20859--20863 [][]\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 20864--20871 []\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- [303] [304] Underfull \hbox (badness 10000) in paragraph at lines 20995--21002 [][][]\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 , [305] Underfull \hbox (badness 10000) in paragraph at lines 21116--21120 []\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 [306] Underfull \hbox (badness 5161) in paragraph at lines 21186--21191 []\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 21186--21191 \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 21186--21191 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21186--21191 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [307] [308] [309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21353--21353 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21357--21357 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [310] Underfull \hbox (badness 3343) in paragraph at lines 21418--21422 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [311] [312] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21559--21559 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21570--21570 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [313] [314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21681--21681 []\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 21684--21684 []\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 21729--21734 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [315] Underfull \hbox (badness 2564) in paragraph at lines 21820--21823 []\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 [316] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21850--21850 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [317] [318] Underfull \hbox (badness 1400) in paragraph at lines 22018--22022 [][][]\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 [319] [320] [321] Underfull \hbox (badness 2469) in paragraph at lines 22188--22194 []\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22188--22194 \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 22188--22194 \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, [322] [323] [324] [325] [326] [327] [328] [329] [330] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22826--22826 []\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 22827--22827 [] \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 22830--22830 []\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)[] [331] [332] Underfull \hbox (badness 1655) in paragraph at lines 22954--22958 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [333] [334] [335] [336] Underfull \hbox (badness 2277) in paragraph at lines 23203--23206 []\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. [337] [338] Underfull \hbox (badness 10000) in paragraph at lines 23332--23335 []\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, [339] [340] [341] [342] [343] [344] [345] Underfull \hbox (badness 1484) in paragraph at lines 23788--23796 []\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 23788--23796 \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 / [346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23866--23866 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [347] [348] [349] [350] [351] [352] [353] Underfull \hbox (badness 1448) in paragraph at lines 24377--24385 \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 = [354] [355] Underfull \hbox (badness 3849) in paragraph at lines 24492--24497 []\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 [356] Underfull \hbox (badness 7308) in paragraph at lines 24569--24575 []\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 24569--24575 \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 24569--24575 [][]\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 24579--24582 []\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 24579--24582 \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 [357] [358] Underfull \hbox (badness 10000) in paragraph at lines 24732--24734 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [359] [360] [361] Underfull \hbox (badness 6188) in paragraph at lines 24952--24955 []\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 [362] [363] [364] Underfull \hbox (badness 1521) in paragraph at lines 25137--25151 \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- [365] [366] [367] [368] [369] Underfull \hbox (badness 2197) in paragraph at lines 25448--25452 []\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 25448--25452 \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 25462--25466 []\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 25462--25466 \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 25504--25504 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25508--25508 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [371] Underfull \hbox (badness 10000) in paragraph at lines 25556--25562 []\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 25556--25562 \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 25569--25571 []\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% Overfull \hbox (4.38043pt too wide) in paragraph at lines 25620--25620 [] \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:[] [372] [373] [374] Underfull \hbox (badness 8189) in paragraph at lines 25815--25821 []\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 [][][] [375] [376] [377] Underfull \hbox (badness 1694) in paragraph at lines 26040--26043 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [378] [379] [380] [381] Underfull \hbox (badness 1603) in paragraph at lines 26287--26289 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [382] [383] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26414--26422 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [384] [385] Underfull \hbox (badness 3271) in paragraph at lines 26633--26636 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [386] [387] [388] Underfull \hbox (badness 3138) in paragraph at lines 26937--26943 []\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 26937--26943 \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 26937--26943 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 26950--26953 []\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 [389] Underfull \hbox (badness 1389) in paragraph at lines 26976--26978 []\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 26996--27002 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27011--27016 []\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 27029--27032 []\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 Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see [390] Underfull \hbox (badness 10000) in paragraph at lines 27053--27059 []\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 27053--27059 \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 27053--27059 \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 27053--27059 \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 27068--27075 []\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 27068--27075 \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 27068--27075 \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 27068--27075 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [391] [392] [393] [394] Underfull \vbox (badness 10000) has occurred while \output is active [395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27416--27416 []\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 27429--27433 []\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 27429--27433 \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)] = [396] [397] Underfull \hbox (badness 10000) in paragraph at lines 27576--27579 []\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 27576--27579 \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 [398] [399] [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27854--27860 [][][]\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 27854--27860 [][]\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 27876--27876 []\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 27888--27888 []\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 27901--27901 []\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 27905--27905 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [402] [403] [404] Underfull \hbox (badness 1360) in paragraph at lines 28071--28075 []\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 = [405] [406] [407] [408] [409] [410] Underfull \hbox (badness 1817) in paragraph at lines 28466--28470 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [411] Underfull \hbox (badness 1796) in paragraph at lines 28534--28537 []\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 [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 28738--28741 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29433--29433 [] \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))[] [425] [426] Underfull \vbox (badness 10000) has occurred while \output is active [427] [428] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29721--29721 []\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 29732--29732 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Underfull \vbox (badness 10000) has occurred while \output is active [429] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29738--29738 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29739--29739 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29744--29744 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [430] Underfull \hbox (badness 7415) in paragraph at lines 29827--29831 []\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 29848--29848 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29894--29894 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [432] Underfull \hbox (badness 3713) in paragraph at lines 30017--30028 []\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 [433] [434] Underfull \hbox (badness 1248) in paragraph at lines 30161--30168 \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 30161--30168 \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 / [435] [436] Underfull \hbox (badness 1533) in paragraph at lines 30279--30282 []\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 [437] [438] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30424--30424 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30442--30453 []\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 [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30586--30586 []\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 30588--30588 []\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 30589--30589 []\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 30590--30590 []\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 30591--30591 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] [441] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30598--30598 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [442] [443] [444] [445] [446] Underfull \hbox (badness 4048) in paragraph at lines 30945--30950 []\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 30945--30950 \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 30945--30950 \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 , [447] [448] [449] [450] [451] [452] [453] [454] Underfull \hbox (badness 2080) in paragraph at lines 31482--31492 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver -sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 31508--31508 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 7558) in paragraph at lines 32026--32030 []\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 32036--32038 []\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 5417) in paragraph at lines 32041--32044 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 32047--32049 []\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 32050--32054 []\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 . [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 10000) in paragraph at lines 32453--32457 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [468] [469] [470] [471] [472] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32809--32809 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32812--32812 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [473] [474] [475] [476] [477] [478] [479] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33252--33252 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [480] [481] [482] [483] [484] [485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33689--33689 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [486] [487] Underfull \hbox (badness 1158) in paragraph at lines 33793--33798 []\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 Underfull \hbox (badness 10000) in paragraph at lines 33820--33826 []\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 33820--33826 \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 [488] [489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33978--33978 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [490] [491] [492] Underfull \hbox (badness 8151) in paragraph at lines 34238--34241 []\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 . [493] [494] [495] [496] Underfull \hbox (badness 10000) in paragraph at lines 34453--34458 []\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 = [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] Overfull \hbox (66.78088pt too wide) in paragraph at lines 35442--35442 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [512] [513] [514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 35694--35694 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 35696--35696 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [515] Underfull \hbox (badness 4954) in paragraph at lines 35739--35745 [][][]\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 35739--35745 [][]\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 [516] [517] Overfull \hbox (20.58041pt too wide) in paragraph at lines 35850--35850 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [518] [519] [520] [521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36185--36185 []\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)[] [522] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36200--36200 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [523] [524] [525] Underfull \hbox (badness 10000) in paragraph at lines 36419--36421 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [526] [527] [528] Overfull \hbox (12.78088pt too wide) in paragraph at lines 36646--36646 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 36647--36647 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [529] [530] [531] [532] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36914--36914 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [533] Underfull \hbox (badness 6110) in paragraph at lines 37005--37015 []\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 37005--37015 \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 37005--37015 \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 37005--37015 \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 37005--37015 \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 Underfull \hbox (badness 10000) in paragraph at lines 37051--37057 []\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 37051--37057 \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 37051--37057 \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 [534] Underfull \hbox (badness 1460) in paragraph at lines 37063--37070 []\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 37063--37070 \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 37063--37070 \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 [535] [536] [537] Underfull \hbox (badness 1484) in paragraph at lines 37295--37299 []\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 [538] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37357--37357 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [539] [540] [541] [542] [543] [544] [545] [546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37937--37937 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [547] [548] [549] [550] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38185--38185 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38229--38229 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [551] [552] [553] [554] [555] [556] [557] Overfull \hbox (52.98038pt too wide) in paragraph at lines 38663--38663 []\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 38666--38666 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [558] Underfull \hbox (badness 10000) in paragraph at lines 38717--38724 []\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 38717--38724 \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 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 38770--38770 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [559] [560] [561] [562] [563] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39081--39081 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [564] [565] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39246--39246 []\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. Overfull \hbox (20.58041pt too wide) in paragraph at lines 39284--39284 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [567] Underfull \hbox (badness 2293) in paragraph at lines 39314--39320 []\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 39314--39320 \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 39333--39338 []\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 39333--39338 \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 [568] Underfull \hbox (badness 2452) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [569] [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39611--39615 []\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 Underfull \hbox (badness 1584) in paragraph at lines 39626--39629 []\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 [572] [573] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39758--39758 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39835--39835 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [575] [576] [577] Underfull \hbox (badness 1082) in paragraph at lines 39979--39982 []\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 [578] [579] [580] Underfull \hbox (badness 1038) in paragraph at lines 40170--40173 []\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 [581] [582] [583] [584] [585] Underfull \hbox (badness 1442) in paragraph at lines 40534--40538 \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 = [586] [587] [588] [589] Underfull \hbox (badness 4096) in paragraph at lines 40784--40787 []\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 , [590] Underfull \hbox (badness 7888) in paragraph at lines 40898--40902 []\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) > [591] [592] [593] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41052--41052 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 41054--41054 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 41056--41056 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/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 41069--41071 []\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 [594] Underfull \hbox (badness 10000) in paragraph at lines 41149--41152 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [595] [596] Underfull \hbox (badness 3872) in paragraph at lines 41267--41270 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [597] Underfull \hbox (badness 5475) in paragraph at lines 41333--41337 [][][]\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 \ [][]$\T1/pcr/m/n/10 https : / / [598] [599] [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41754--41761 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 41810--41819 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 41810--41819 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [604] Underfull \hbox (badness 1082) in paragraph at lines 41820--41832 \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' in that di-rec-tory states the ver-sion. That op-tion is Underfull \hbox (badness 1337) in paragraph at lines 41893--41901 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or [605] Underfull \hbox (badness 10000) in paragraph at lines 41902--41905 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 41956--41959 [][][]$\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 41960--41962 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 41969--41969 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [606] [607] [608] Underfull \hbox (badness 10000) in paragraph at lines 42190--42192 []\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 [609] [610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42312--42312 []\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 42314--42314 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [611] [612] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42415--42415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42417--42417 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [613] [614] [615] Underfull \hbox (badness 6542) in paragraph at lines 42691--42693 []\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 [616] [617] Overfull \hbox (30.78088pt too wide) in paragraph at lines 42810--42810 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [618] Underfull \hbox (badness 1708) in paragraph at lines 42878--42886 []\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 42878--42886 \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 [619] Underfull \hbox (badness 4859) in paragraph at lines 42908--42913 [][][]\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; [620] Underfull \hbox (badness 3895) in paragraph at lines 42970--42982 []\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 42970--42982 \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 , [621] [622] [623] [624] [625] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43292--43292 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [626] [627] [628] [629] [630] [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43760--43760 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [632] Overfull \hbox (25.98041pt too wide) in paragraph at lines 43769--43769 []\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 43835--43841 [][][]\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 , [633] Underfull \hbox (badness 3861) in paragraph at lines 43844--43849 [][][]\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 , [634] [635] Underfull \hbox (badness 1803) in paragraph at lines 43990--43993 []\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 43994--44001 []\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 [636] [637] [638] Underfull \hbox (badness 3668) in paragraph at lines 44209--44211 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [639] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44315--44315 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44390--44390 []\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[] [641] Overfull \hbox (90.78033pt too wide) in paragraph at lines 44398--44398 []\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 ...[] [642] Underfull \hbox (badness 6220) in paragraph at lines 44528--44533 []\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 44528--44533 \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, [643] Underfull \hbox (badness 10000) in paragraph at lines 44549--44554 []\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 44549--44554 \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 [644] Underfull \hbox (badness 2818) in paragraph at lines 44645--44651 []\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 [645] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44680--44680 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [646] [647] [648] [649] [650] [651] Underfull \hbox (badness 2846) in paragraph at lines 45137--45141 []\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 [652] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45177--45177 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 45198--45202 []\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 [653]) (./compiler-pkg.tex [654] Chapter 2. [655] 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 [656] [657] [658]) (./datasets-pkg.tex Chapter 3. [659] [660] [661] [662] [663] 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,[] [664] 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 [665] [666] [667] [668] 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)[] [669] 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") [670] [671] 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") [672] [673] [674] 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. [675] 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") [676] [677] [678] [679] [680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [681] [682] Underfull \hbox (badness 10000) in paragraph at lines 1547--1550 []\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 1547--1550 \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 [683] [684] [685] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1736--1739 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [686] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1830--1830 []\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 1838--1838 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [687] [688] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1954--1954 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [689] [690] [691] [692] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2158--2161 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [693] [694] [695] Overfull \vbox (4.29591pt too high) has occurred while \output is active [696] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2723--2726 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] Overfull \vbox (13.87083pt too high) has occurred while \output is active [702] Underfull \vbox (badness 2376) has occurred while \output is active [703] [704] Overfull \vbox (12.25539pt too high) has occurred while \output is active [705] [706] Overfull \vbox (17.12102pt too high) has occurred while \output is active [707] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3152--3152 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [708] [709] [710] [711] [712] [713] [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [715] [716] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3757--3760 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [717] Overfull \vbox (10.49593pt too high) has occurred while \output is active [718] Overfull \vbox (15.49593pt too high) has occurred while \output is active [719] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3966--3966 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4004--4006 []\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 4004--4006 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733]) (./grDevices-pkg.tex [734] Chapter 4. [735] [736] [737] [738] 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 [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\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 379--387 \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 [741] [742] Overfull \hbox (6.78088pt too wide) in paragraph at lines 516--516 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \hbox (badness 5175) in paragraph at lines 1189--1191 []\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 [753] [754] [755] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] Underfull \hbox (badness 1173) in paragraph at lines 1402--1405 []\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 [756] [757] [758] [759] [760] [761] [762] [763] Underfull \hbox (badness 1565) in paragraph at lines 1890--1895 []\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 1890--1895 \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 [764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1973--1973 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2014--2024 []\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 2014--2024 \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 , [765] [766] Underfull \hbox (badness 10000) in paragraph at lines 2126--2128 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [767] [768] Underfull \hbox (badness 6758) in paragraph at lines 2305--2308 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [769] [770] Underfull \hbox (badness 2326) in paragraph at lines 2423--2433 \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 2423--2433 \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 2423--2433 \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 2423--2433 \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 [771] [772] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2526--2526 []\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 [773] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2642--2642 []\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 2643--2643 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [774] [775] [776] [777] [778] Underfull \hbox (badness 10000) in paragraph at lines 2914--2915 Underfull \vbox (badness 10000) has occurred while \output is active [779] [780] [781] [782] [783] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3247--3247 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [784] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3331--3331 []\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 3332--3332 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 3488--3493 []\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 3488--3493 \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- [787] [788] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3562--3562 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3666--3666 []\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 3673--3673 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [790] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3729--3729 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [791] Underfull \hbox (badness 8170) in paragraph at lines 3758--3761 []\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 , [792] Underfull \hbox (badness 2189) in paragraph at lines 3819--3824 []\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 3857--3861 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [793] Underfull \vbox (badness 10000) has occurred while \output is active [794] Underfull \hbox (badness 5260) in paragraph at lines 3987--3990 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [795] [796] [797] [798] [799] Underfull \hbox (badness 5939) in paragraph at lines 4320--4325 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 10000) in paragraph at lines 4724--4729 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [806] [807] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4839--4839 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [808] [809] Underfull \hbox (badness 1348) in paragraph at lines 5044--5047 []\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 [810] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5068--5068 []\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 5109--5115 []\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 [811] Underfull \hbox (badness 1112) in paragraph at lines 5142--5146 []\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" [812] Underfull \hbox (badness 1755) in paragraph at lines 5284--5286 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [813] [814] [815] Underfull \hbox (badness 7344) in paragraph at lines 5464--5466 []\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 5475--5479 [][][]\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 [816] [817] Underfull \hbox (badness 1552) in paragraph at lines 5602--5611 \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 5602--5611 \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 5602--5611 \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 5612--5614 []\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 5644--5650 \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 [818] Underfull \hbox (badness 10000) in paragraph at lines 5670--5677 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [819] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5771--5771 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\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 [824] [825] [826] [827] [828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6336--6336 []\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 6350--6353 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [829] [830] [831] [832] [833] [834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6685--6685 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 6955--6960 []\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 6955--6960 \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 6955--6960 \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 [839] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7061--7061 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [840] Underfull \hbox (badness 3590) in paragraph at lines 7100--7103 []\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 7100--7103 \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 7111--7111 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [841] Underfull \hbox (badness 1189) in paragraph at lines 7175--7177 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [842] Underfull \hbox (badness 10000) in paragraph at lines 7280--7282 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [843] Underfull \hbox (badness 10000) in paragraph at lines 7326--7333 []\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 7326--7333 \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 [844] Underfull \hbox (badness 5607) in paragraph at lines 7410--7414 []\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 [845] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7462--7462 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [846] [847] Underfull \hbox (badness 5637) in paragraph at lines 7594--7600 \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 7627--7630 []\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 / [848] [849] [850] Underfull \hbox (badness 1231) in paragraph at lines 7796--7798 []\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 [851] [852]) (./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 = [853] [854] [855] 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 [856] [857] [858] [859] 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 [860] [861] 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[] [862] 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 [863] [864] 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, ...)[] [865] [866] [867] 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 (106.98032pt too wide) in paragraph at lines 981--981 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = 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)[] [868] [869] [870] [871] 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"):[] [872] [873] [874] Underfull \hbox (badness 1024) in paragraph at lines 1431--1439 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1465--1467 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [875] [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535 []\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 1536--1536 []\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 1542--1542 []\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 1543--1543 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 1846--1852 [][][]\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 (42.18039pt too wide) in paragraph at lines 1878--1878 []\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 1894--1894 []\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 1903--1903 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [882] [883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1988--1988 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [884] [885] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2117--2117 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2122--2122 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [886] [887] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296 []\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 2297--2297 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [888] Underfull \hbox (badness 1430) in paragraph at lines 2328--2330 []\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 [889] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2421--2428 \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 [890] Underfull \hbox (badness 7273) in paragraph at lines 2503--2507 [][][]\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 [891] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2516--2516 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [892] [893] [894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2750--2750 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2787--2787 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [896] [897] Underfull \hbox (badness 1226) in paragraph at lines 2912--2916 \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 2965--2965 []\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 :[] [898] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2969--2969 []\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 3021--3024 [][][]\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 [899] [900] [901] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3226--3226 []\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 3231--3231 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 3373--3378 []\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 3373--3378 [][]\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 3373--3378 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [904] [905] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3559--3559 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3578--3578 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [907] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3582--3582 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3759--3759 [] \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 3760--3760 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3799--3799 [] \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 [911] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3851--3851 []\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 3859--3859 []\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 3861--3861 []\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 3869--3869 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [912] Underfull \hbox (badness 10000) in paragraph at lines 3932--3936 [][][]\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% [913] [914] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [915] [916] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4198--4198 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [917] Underfull \hbox (badness 3930) in paragraph at lines 4277--4279 []\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 [918] [919] [920] [921] [922] Underfull \hbox (badness 1286) in paragraph at lines 4588--4591 \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 4596--4601 []\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 [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693 []\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 4698--4698 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [925] Underfull \hbox (badness 1264) in paragraph at lines 4889--4902 \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 , [926] [927] Underfull \hbox (badness 10000) in paragraph at lines 5026--5032 []\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. [928] [929] Underfull \hbox (badness 10000) in paragraph at lines 5157--5160 [930 ] Underfull \hbox (badness 10000) in paragraph at lines 5218--5220 [931 ] [932] Underfull \hbox (badness 10000) in paragraph at lines 5408--5410 []\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 [933] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5464--5464 []\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 5465--5465 [] \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 [934] [935] [936] [937] [938] [939] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830 []\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 5831--5831 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [940]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5890 \aliasA{plot}{plot.default}{plot} [941] [942] [943] [944] [945] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [946] [947] [948] [949] [950] [951] Underfull \hbox (badness 10000) in paragraph at lines 6658--6660 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [952] [953] Underfull \hbox (badness 1028) in paragraph at lines 6752--6754 []\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 6795--6796 [][] [954 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6889--6889 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [955] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6920--6920 [] \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 [956] [957] Underfull \hbox (badness 10000) in paragraph at lines 7042--7044 []\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 7069--7069 [] \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 7075--7075 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [958] Underfull \hbox (badness 2600) in paragraph at lines 7135--7137 []\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 [959] [960] [961] [962] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [963] [964] [965] [966] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754 []\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 7758--7758 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [969] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7770--7770 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [970] [971] [972] [973] [974] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8119--8119 []\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 8122--8122 []\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 8126--8126 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [975] [976] [977] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8297--8297 []\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 8298--8298 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [978] [979] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8402--8402 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8413--8418 []\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 [980] Underfull \hbox (badness 1112) in paragraph at lines 8461--8465 []\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 [981] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8521--8521 []\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 8536--8536 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [982] [983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8858--8858 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [986] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8888--8890 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8920--8926 []\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 [987]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8968 \HeaderA{units}{Graphical Units}{units} [988] Underfull \hbox (badness 1205) in paragraph at lines 9033--9035 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [989] [990] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9152--9152 []\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)[] [991]) (./grid-pkg.tex [992] Chapter 6. [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \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 476--482 \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 [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\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- [1011] [1012] [1013] [1014] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\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 [1015] [1016] [1017] [1018] [1019] [1020] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1768--1768 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1021] [1022] [1023] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1982--1982 []\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 1983--1983 []\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 1984--1984 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1024] Underfull \hbox (badness 2961) in paragraph at lines 2019--2024 []\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 , [1025] Underfull \hbox (badness 1430) in paragraph at lines 2078--2083 []\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 2107--2110 []\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 [1026] [1027] [1028] Underfull \hbox (badness 2894) in paragraph at lines 2314--2321 []\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 [1029] [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2470--2470 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2482--2487 []\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- [1032] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2541--2541 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1033] [1034] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2693--2693 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1035] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1036] [1037] [1038] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2967--2967 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1039] [1040] [1041] [1042] [1043] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3282--3282 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1044] [1045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3412--3418 []\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 [1046] [1047] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3504--3504 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1048] [1049] [1050] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3712--3712 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3727--3727 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1051] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3748--3748 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \hbox (badness 1067) in paragraph at lines 4489--4492 []\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 [1064] Underfull \hbox (badness 1430) in paragraph at lines 4535--4540 []\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- [1065] [1066] [1067] Underfull \hbox (badness 7256) in paragraph at lines 4734--4736 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 10000) in paragraph at lines 5371--5373 []\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 [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] Underfull \hbox (badness 6859) in paragraph at lines 6059--6065 []\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 6059--6065 \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") [1088] [1089] [1090] [1091] [1092] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1093] Underfull \hbox (badness 1867) in paragraph at lines 6437--6439 []\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 [1094] Underfull \hbox (badness 10000) in paragraph at lines 6474--6480 [][][]\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 , [1095] [1096] Underfull \hbox (badness 1371) in paragraph at lines 6606--6609 []\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 [1097] Underfull \vbox (badness 10000) has occurred while \output is active [1098] [1099] [1100] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6810--6810 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1101]) (./methods-pkg.tex [1102] Chapter 7. [1103] [1104] 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 [1105] [1106] [1107] 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- [1108] [1109] 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[] [1110] 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 [1111] 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 [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] 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[] [1127] [1128] 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 [1129] [1130] [1131] 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 = [1132] [1133] 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 [1134] [1135] [1136] 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 [1137] 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))[] [1138] [1139] [1140] 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:[] [1141] [1142] [1143] [1144] [1145] [1146] [1147] 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 [1148] [1149] 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 [1150] 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 [] [1151] [1152] 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,...) { [1153] 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 [1154] [1155] [1156] 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 [1157] [1158] [1159] 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,[] [1160] 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) [1161] [1162] [1163] 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 , [1164] [1165] [1166] 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 [1167] [1168] [1169] [1170] 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[] [1171] 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 [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1174] [1175] 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 [1176] [1177] [1178] 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 [1179] [1180] [1181] [1182] [1183] [1184] 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 [1185] [1186] 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 [1187] 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 [1188] [1189] 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 [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] [1193]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1194] 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().[] [1195] [1196] 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")[] [1197]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 [1198] 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 , [1199] [1200] 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 [1201] [1202] 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 [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] 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 [1214] 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(), [1215] 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 =,[] [1216] [1217] [1218] [1219] 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[] [1220] [1221] [1222] 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")[] [1223] [1224] [1225] 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[] [1226] [1227] [1228] [1229] 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[] [1230] 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][] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] 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 [1241] [1242] [1243]) (./parallel-pkg.tex [1244] 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 [1245] 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 [1246] [1247] 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 [1248] [1249] [1250] 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 [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 1917) in paragraph at lines 770--779 []\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 770--779 \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 [1256] [1257] Overfull \hbox (60.78088pt too wide) in paragraph at lines 863--863 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1258] [1259] [1260] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1054--1054 []\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 1058--1058 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1261] Underfull \hbox (badness 5388) in paragraph at lines 1173--1178 []\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 [1262] Underfull \hbox (badness 10000) in paragraph at lines 1197--1205 []\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 1234--1234 []\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)[] [1263] [1264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1350--1350 [] \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 1364--1364 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1265] Underfull \hbox (badness 1577) in paragraph at lines 1393--1396 []\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 1440--1442 []\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 [1266] [1267]) (./splines-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] 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))[] [1277] 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 [1278] [1279] 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)))[] [1280] [1281] [1282]) (./stats-pkg.tex Chapter 10. [1283] 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[] [1284] [1285] [1286] [1287] [1288] 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[] [1289] 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) [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 1024) in paragraph at lines 882--884 []\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 [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 10000) in paragraph at lines 1544--1548 []\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 1544--1548 \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 1544--1548 \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 [1306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620 [] \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 1623--1623 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1307] [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1770--1770 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1309] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1782--1782 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[ ] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2800--2800 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1324] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3040--3040 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1328] [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 3251--3253 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1331] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3300--3300 []\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 3301--3301 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1332] [1333] [1334] [1335] [1336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3692--3692 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1337] [1338] [1339] [1340] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1341] [1342] [1343] [1344] [1345] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4260--4260 []\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 4261--4261 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1346] [1347] [1348] [1349] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4501--4501 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1350] [1351] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4676--4676 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1352] [1353] Underfull \hbox (badness 3989) in paragraph at lines 4770--4777 []\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 = [1354] [1355] [1356] [1357] [1358] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5155--5155 []\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 5157--5157 []\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))[] [1359] [1360] [1361] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5378--5378 []\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 5396--5396 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1362] Underfull \hbox (badness 2680) in paragraph at lines 5423--5425 []\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 [1363] [1364] [1365] Underfull \hbox (badness 1436) in paragraph at lines 5606--5611 []\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 5606--5611 \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 5606--5611 \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 , [1366] [1367] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5809--5809 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1368] [1369] [1370] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5976--5976 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1371] [1372] [1373] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6161--6161 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1374] [1375] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6269--6269 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1376] Underfull \hbox (badness 10000) in paragraph at lines 6336--6341 []\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 [1377] [1378] [1379] Underfull \hbox (badness 5954) in paragraph at lines 6532--6534 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1380] Underfull \hbox (badness 2503) in paragraph at lines 6614--6617 []\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 6618--6620 []\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 6621--6626 \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, [1381] Underfull \hbox (badness 7238) in paragraph at lines 6657--6660 [][][]\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 6692--6692 []\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 6707--6707 []\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):[] [1382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6722--6722 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1383] [1384] [1385] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6967--6967 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1386] [1387] [1388] Underfull \vbox (badness 10000) has occurred while \output is active [1389] [1390] [1391] [1392] Underfull \hbox (badness 10000) in paragraph at lines 7366--7370 \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 [1393] Underfull \hbox (badness 6493) in paragraph at lines 7465--7468 []\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 [1394] [1395] Underfull \hbox (badness 10000) in paragraph at lines 7602--7605 []\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 = [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 8014--8019 []\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 , ..., [1402] [1403] [1404] [1405] [1406] [1407] Underfull \hbox (badness 1210) in paragraph at lines 8369--8371 []\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 [1408] [1409] [1410] [1411] [1412] [1413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8832--8832 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1414] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8877--8877 []\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 8880--8880 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1415] [1416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9018--9018 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1417] [1418] [1419] [1420] [1421] [1422] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9445--9445 [] \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 9446--9446 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1423] [1424] [1425] Underfull \hbox (badness 7291) in paragraph at lines 9625--9627 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1426] [1427] [1428] [1429] [1430] [1431] [1432] Underfull \hbox (badness 6944) in paragraph at lines 10103--10109 [][][]\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); [1433] [1434] [1435] Underfull \hbox (badness 3758) in paragraph at lines 10317--10320 []\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 [1436] [1437] [1438] [1439] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10561--10561 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10587--10592 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] Underfull \hbox (badness 4132) in paragraph at lines 10626--10630 []\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 10680--10686 []\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- [1441] Underfull \hbox (badness 10000) in paragraph at lines 10731--10734 []\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 [1442] [1443] [1444] Underfull \hbox (badness 2142) in paragraph at lines 10948--10951 []\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 ^^@ [1445] Underfull \hbox (badness 1708) in paragraph at lines 11029--11033 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1446] Underfull \hbox (badness 10000) in paragraph at lines 11071--11077 [][][]\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 11109--11114 \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 (= [1447] [1448] Underfull \hbox (badness 2635) in paragraph at lines 11242--11245 \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 [1449] [1450] [1451] Underfull \hbox (badness 1694) in paragraph at lines 11425--11428 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11526--11526 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1453] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11559--11559 [] \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 11572--11576 []\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 [1454] [1455] [1456] [1457] [1458] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1459]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11909 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11969--11969 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1460] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12034--12039 []\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 12051--12053 []\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 [1461] [1462] [1463] [1464] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1465] [1466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1467] [1468] [1469] [1470] Underfull \hbox (badness 10000) in paragraph at lines 12649--12651 []\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 12672--12674 []\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 [1471] Underfull \hbox (badness 2753) in paragraph at lines 12741--12743 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1472] [1473] [1474] [1475] Underfull \hbox (badness 6910) in paragraph at lines 12979--12981 []\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 12985--12989 []\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 12985--12989 \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 [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13692--13692 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1486] Underfull \hbox (badness 4518) in paragraph at lines 13736--13741 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 13935--13939 []\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 , [1490] [1491] [1492] [1493] [1494] Underfull \hbox (badness 1163) in paragraph at lines 14269--14277 \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 , [1495] Underfull \hbox (badness 4518) in paragraph at lines 14389--14394 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1496] [1497] [1498] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14577--14577 []\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 14578--14578 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1499] [1500] [1501] [1502] [1503] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14921--14921 []\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 14922--14922 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1504] [1505] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15015--15015 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2726) in paragraph at lines 15421--15424 []\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 , [1512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15515--15515 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16141--16141 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1523] [1524] Underfull \hbox (badness 1490) in paragraph at lines 16279--16284 \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 [1525] Underfull \hbox (badness 1648) in paragraph at lines 16345--16347 []\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 16360--16369 \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 16360--16369 \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 [1526] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16430--16430 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16988--16988 []\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[] [1536] [1537] [1538] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17220--17220 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] Underfull \vbox (badness 10000) has occurred while \output is active [1550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17981--17981 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1551] [1552] [1553] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18144--18144 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18191--18191 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18238--18238 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] Underfull \hbox (badness 1248) in paragraph at lines 18736--18739 []\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 18749--18753 []\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 [1563] Underfull \hbox (badness 1478) in paragraph at lines 18757--18761 \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 Underfull \hbox (badness 2042) in paragraph at lines 18815--18817 []\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 [1564] [1565] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18921--18921 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1566] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18964--18964 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18982--18982 []\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 18985--18985 []\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 19005--19005 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 19008--19008 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1567] Underfull \hbox (badness 2564) in paragraph at lines 19043--19054 []\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 19043--19054 \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 [1568] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1569] [1570] [1571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19333--19333 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1572] [1573] Underfull \hbox (badness 1337) in paragraph at lines 19444--19447 []\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 [1574] [1575] [1576] [1577] [1578] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19763--19763 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1579] [1580] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19851--19851 [] \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 19853--19853 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19855--19855 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1581] Underfull \hbox (badness 10000) in paragraph at lines 19901--19907 []\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 19942--19946 []\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 [1582] [1583] [1584] [1585] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20195--20195 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20205--20208 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1586] Underfull \hbox (badness 1107) in paragraph at lines 20263--20265 []\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 [1587] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20318--20318 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20325--20325 []\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)[] [1589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20419--20419 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1590] [1591] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1592] Underfull \hbox (badness 7740) in paragraph at lines 20611--20613 []\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 [1593] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20659--20659 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1594] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20751--20751 [] \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 20756--20756 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21611--21611 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1608] Underfull \hbox (badness 6859) in paragraph at lines 21678--21685 [][][]\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 21689--21695 []\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 , [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22435--22435 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1621] [1622] [1623] [1624] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22719--22719 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22720--22720 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 23046--23052 []\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 [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] Underfull \hbox (badness 10000) in paragraph at lines 23602--23604 []\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 23602--23604 \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 23609--23610 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1639] [1640] [1641] Underfull \hbox (badness 1028) in paragraph at lines 23772--23775 []\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 [1642] Underfull \hbox (badness 10000) in paragraph at lines 23882--23885 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] Underfull \hbox (badness 7944) in paragraph at lines 23937--23939 []\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 = [1644] Underfull \hbox (badness 7944) in paragraph at lines 23999--24001 []\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 = [1645] [1646] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24101--24101 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1647] [1648] [1649] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24321--24321 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1650] [1651] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24425--24425 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24468--24474 \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 24489--24492 []\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] = [1652] Underfull \hbox (badness 2134) in paragraph at lines 24558--24562 [][][]\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 24571--24571 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1653] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24600--24600 []\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 24612--24612 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 6268) in paragraph at lines 25067--25072 [][]\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 , [1661] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25095--25095 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1662] [1663] [1664] Underfull \hbox (badness 1867) in paragraph at lines 25272--25274 []\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 25287--25291 []\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 25287--25291 \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 25323--25323 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1665] [1666] [1667] Underfull \hbox (badness 2495) in paragraph at lines 25513--25522 []\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 . [1668] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25595--25595 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1669] Underfull \hbox (badness 1412) in paragraph at lines 25602--25604 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1670] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25689--25689 []\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 25714--25714 []\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 25717--25717 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1671] [1672] [1673] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25941--25941 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25945--25951 []\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 [1674] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25991--25991 []\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 26012--26012 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1675] Underfull \hbox (badness 1019) in paragraph at lines 26074--26079 \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 [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26204--26204 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1678] [1679] [1680] [1681] [1682] [1683] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26584--26584 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1684] [1685] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26765--26765 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1686] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26771--26771 []\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 26780--26780 []\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 26781--26781 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1687] Underfull \hbox (badness 2922) in paragraph at lines 26850--26855 []\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 26887--26887 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1688] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26890--26890 [] \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 26899--26899 [] \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 26900--26900 [] \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 26904--26904 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1689] Underfull \hbox (badness 3240) in paragraph at lines 26958--26961 [][][]\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 26979--26979 [] \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 26982--26982 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1690] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27065--27065 [] \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 27069--27069 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1691] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27079--27079 [] \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 27084--27084 [] \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 27120--27126 []\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 [1692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27142--27142 []\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 27158--27158 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1693] [1694] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27272--27272 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1695] Underfull \hbox (badness 2922) in paragraph at lines 27334--27339 []\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 (69.18036pt too wide) in paragraph at lines 27372--27372 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1696] Underfull \hbox (badness 2922) in paragraph at lines 27421--27426 []\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 [1697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27452--27452 []\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 27486--27491 []\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 [1698] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27511--27511 []\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 27515--27515 []\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 27535--27535 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27545--27545 [] \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[] [1699] Underfull \hbox (badness 2922) in paragraph at lines 27580--27585 []\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 27602--27602 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1700] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27620--27620 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 27672--27677 []\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 [1701] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27700--27700 []\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 27703--27703 []\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 27706--27706 []\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 27709--27709 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 3396) in paragraph at lines 28631--28633 []\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 [1716] [1717] [1718] Underfull \hbox (badness 2237) in paragraph at lines 28808--28810 []\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 [1719] [1720] Underfull \hbox (badness 2591) in paragraph at lines 28972--28974 []\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 [1721] Underfull \hbox (badness 2237) in paragraph at lines 29018--29021 []\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 [1722] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29091--29091 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1723] [1724] Underfull \hbox (badness 3407) in paragraph at lines 29200--29204 []\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) [1725] [1726] Underfull \hbox (badness 1337) in paragraph at lines 29333--29337 []\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 [1727] [1728] [1729] [1730] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29591--29591 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29619--29619 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1731] Underfull \hbox (badness 1616) in paragraph at lines 29645--29648 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1732] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29724--29724 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1733] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29801--29801 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1734] [1735] Underfull \hbox (badness 2205) in paragraph at lines 29890--29895 []\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 [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30489--30489 []\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 30490--30490 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1745] [1746] [1747] [1748] [1749] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30790--30790 [] \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 30791--30791 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1750] [1751] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30917--30917 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30926--30926 []\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 [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 31143--31147 []\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 [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] Underfull \hbox (badness 1337) in paragraph at lines 31672--31676 []\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 31686--31688 []\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 [1764] [1765] [1766] Overfull \hbox (117.7803pt too wide) in paragraph at lines 31879--31879 []\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 31881--31881 []\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)[] [1767] [1768] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32040--32040 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1769] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32124--32124 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1770] Underfull \hbox (badness 6775) in paragraph at lines 32181--32186 []\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 [1771] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32244--32244 []\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 "")[] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] 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 [1776] 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[] [1777] [1778] [1779] [1780]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} [1781] [1782] [1783]) (./tcltk-pkg.tex [1784] Chapter 12. [1785] [1786] [1787] [1788] Overfull \hbox (36.7804pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1789] [1790] [1791] Underfull \vbox (badness 10000) has occurred while \output is active [1792] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\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 [1793] [1794] [1795] [1796] [1797] [1798] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1799] [1800] [1801] [1802] [1803] Underfull \hbox (badness 1189) in paragraph at lines 1406--1409 [][][]\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 [1804]) (./tools-pkg.tex Chapter 13. [1805] 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.[] [1806] 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 [1807] 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)[] [1808] 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 , [1809] 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 [1810] [1811] 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 [1812] [1813] [1814] [1815] [1816] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1817] [1818] 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")[] [1819] [1820] [1821] 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, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1150--1160 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1150--1160 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1822] 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 [1823] 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 [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1697--1697 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] 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--1712 []\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--1712 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1911 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] [1836] [1837] Underfull \hbox (badness 1142) in paragraph at lines 2179--2185 []\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 2213--2213 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2214--2214 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2241--2248 []\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 2241--2248 \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 2241--2248 \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 [1839] Underfull \hbox (badness 1342) in paragraph at lines 2293--2299 \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 [1840] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2369--2369 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2382--2388 []\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 2382--2388 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2424--2424 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2441--2441 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1842] [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1846] Underfull \hbox (badness 2486) in paragraph at lines 2770--2778 []\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 [1847] [1848] [1849] [1850] [1851] Underfull \hbox (badness 1072) in paragraph at lines 3150--3152 []\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 [1852] [1853] [1854] [1855] [1856] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3483--3483 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 4108) in paragraph at lines 3731--3738 []\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 [1861] [1862] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3831--3831 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3834--3834 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3851--3853 []\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 3868--3874 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1863] [1864] Underfull \hbox (badness 7832) in paragraph at lines 3990--3993 []\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 [1865] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4066--4066 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1866] Underfull \hbox (badness 1137) in paragraph at lines 4092--4094 []\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 [1867] [1868] [1869] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4277--4277 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1870] [1871] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4439--4439 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4450--4453 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1872] Underfull \hbox (badness 6859) in paragraph at lines 4466--4471 []\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 4474--4480 []\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 4474--4480 \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 [1873] [1874] [1875] [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4745--4748 []\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 4749--4759 \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 4784--4790 []\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 4784--4790 \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 ', [1877] Underfull \hbox (badness 1571) in paragraph at lines 4812--4816 []\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 4838--4843 \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 [1878] [1879] [1880]) (./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 ', [1881] [1882] [1883] [1884] 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[] [1885] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1886] 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 [1887] 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"))),[] [1888] [1889] Underfull \hbox (badness 1946) in paragraph at lines 626--630 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676 []\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 682--682 []\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 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684 []\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 685--685 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 719--725 []\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 719--725 \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- [1891] [1892] Underfull \hbox (badness 4505) in paragraph at lines 855--861 \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 [1893] [1894] [1895] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1896] Underfull \hbox (badness 1748) in paragraph at lines 1094--1102 []\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 1094--1102 \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 1094--1102 \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 1094--1102 \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 1106--1108 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1897] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1898] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1907] [1908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1909] [1910] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1911] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1912] [1913] [1914] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353 [] \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")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1915] [1916] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1917] Underfull \hbox (badness 1082) in paragraph at lines 2570--2574 [][][]\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.2575 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2606--2608 []\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 . [1918] [1919] Underfull \hbox (badness 10000) in paragraph at lines 2694--2696 []\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 [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 2911--2913 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1923] [1924] [1925] [1926] Underfull \hbox (badness 1762) in paragraph at lines 3205--3208 []\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 = [1927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298 []\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 '[] [1928] Underfull \hbox (badness 2452) in paragraph at lines 3374--3377 []\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 [1929] [1930] [1931] [1932] [1933] [1934] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 3867--3871 []\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 3935--3943 []\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 [1937] Underfull \hbox (badness 1231) in paragraph at lines 4012--4024 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1938] Underfull \hbox (badness 10000) in paragraph at lines 4026--4031 []\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 4026--4031 \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 4026--4031 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1939] Underfull \hbox (badness 4660) in paragraph at lines 4146--4149 \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 4170--4172 []\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 [1940] [1941] [1942] Underfull \hbox (badness 1565) in paragraph at lines 4355--4359 []\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 [1943] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4438--4438 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1944] Underfull \hbox (badness 1931) in paragraph at lines 4473--4480 []\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) [1945] [1946] [1947] [1948] [1949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4797--4797 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4868 ...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.4868 ...mat Unordered and Ordered Lists}{format} [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1622) in paragraph at lines 5387--5391 []\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 [1959] [1960] [1961] [1962] [1963] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5709--5709 []\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 5721--5721 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1964] [1965] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5854--5854 [] \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 5855--5855 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1966] [1967] [1968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6065--6065 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1969] Underfull \hbox (badness 10000) in paragraph at lines 6149--6151 []\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 [1970] Underfull \hbox (badness 1502) in paragraph at lines 6198--6203 []\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 6198--6203 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1971] [1972] Underfull \hbox (badness 10000) in paragraph at lines 6371--6380 []\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 6371--6380 \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 [1973] Underfull \hbox (badness 2150) in paragraph at lines 6435--6438 []\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 6451--6454 []\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 [1974] [1975] Underfull \hbox (badness 3118) in paragraph at lines 6573--6575 []\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 [1976] [1977] Underfull \hbox (badness 5091) in paragraph at lines 6747--6749 []\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 [1978] Underfull \hbox (badness 5331) in paragraph at lines 6763--6769 []\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 6763--6769 \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 6763--6769 \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 6777--6784 []\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 6792--6802 \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 [1979] Underfull \hbox (badness 10000) in paragraph at lines 6835--6838 []\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 6835--6838 \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 6843--6846 []\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 [1980] Underfull \hbox (badness 2376) in paragraph at lines 6914--6921 []\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 6914--6921 \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 6914--6921 \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 6922--6925 []\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 [1981] Underfull \hbox (badness 1314) in paragraph at lines 7001--7008 []\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 7048--7051 []\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 7048--7051 \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 7081--7086 [][][]\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 , [1982] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7104--7104 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7140--7144 []\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 7154--7157 []\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 [1983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7201--7201 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1984] [1985] Underfull \hbox (badness 4132) in paragraph at lines 7325--7327 []\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 [1986] [1987] [1988] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7492--7492 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1989] [1990] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7635--7635 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1991] Underfull \hbox (badness 10000) in paragraph at lines 7675--7677 []\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 [1992] [1993] Underfull \hbox (badness 10000) in paragraph at lines 7863--7865 []\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 7868--7870 []\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 [1994] [1995] [1996] [1997] Underfull \hbox (badness 1859) in paragraph at lines 8096--8099 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1998] Underfull \hbox (badness 1655) in paragraph at lines 8190--8193 []\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 8201--8201 []\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 8209--8209 []\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):[] [1999] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8217--8217 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2000] Underfull \hbox (badness 1917) in paragraph at lines 8304--8306 []\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 , [2001] [2002] [2003] [2004] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8576--8576 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8577--8577 [] \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 8578--8578 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2005] Underfull \hbox (badness 10000) in paragraph at lines 8606--8608 []\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 8620--8622 []\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 8628--8633 []\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, [2006] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8674--8674 [] \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 8675--8675 [] \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[] [2007] [2008] Underfull \hbox (badness 10000) in paragraph at lines 8804--8809 []\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 8804--8809 [][]\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 8804--8809 \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 8811--8814 \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 [2009] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8927--8927 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8928--8928 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2010] [2011] [2012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/9 "S original, "),[] [2013] Underfull \hbox (badness 1789) in paragraph at lines 9232--9234 []\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 [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 5203) in paragraph at lines 9805--9808 []\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 [2023] [2024] Underfull \hbox (badness 1394) in paragraph at lines 10031--10038 \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 [2025] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10055--10055 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2026] [2027] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10216--10216 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2028] [2029] [2030] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10397--10397 []\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[] [2031] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10483--10483 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10486--10486 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10491--10491 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2032] Underfull \hbox (badness 2027) in paragraph at lines 10563--10566 []\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 [2033] [2034] [2035] [2036] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10835--10835 []\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 10836--10836 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10843--10848 []\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 10843--10848 \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 10843--10848 \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 [2037] [2038] [2039] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11076--11076 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2040] [2041] [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 \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 11355--11355 []\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 11360--11360 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2045] [2046] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11493--11493 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11494--11494 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2047] [2048] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11629--11629 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2049] Underfull \hbox (badness 1917) in paragraph at lines 11753--11756 []\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 11753--11756 \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 [2050] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11776--11776 []\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 '[] [2051] Underfull \hbox (badness 10000) in paragraph at lines 11839--11841 []\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 [2052] Underfull \hbox (badness 6725) in paragraph at lines 11889--11898 \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 11889--11898 \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 11889--11898 \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 11889--11898 \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 [2053] Underfull \hbox (badness 3646) in paragraph at lines 12015--12017 [][][]$\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 / [2054] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12053--12053 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2055] [2056] [2057] Underfull \hbox (badness 10000) in paragraph at lines 12234--12238 []\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 12265--12271 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2058] [2059] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12441--12441 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2060] Underfull \hbox (badness 1009) in paragraph at lines 12459--12471 []\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 12499--12501 []\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 [2061] Underfull \hbox (badness 1043) in paragraph at lines 12542--12547 []\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 [2062] [2063] [2064] [2065] Underfull \hbox (badness 1888) in paragraph at lines 12835--12838 []\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 12852--12855 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2066] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12898--12898 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2067] Underfull \hbox (badness 2158) in paragraph at lines 12953--12956 []\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 13001--13001 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2068] [2069] [2070] Underfull \hbox (badness 2302) in paragraph at lines 13158--13160 []\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 [2071] Underfull \hbox (badness 3333) in paragraph at lines 13265--13267 []\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- [2072] [2073] [2074] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13432--13432 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13456--13461 []\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 13465--13468 []\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 13465--13468 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2075] Underfull \hbox (badness 1442) in paragraph at lines 13492--13496 []\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 13524--13524 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2076] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13555--13555 []\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 13562--13562 []\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 13564--13564 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2077] [2078] Underfull \hbox (badness 10000) in paragraph at lines 13732--13734 []\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 [2079] [2080] [2081] Underfull \hbox (badness 6300) in paragraph at lines 13889--13896 []\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 13889--13896 \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 13889--13896 \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 [2082] [2083] Underfull \hbox (badness 2020) in paragraph at lines 14058--14074 \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 14058--14074 \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 [2084] [2085] Underfull \hbox (badness 5022) in paragraph at lines 14198--14202 []\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 14205--14208 [][][]$\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 14205--14208 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2086] [2087] [2088] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14369--14369 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2089] [2090] [2091] [2092] [2093] [2094] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14809--14809 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14815--14815 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14836--14838 []\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 14851--14855 \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 14865--14869 []\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 14871--14876 []\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 14871--14876 \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 14871--14876 \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 14877--14879 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2095] Underfull \hbox (badness 10000) in paragraph at lines 14907--14912 \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 14907--14912 \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 14928--14933 []\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 14936--14939 [][][]\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 , [2096] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14990--14990 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2097] [2098] [2099] Underfull \hbox (badness 10000) in paragraph at lines 15192--15195 [][][]\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 15192--15195 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2100] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15208--15208 []\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:[] [2101] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15275--15275 [] \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 15297--15297 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2102] [2103] Underfull \hbox (badness 1297) in paragraph at lines 15428--15430 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2104] Underfull \hbox (badness 4036) in paragraph at lines 15475--15477 []\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. [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15612--15612 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2107] Underfull \hbox (badness 1715) in paragraph at lines 15664--15667 []\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 15709--15711 []\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 = [2108] [2109] [2110]) [2111] [2112] (./KernSmooth-pkg.tex Chapter 15. [2113] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2114] [2115] [2116] [2117] [2118] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2119] [2120] [2121] [2122]) (./MASS-pkg.tex Chapter 16. [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] 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))[] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] 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"),[] [2157] [2158] [2159] [2160] 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 [2161] [2162] [2163] 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 , [2164] [2165] 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 [2166] [2167] [2168] 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, ...)[] [2169] 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")[] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] 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 [2182] [2183] [2184] [2185] [2186] [2187] [2188] 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", ...)[] [2189] [2190] [2191] 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, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] 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) [2206] 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") [2207] [2208]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} [2209] [2210] 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 [2211] [2212] [2213] [2214] 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)))[] [2215] 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"))[] [2216] [2217] [2218] [2219] [2220] [2221] 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"))[] [2222] 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 ) = [2223] 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)[] [2224] [2225] 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 [2226] [2227] 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")[] [2228] 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"), ...)[] [2229] [2230] [2231] [2232] [2233] [2234] 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 [2235] [2236] 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 [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254] [2255] [2256] 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, ...)[] [2257] 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), [2258] 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)[] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271]) (./Matrix-pkg.tex [2272] 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 [2273] 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 [2274] 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 [2275] 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 [2276] [2277] Underfull \hbox (badness 5147) in paragraph at lines 496--499 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2278] Underfull \hbox (badness 5119) in paragraph at lines 509--513 []\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 513--518 [][][]\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 543--543 []\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 545--545 []\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 554--554 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2279] [2280] Overfull \hbox (52.98038pt too wide) in paragraph at lines 668--668 []\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 669--669 []\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 670--670 []\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 683--683 [] \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 684--684 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 689--689 []\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 758--762 \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 / [2282] [2283] [2284] Overfull \hbox (72.78088pt too wide) in paragraph at lines 973--973 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2285] [2286] [2287]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) has been already used, duplicate ignored \relax l.1160 ...- '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.1160 ...- 'Matrix' S4 Generic and Methods}{chol} [2288pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} ] Underfull \hbox (badness 2285) in paragraph at lines 1249--1254 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the Overfull \hbox (31.3804pt too wide) in paragraph at lines 1295--1295 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2289] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1390--1390 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2290] Underfull \hbox (badness 2277) in paragraph at lines 1418--1421 []\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 [2291] Underfull \hbox (badness 1609) in paragraph at lines 1465--1469 []\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 1492--1492 []\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 1506--1506 []\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[] [2292] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1514--1514 []\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 1561--1568 []\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 1561--1568 \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 [2293] Underfull \hbox (badness 1783) in paragraph at lines 1596--1600 []\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 1612--1618 \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.1653 ... 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.1653 ... 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.1654 \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.1675 \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.1686 \aliasA{rowSums}{colSums}{rowSums} [2294] Underfull \hbox (badness 2922) in paragraph at lines 1740--1744 []\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 1740--1744 \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 1751--1754 [][][]\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 [2295] [2296] [2297] Underfull \hbox (badness 3547) in paragraph at lines 1905--1908 []\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 [2298] [2299] [2300] [2301] Underfull \hbox (badness 1484) in paragraph at lines 2267--2269 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2302] Underfull \hbox (badness 7379) in paragraph at lines 2363--2365 []\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 [2303] [2304] [2305] Underfull \hbox (badness 4846) in paragraph at lines 2639--2643 []\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 2644--2648 []\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 2651--2654 []\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 ; [2306] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2698--2698 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2707--2709 []\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 2711--2716 []\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 2711--2716 [][]\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 [2307] Underfull \hbox (badness 1097) in paragraph at lines 2734--2737 []\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 2747--2752 [][]\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 [2308] Underfull \hbox (badness 3646) in paragraph at lines 2986--2989 []\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 3018--3020 []\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 3021--3025 []\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 3030--3036 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2309] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 []\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 3047--3051 [][][]\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 [2310] [2311] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\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 3278--3280 [][][]\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) [2312] Underfull \hbox (badness 2469) in paragraph at lines 3398--3401 []\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 [2313] [2314] Underfull \hbox (badness 10000) in paragraph at lines 3563--3567 []\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 3563--3567 \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 , [2315] Underfull \hbox (badness 2285) in paragraph at lines 3613--3616 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2316] [2317] Underfull \hbox (badness 10000) in paragraph at lines 3760--3765 []\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 3760--3765 \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 3772--3775 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2318] Underfull \hbox (badness 10000) in paragraph at lines 3848--3850 []\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 [2319] [2320] [2321] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4058--4058 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4126--4130 []\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 [2322] Underfull \hbox (badness 10000) in paragraph at lines 4135--4138 []\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 4135--4138 \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 4140--4144 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2323] [2324] Underfull \hbox (badness 3158) in paragraph at lines 4323--4327 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2325] [2326] [2327] [2328] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4562--4562 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4565--4565 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4569--4569 []\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 4572--4572 []\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 4582--4582 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 4884--4889 []\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 , [2333] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4965--4965 []\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 4967--4967 [] \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 4971--4971 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2334] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4978--4978 [] \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 '[] [2335] [2336] Underfull \hbox (badness 4120) in paragraph at lines 5122--5125 []\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 5159--5159 []\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 5165--5165 [] \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 5166--5166 [] \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 5170--5170 []\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 5172--5172 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 []\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 5182--5182 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2338] Underfull \hbox (badness 1817) in paragraph at lines 5271--5280 []\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 5313--5315 []\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 5315--5318 []\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 5328--5331 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2339] Underfull \hbox (badness 4765) in paragraph at lines 5346--5349 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5406--5406 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2341] [2342] [2343] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5664--5664 []\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[] [2344] Underfull \hbox (badness 10000) in paragraph at lines 5747--5750 [][][]\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 5758--5758 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2345] Underfull \hbox (badness 1622) in paragraph at lines 5795--5800 []\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 5795--5800 \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 [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5856--5856 []\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 5857--5857 [] \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 5864--5864 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2347] Underfull \hbox (badness 1062) in paragraph at lines 5993--5996 []\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 [2348] Underfull \hbox (badness 6063) in paragraph at lines 6022--6025 []\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 [2349] Underfull \hbox (badness 2635) in paragraph at lines 6134--6139 []\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 6134--6139 \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 Underfull \hbox (badness 10000) in paragraph at lines 6142--6145 []\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., [2350] Underfull \hbox (badness 10000) in paragraph at lines 6252--6262 \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 6252--6262 [][]\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 [2351] Underfull \hbox (badness 3179) in paragraph at lines 6334--6337 []\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 [2352] Underfull \hbox (badness 10000) in paragraph at lines 6432--6435 []\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., [2353] Underfull \hbox (badness 10000) in paragraph at lines 6507--6510 []\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., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6523--6523 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2354] Underfull \hbox (badness 2443) in paragraph at lines 6562--6568 []\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 6562--6568 [][]\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 6583--6586 []\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 [2355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6653--6653 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2356] [2357] Underfull \hbox (badness 10000) in paragraph at lines 6794--6797 []\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 Underfull \hbox (badness 1490) in paragraph at lines 6816--6818 []\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) [2358] [2359] Underfull \hbox (badness 5036) in paragraph at lines 6896--6900 []\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 6896--6900 \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 [2360]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6995 \aliasA{det}{Matrix-class}{det} [2361] Underfull \hbox (badness 10000) in paragraph at lines 7098--7101 Underfull \hbox (badness 10000) in paragraph at lines 7108--7110 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2362]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7171 ...*\%}{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.7279 ...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.7379 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7477--7483 \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 [2363pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 ] Underfull \hbox (badness 10000) in paragraph at lines 7550--7553 []\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 7550--7553 \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 7553--7558 []\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 7553--7558 \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 7558--7562 []\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 7558--7562 \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 7568--7569 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2364] [2365] Underfull \hbox (badness 1009) in paragraph at lines 7704--7706 []\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 Underfull \hbox (badness 1062) in paragraph at lines 7749--7752 []\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 [2366] Underfull \hbox (badness 6063) in paragraph at lines 7783--7786 []\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 10000) in paragraph at lines 7839--7841 []\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 [2368] [2369] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7941--7941 [] \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 7981--7981 []\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 [2370] Underfull \hbox (badness 2635) in paragraph at lines 8046--8051 []\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 8046--8051 \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 8054--8057 []\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., [2371] Underfull \hbox (badness 3482) in paragraph at lines 8128--8134 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2372] Underfull \hbox (badness 1867) in paragraph at lines 8248--8250 []\T1/ptm/m/n/10 fast sim- [2373]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8288 \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.8288 \HeaderA{norm}{Matrix Norms}{norm} [2374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8375--8375 []\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 8376--8376 []\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 8377--8377 []\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 8490--8500 []\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 , [2375] Underfull \hbox (badness 3179) in paragraph at lines 8561--8564 []\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 [2376] Underfull \hbox (badness 10000) in paragraph at lines 8651--8654 []\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., [2377] Underfull \hbox (badness 10000) in paragraph at lines 8727--8730 []\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., [2378] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8743--8743 []\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 [2379] Underfull \hbox (badness 10000) in paragraph at lines 8853--8855 []\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 8855--8858 []\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 8861--8868 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2380] [2381] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8954--8954 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8957--8957 []\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 8959--8959 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8963--8963 []\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 8964--8964 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8989--8999 []\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 8989--8999 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2382] [2383]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9090 \aliasA{qr}{qr-methods}{qr} [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9163--9163 []\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 9174--9174 []\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 9178--9178 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9203--9203 []\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 [2385] Underfull \hbox (badness 10000) in paragraph at lines 9260--9266 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9277--9280 []\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 [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9376--9376 []\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 9392--9392 []\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 9398--9398 []\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 9399--9399 []\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.9418 ... the Reciprocal Condition Number}{rcond} [2388] [2389] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9531--9531 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2390] [2391] [2392] Underfull \hbox (badness 2351) in paragraph at lines 9722--9730 []\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 9722--9730 \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 [2393] [2394] Underfull \hbox (badness 1558) in paragraph at lines 9867--9870 []\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 [2395] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9929--9929 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9933--9933 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2396]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9995 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10092--10092 [] \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 10097--10097 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2397] Underfull \hbox (badness 1616) in paragraph at lines 10132--10144 []\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 10149--10152 []\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 10158--10165 []\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 10171--10181 []\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 10171--10181 \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 10198--10202 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10205--10207 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2398] Underfull \hbox (badness 10000) in paragraph at lines 10228--10229 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10234--10236 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10238--10239 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10246--10249 [][][]\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 10264--10264 []\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 10268--10268 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2399] Underfull \hbox (badness 10000) in paragraph at lines 10289--10292 []\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 10317--10319 []\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 10325--10328 []\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 10325--10328 \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 10336--10340 []\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 10336--10340 \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 [2400] Underfull \hbox (badness 1668) in paragraph at lines 10351--10356 [][][]\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 10372--10378 []\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- [2401] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10431--10431 [] \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 10432--10432 [] \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 10433--10433 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2402] [2403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10617--10617 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2404] Underfull \hbox (badness 1668) in paragraph at lines 10659--10664 [][][]\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 [2405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10756--10756 []\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 10760--10760 []\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 10761--10761 []\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 10766--10766 []\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 10769--10769 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10792--10792 []\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 10793--10793 []\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 10819--10819 []\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 10821--10821 [] \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 10823--10823 [] \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 [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 10968--10972 [][][]\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.11008 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2409] [2410] Underfull \hbox (badness 10000) in paragraph at lines 11138--11140 []\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 11166--11166 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2411] Underfull \hbox (badness 5036) in paragraph at lines 11194--11196 []\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 11328--11334 []\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 11328--11334 \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 , [2412] Underfull \hbox (badness 10000) in paragraph at lines 11401--11404 []\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 [2413] Underfull \hbox (badness 10000) in paragraph at lines 11419--11424 []\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 11434--11436 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2414] [2415] Underfull \hbox (badness 2698) in paragraph at lines 11559--11565 [][][]\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, [2416] Underfull \hbox (badness 10000) in paragraph at lines 11652--11654 []\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 11670--11675 []\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 11670--11675 \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 [2417] Underfull \hbox (badness 2591) in paragraph at lines 11678--11683 \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 11750--11752 []\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., [2418] [2419] Underfull \hbox (badness 6641) in paragraph at lines 11836--11839 []\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 11876--11880 []\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 11876--11880 \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 [2420] [2421] Underfull \hbox (badness 7649) in paragraph at lines 11983--11985 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2422] [2423] [2424] Underfull \hbox (badness 7362) in paragraph at lines 12184--12186 []\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 12222--12222 []\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 12223--12223 []\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)[] [2425] [2426] [2427] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12365--12365 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12378--12378 [] \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 12383--12383 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2428] Underfull \hbox (badness 6910) in paragraph at lines 12557--12559 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2429] [2430] [2431]) (./boot-pkg.tex [2432] Chapter 18. [2433] [2434] [2435] [2436] [2437] [2438] [2439] 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"), [2440] 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- [2441] [2442] [2443] 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 , [2444] 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 [2445] [2446] 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" [2447] 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 [2448] [2449] [2450] [2451] 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- [2452] [2453] [2454] [2455] [2456] 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), [2457] [2458] [2459] Underfull \vbox (badness 10000) has occurred while \output is active [2460] 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),[] [2461] 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. [2462] [2463] [2464] 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 [2465] 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 , [2466] [2467] 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 [2468] [2469] [2470] [2471] [2472] 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,[] [2473] [2474] [2475] 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 , [2476] 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)) [2477] [2478] [2479] 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 [2480] [2481] [2482] [2483] [2484] [2485] [2486] 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)[] [2487] [2488] 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])[] [2489] [2490] [2491] 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 [2492] 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 [2493] [2494] 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 [2495] [2496] [2497] [2498] [2499] [2500] [2501] [2502] [2503] 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 [2504] [2505] [2506] [2507] 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 [2508] 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])[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] 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][] [2517] 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 [2518] 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 [2519] [2520] [2521] [2522] 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). [2523] [2524] 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[] [2525] [2526] [2527] 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 [2528] [2529] 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),[] [2530] [2531] [2532] [2533] [2534] [2535] [2536] [2537]) (./class-pkg.tex [2538] Chapter 19. [2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554]) (./cluster-pkg.tex Chapter 20. [2555] 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 [2556] [2557] 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]))[] [2558] [2559] Underfull \vbox (badness 10000) has occurred while \output is active [2560] [2561] 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, ...)[] [2562] [2563] 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)[] [2564] 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 [2565] [2566] 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 , [2567] 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 [2568] 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), ...)[] [2569] 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, [2570] [2571] 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 [2572] 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 [2573] 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."),[] [2574] [2575] 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 [2576] 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[] [2577] 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 [2578] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2579] [2580] 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 = [2581] 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, [2582] [2583] [2584] [2585] [2586] 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. [2587] [2588] 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 , [2589] 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 [2590] 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 , [2591] [2592] [2593] 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 ):[] [2594] 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"),[] [2595] [2596] [2597] 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):[] [2598] [2599] 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")[] [2600] [2601] [2602] 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, ...)[] [2603] 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 [2604] 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, ...)[] [2605] [2606] [2607] 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 [2608] 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 , [2609] 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 , [2610] [2611] [2612] 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 , [2613] 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 [2614] [2615] [2616] [2617] 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, ...)[] [2618] [2619] 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[] [2620] [2621] [2622] [2623] [2624] [2625] [2626] 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:[] [2627] 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:[] [2628]) (./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,[] [2629] 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 [2630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2631] [2632] [2633]) (./foreign-pkg.tex [2634] Chapter 22. [2635] 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 [2636] [2637] 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 , [2638] 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, [2639] [2640] [2641] 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,[] [2642] 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 [2643] 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 [2644] 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,[] [2645] 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="")[] [2646] [2647] 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])[] [2648] [2649] 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) [2650] 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))) [2651] [2652] 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"))[] [2653] [2654] 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 , [2655] 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 [2656]) (./lattice-pkg.tex Chapter 23. [2657] 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 / [2658] [2659] 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"),[] [2660] 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"),[] [2661] [2662] [2663] [2664] 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 [2665] [2666] [2667] [2668] 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. [2669] 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 [2670] [2671] 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 [2672] [2673] [2674] 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 , [2675] 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 , [2676] Underfull \vbox (badness 10000) has occurred while \output is active [2677] 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 [2678] 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 [2679] [2680] [2681] [2682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2683] 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 [2684] [2685] [2686] 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"),[] [2687] [2688] [2689] [2690] [2691] 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"),[] [2692] [2693] 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 [2694] Underfull \hbox (badness 6758) in paragraph at lines 2888--2892 []\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 2888--2892 \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 2894--2896 []\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 2946--2952 []\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 2946--2952 \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 2946--2952 \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 Underfull \hbox (badness 2486) in paragraph at lines 2970--2974 []\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 [2695] [2696] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3073--3073 [] \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 3074--3074 [] \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 3075--3075 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3086--3086 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2697] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3098--3098 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] Underfull \hbox (badness 2913) in paragraph at lines 3156--3163 []\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 3156--3163 \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 [2698] [2699] [2700] [2701]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3444 \aliasA{parallel}{B\_08\_splom}{parallel} [2702] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2703] [2704] [2705] [2706] [2707] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2708] Underfull \hbox (badness 2277) in paragraph at lines 3935--3939 []\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 3935--3939 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2709] [2710] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4065--4065 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4074--4078 []\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 Underfull \hbox (badness 3219) in paragraph at lines 4101--4103 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2711] Underfull \hbox (badness 1728) in paragraph at lines 4118--4122 \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 Underfull \hbox (badness 5161) in paragraph at lines 4183--4187 []\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 4183--4187 \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 [2712] [2713] Underfull \hbox (badness 1067) in paragraph at lines 4297--4307 []\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 4297--4307 \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 4297--4307 \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 4297--4307 \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 4297--4307 \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 [2714] Underfull \hbox (badness 1701) in paragraph at lines 4322--4325 []\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 4325--4327 []\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 [2715] [2716] [2717] [2718] [2719] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4729--4729 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 []\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 . [2722] [2723] Underfull \hbox (badness 1442) in paragraph at lines 5048--5051 []\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 [2724] [2725] [2726] [2727] [2728] [2729] Underfull \hbox (badness 3646) in paragraph at lines 5382--5385 [][][]\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 5412--5412 [] \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 5413--5413 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2730] Underfull \hbox (badness 10000) in paragraph at lines 5501--5504 []\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 5501--5504 \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 [2731] Underfull \hbox (badness 1635) in paragraph at lines 5527--5532 []\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 [2732] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5678--5678 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2733] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5692--5692 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5701--5701 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5707--5707 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5711--5711 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5727--5729 []\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 5738--5740 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2734] [2735] Underfull \hbox (badness 2538) in paragraph at lines 5863--5867 \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 5874--5881 []\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 5874--5881 \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 [2736] [2737] Underfull \hbox (badness 10000) in paragraph at lines 6027--6031 [][][]\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 , [2738] [2739] Underfull \hbox (badness 4242) in paragraph at lines 6174--6179 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2740] [2741] Underfull \hbox (badness 3601) in paragraph at lines 6290--6295 []\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 6290--6295 \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 [2742] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2743] [2744] Underfull \hbox (badness 1888) in paragraph at lines 6509--6516 \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 [2745] Underfull \hbox (badness 10000) in paragraph at lines 6566--6569 []\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 6566--6569 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 1320) in paragraph at lines 6972--6979 []\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 6972--6979 \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 [2752] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2753] Underfull \hbox (badness 10000) in paragraph at lines 7072--7076 []\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 7072--7076 \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 [2754] Underfull \hbox (badness 10000) in paragraph at lines 7177--7180 \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 [2755] [2756] Underfull \hbox (badness 2012) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2757] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2758] [2759] Underfull \hbox (badness 2644) in paragraph at lines 7530--7534 \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 7543--7546 []\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 [2760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613 [] \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 7623--7623 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7684--7684 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2762] [2763] [2764] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2765] Underfull \hbox (badness 1436) in paragraph at lines 7929--7935 []\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 [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 8487--8490 []\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 8487--8490 \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 [2774] [2775] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662 []\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 8663--8663 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2776] Underfull \hbox (badness 3118) in paragraph at lines 8694--8697 []\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 [2777] Underfull \hbox (badness 1515) in paragraph at lines 8770--8774 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2778] Underfull \hbox (badness 6316) in paragraph at lines 8876--8881 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2779] [2780] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2781] [2782] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2783] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185 []\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 9181--9185 \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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] Underfull \hbox (badness 7238) in paragraph at lines 9639--9643 []\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 9639--9643 \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 , [2791] [2792] [2793]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma} [2794] [2795] [2796] Underfull \hbox (badness 10000) in paragraph at lines 10032--10037 \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 10105--10105 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2797] [2798]) (./mgcv-pkg.tex Chapter 24. [2799] [2800] 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,[] [2801] 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. [2802] [2803] [2804] [2805] Underfull \hbox (badness 10000) in paragraph at lines 377--384 [][][]\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 377--384 [][]\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 377--384 [][]\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 , [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 420--420 []\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)+[] [2807] [2808] [2809] Underfull \hbox (badness 2922) in paragraph at lines 632--633 []\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 [2810] [2811] Underfull \hbox (badness 1406) in paragraph at lines 702--703 []\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 [2812] [2813] Underfull \hbox (badness 1158) in paragraph at lines 812--814 []\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 [2814] Underfull \hbox (badness 1259) in paragraph at lines 875--876 []\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). [2815] Underfull \vbox (badness 10000) has occurred while \output is active [2816] [2817] [2818] [2819] [2820] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224 []\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 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)[] [2821] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \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 1254--1254 []\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 1263--1263 []\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 1265--1265 [] \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 [2822] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 []\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)[] [2823] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1379--1379 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2824] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1390--1390 [] \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 1424--1424 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] [2833] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1930--1930 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2834] [2835] [2836] [2837] [2838] [2839] Underfull \hbox (badness 1052) in paragraph at lines 2318--2326 \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 2335--2335 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2347--2350 []\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 2360--2364 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2840] Underfull \hbox (badness 1043) in paragraph at lines 2386--2391 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2841] [2842] [2843] Underfull \hbox (badness 1043) in paragraph at lines 2551--2557 \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 [2844] Underfull \hbox (badness 10000) in paragraph at lines 2687--2693 [][][]\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 2687--2693 [][]\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 2687--2693 [][]\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 , [2845] [2846] Underfull \vbox (badness 10000) has occurred while \output is active [2847] Underfull \vbox (badness 10000) has occurred while \output is active [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3343--3343 [] \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 3346--3346 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] Underfull \hbox (badness 5189) in paragraph at lines 3821--3825 []\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 [2865] [2866] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3938--3938 []\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 [2867] [2868] [2869] Underfull \hbox (badness 1184) in paragraph at lines 4107--4111 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2870] [2871] [2872] [2873] [2874] [2875] [2876] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4553--4553 [] \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)+[] [2877] [2878] [2879] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4703--4703 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2880] [2881] Underfull \hbox (badness 1142) in paragraph at lines 4828--4832 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2882] Underfull \hbox (badness 10000) in paragraph at lines 4900--4909 []\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 [2883] [2884] Underfull \hbox (badness 5970) in paragraph at lines 5017--5023 [][][]\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 5017--5023 [][]\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 . [2885] Underfull \vbox (badness 10000) has occurred while \output is active [2886] [2887] [2888] [2889] Underfull \hbox (badness 1577) in paragraph at lines 5369--5372 []\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 5376--5377 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2890] [2891] [2892] [2893] [2894] [2895] [2896] Underfull \hbox (badness 6708) in paragraph at lines 5765--5766 []\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 [2897] [2898] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5814--5814 [] \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 5839--5839 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5868--5868 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2900] [2901] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5990--5990 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2902] [2903] [2904] [2905] [2906] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6327--6327 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2907] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6329--6329 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6350--6354 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2908] [2909] [2910] Underfull \vbox (badness 10000) has occurred while \output is active [2911] [2912] [2913] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6669--6669 []\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) [2914] [2915] [2916] [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] Underfull \vbox (badness 10000) has occurred while \output is active [2919] [2920] [2921] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7098--7098 []\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 7125--7125 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] Underfull \hbox (badness 1242) in paragraph at lines 7668--7669 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2931] [2932] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7755--7755 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2933] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7818--7818 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] [2934] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7837--7837 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \hbox (badness 10000) in paragraph at lines 9057--9060 []\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 9057--9060 \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 9057--9060 \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 . [2954] Underfull \hbox (badness 10000) in paragraph at lines 9113--9116 []\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 9113--9116 \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 [2955] [2956] [2957] [2958] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9333--9333 []\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 9334--9334 [] \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 9337--9337 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2959] [2960] Underfull \hbox (badness 1629) in paragraph at lines 9495--9500 \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 [2961] [2962] Underfull \vbox (badness 10000) has occurred while \output is active [2963] [2964] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9706--9706 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2965] Underfull \hbox (badness 1062) in paragraph at lines 9743--9747 []\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 9743--9747 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2966] [2967] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9874--9874 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10147--10147 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [2972] Underfull \hbox (badness 1205) in paragraph at lines 10185--10187 []\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 10185--10187 \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 10191--10196 []\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 [2973] Underfull \hbox (badness 1205) in paragraph at lines 10275--10277 []\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 10275--10277 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2974] Underfull \hbox (badness 10000) in paragraph at lines 10344--10347 []\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 10344--10347 [][]\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, [2975] [2976] [2977] Underfull \hbox (badness 1253) in paragraph at lines 10474--10476 []\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, [2978] [2979] [2980] [2981] [2982] Underfull \hbox (badness 1946) in paragraph at lines 10727--10734 []\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 10727--10734 \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 10727--10734 \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 Underfull \hbox (badness 2846) in paragraph at lines 10735--10738 []\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 10735--10738 \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. [2983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10801--10801 []\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 10811--10811 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 10842--10845 []\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 , [2985] [2986] [2987] [2988] [2989] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11143--11143 []\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) [2990] [2991] [2992] [2993] [2994] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11474--11474 []\T1/pcr/m/n/9 dat <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(runif( n))) + (eps/del))[] [2995] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11513--11513 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~ s(times, k = 10), ~ 1, ~ 1),[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 11531--11531 []\T1/pcr/m/n/9 xSeq <- data.frame(cbind("accel" = rep(0, 1e3), "times" = seq( 2, 58, length.out = 1e3)))[] Underfull \vbox (badness 10000) has occurred while \output is active [2996] [2997] Underfull \hbox (badness 3861) in paragraph at lines 11628--11631 []\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 11637--11637 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [2998] Underfull \hbox (badness 10000) in paragraph at lines 11654--11658 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11694--11698 []\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- [2999] [3000] [3001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11838--11838 [] \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 11849--11854 []\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 [3002] Underfull \hbox (badness 1803) in paragraph at lines 11926--11930 \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 11938--11950 \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 [3003] Underfull \hbox (badness 2401) in paragraph at lines 11955--11959 \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 11955--11959 \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 , [3004] [3005] [3006] Underfull \hbox (badness 6876) in paragraph at lines 12150--12156 [][][]\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 [3007] Underfull \hbox (badness 10000) in paragraph at lines 12191--12192 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3008] [3009] Underfull \hbox (badness 10000) in paragraph at lines 12308--12309 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12362--12362 [] \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 12374--12374 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12386--12386 [] \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 12391--12391 [] \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 12397--12397 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3012] Underfull \hbox (badness 10000) in paragraph at lines 12467--12469 []\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 12467--12469 \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 [3013] [3014] Underfull \hbox (badness 10000) in paragraph at lines 12597--12598 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3015] [3016] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12678--12678 []\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 12679--12679 []\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[] [3017] [3018] Underfull \hbox (badness 10000) in paragraph at lines 12830--12831 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3019] [3020] [3021] [3022] [3023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13080--13080 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3024] Underfull \hbox (badness 10000) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 13300--13303 []\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 13300--13303 \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 13300--13303 \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" [3027] [3028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13384--13384 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3029] Underfull \hbox (badness 10000) in paragraph at lines 13429--13435 []\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 13429--13435 \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- [3030] [3031] [3032] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13643--13643 []\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 [3033] Underfull \vbox (badness 10000) has occurred while \output is active [3034] Underfull \hbox (badness 10000) in paragraph at lines 13746--13754 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13772--13773 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3035] [3036] [3037] [3038] [3039] Underfull \hbox (badness 3396) in paragraph at lines 14032--14035 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 14077--14079 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3040] [3041] [3042] [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 14358--14361 []\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 14358--14361 \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 Underfull \hbox (badness 10000) in paragraph at lines 14391--14395 [][][]\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 14391--14395 [][]\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 14391--14395 [][]\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 , [3046] [3047] [3048] [3049] [3050] Underfull \hbox (badness 2158) in paragraph at lines 14681--14681 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3051] [3052] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14760--14760 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3053] [3054] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14894--14894 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3055] [3056] Underfull \hbox (badness 4846) in paragraph at lines 15025--15028 []\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 [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16228--16228 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3077] [3078] [3079] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16438--16438 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16440--16440 []\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 16442--16442 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3080] Underfull \hbox (badness 10000) in paragraph at lines 16462--16463 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16462--16463 \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 [3081] [3082] [3083] [3084] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16650--16650 []\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 16651--16651 []\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 16663--16663 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3085] [3086] [3087]) (./nlme-pkg.tex [3088] Chapter 25. [3089] 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 [3090] 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 [3091] [3092] [3093] [3094] [3095] 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,[] [3096] [3097] 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 --------------------------- ---------------[] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] 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"),[] [3106] 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 [3107] [3108] [3109] [3110] [3111] [3112] [3113] 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 , [3114] 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 [3115] [3116] [3117] [3118] [3119] 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 , [3120] 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")[] [3121] 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 [3122] [3123] 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 , [3124] 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,[] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] 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 , [3133] [3134] [3135] [3136] [3137] [3138pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3139] [3140] [3141] [3142] [3143] [3144] 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 , [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] 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 , [3169] [3170] [3171] [3172] [3173] [3174] [3175] 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 , [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] 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 [3185] 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 , [3186] 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 , [3187] 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[] [3188] [3189] [3190] [3191] 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 , [3192] 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, [3193] 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 [3194] 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[] [3195] [3196] [3197] 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 , [3198] 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 [3199] [3200] [3201] 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 , [3202] [3203] [3204] 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 , [3205] [3206] [3207] 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 [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] 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 [3216] [3217] [3218] [3219] [3220] 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 [3221] 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} [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] 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") [3234] 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 [3235] [3236] [3237] [3238]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} [3239] 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 [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] 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 [3248] [3249] [3250] 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, [3251] 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 [3252] [3253] [3254] 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,[] [3255] [3256] 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[][][] [3257] 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[] [3258] [3259] [3260] [3261] 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)[] [3262] [3263] [3264] [3265] [3266] [3267] 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(*)) [3268] [3269] [3270] [3271] [3272] [3273] 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 , [3274] [3275] [3276] [3277] 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 , [3278] [3279] [3280] [3281] [3282] 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 [3283] [3284] 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 , [3285] 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 , [3286] [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] 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(*)) [3295] [3296] [3297] [3298] [3299] 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)[] [3300] 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 [3301] 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,[] [3302] 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 [3303] 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 [3304] 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 , [3305] 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 , [3306] [3307] [3308] [3309] 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 [3310] [3311] [3312] [3313] 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"),[] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322]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} [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] 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- [3333] 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)[] [3334] 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 [3335] [3336] 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, ...)[] [3337] [3338] [3339] [3340] [3341] 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 , [3342] 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, ...)[] [3343] [3344] [3345] [3346] [3347] [3348] [3349] 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 [3350] [3351] [3352] [3353] [3354] 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 [3355] 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 [3356] [3357] [3358] [3359] 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 , [3360] [3361] [3362] [3363] 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[] [3364] [3365] [3366] [3367] [3368] [3369] 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 , [3370] 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 [3371] 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 [3372] 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 [3373] 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 [3374] 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 , [3375] 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 [3376] [3377] 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 [3378] [3379] 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 [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388]) (./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} [3389] 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,[] [3390] [3391] [3392] 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,[] [3393] 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)[] [3394] [3395] 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,[] [3396]) (./rpart-pkg.tex Chapter 27. [3397] [3398] [3399] [3400] 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, ...)[] [3401] [3402] [3403] [3404] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\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 [3405] [3406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3407] [3408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3409] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3410] [3411] [3412] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\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 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3413] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\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 [3414] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\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 1288--1288 []\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 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3415] [3416] [3417] [3418] [3419] [3420] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\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 ', [3421] [3422] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3423] [3424] [3425]) (./spatial-pkg.tex [3426] Chapter 28. [3427] [3428] [3429] [3430] [3431] [3432] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3433] [3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445]) (./survival-pkg.tex [3446] Chapter 29. [3447] [3448] 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.[] [3449] [3450] 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 [3451] [3452]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} [3453] 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)[] [3454] 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)[] [3455] [3456] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3457] [3458] 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"),[] [3459] [3460] 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,[] [3461] [3462] [3463] 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[] [3464] [3465] 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) [3466] 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} [3467] 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, ...)[] [3468] [3469] [3470] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1572--1572 [] \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 1619--1619 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3471] [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 1935--1950 []\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 1935--1950 \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 1935--1950 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3476] Underfull \hbox (badness 1337) in paragraph at lines 2019--2023 [][][]\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 , [3477] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2074--2074 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2646--2646 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2673--2673 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3486] [3487] [3488] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2905--2905 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3489] [3490] [3491] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3492] [3493] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3246--3246 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3494] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3281--3281 [] \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 3295--3297 []\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 3306--3306 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3495] [3496] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3440--3440 [] \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 )))[] [3497] [3498] Overfull \hbox (467.89665pt too wide) in alignment at lines 3581--3581 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3499] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3500] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3703--3703 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3501] [3502] [3503] [3504] [3505] [3506] [3507] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4092--4092 [] \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 )))[] [3508] [3509] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4238--4238 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4243--4243 []\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 4247--4247 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3510] Underfull \vbox (badness 1527) has occurred while \output is active [3511] [3512] [3513] [3514] [3515] [3516] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4664--4664 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3517] [3518] [3519] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4894--4894 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5020--5020 []\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[] [3521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5028--5028 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3522] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5114--5114 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5192--5192 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3524] Underfull \hbox (badness 1852) in paragraph at lines 5264--5266 []\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 [3525] [3526] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5389--5389 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3527] [3528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5491--5491 []\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 5492--5492 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3529] [3530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5656--5656 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5758--5758 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3532] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5779--5779 []\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 5781--5781 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3533] [3534] [3535] [3536] [3537] [3538] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6296--6296 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3539] [3540] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6476--6476 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6488--6491 \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 [3542] [3543] [3544] [3545] [3546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6796--6796 []\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 6797--6797 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3547] [3548] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6927--6927 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3549] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7001--7001 []\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.7005 ...ata from a soldering experiment}{solder} [3550] [3551] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7111--7111 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7475--7475 []\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 7476--7476 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3557] [3558] [3559] [3560] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7787--7787 [] \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 ),[] [3561] [3562] [3563] [3564] Underfull \hbox (badness 1253) in paragraph at lines 8076--8079 []\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 [3565] [3566] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3567] Underfull \hbox (badness 10000) in paragraph at lines 8328--8337 []\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 8328--8337 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3568] [3569] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8424--8424 [] \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 8442--8442 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8484--8490 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3570] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8536--8536 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3572] [3573] [3574] Underfull \hbox (badness 10000) in paragraph at lines 8847--8852 [][][]\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 , [3575] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8865--8865 [] \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 8866--8866 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3576] [3577] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9062--9062 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3578] [3579] Underfull \hbox (badness 3058) in paragraph at lines 9195--9200 []\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 9195--9200 \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 9195--9200 \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 9195--9200 \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 [3580] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9325--9325 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3581] [3582] [3583] [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9710--9710 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3586] Underfull \hbox (badness 1354) in paragraph at lines 9751--9755 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3587] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9797--9797 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3588] [3589] Underfull \hbox (badness 2035) in paragraph at lines 9961--9968 \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 9961--9968 \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 9961--9968 \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 [3590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10041--10041 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3591] [3592] [3593] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10198--10198 [] \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 )[] [3594] [3595] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10330--10330 [] \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 10333--10333 [] \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 )[] [3596] [3597] [3598] [3599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10643--10643 []\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 10644--10644 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10650--10650 [] \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 10652--10652 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3601] [3602] [3603] [3604] [3605] [3606] [3607] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11093--11093 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3608] [3609] [3610]) 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 2019] (kpathsea + Thai support). Scanning input file fullrefman.idx............................done (24949 entries accepted, 78 rejected). Sorting entries.....................................................................................................................................................................................................................................................................................done (410884 comparisons). Generating output file fullrefman.ind...........................done (26059 lines written, 114 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-12-01> (/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2018/09/03 v1.4i 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/ts1enc.def (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/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/oberdiek/hobsub-hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 377. 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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 2435) in paragraph at lines 212--217 []\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/ ptm/m/n/10 is true, there are 10 such Underfull \hbox (badness 3009) in paragraph at lines 221--233 \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 363--366 [][][]\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 561--567 []\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] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 903--903 []\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 921--921 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1532--1538 Underfull \hbox (badness 10000) in paragraph at lines 1545--1547 []\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 1724--1724 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1752--1755 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1871--1873 []\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 [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2008--2008 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\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 2318--2318 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2446--2448 []\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 2449--2454 [][][]\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 2517--2519 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2684--2684 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3353--3353 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3384--3384 []\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 3385--3385 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3392--3392 []\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 3393--3393 [] \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 3396--3396 []\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 3836--3838 []\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] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] Underfull \hbox (badness 4927) in paragraph at lines 4335--4339 []\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 4335--4339 \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 [66] [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4419--4419 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4484--4487 []\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 4644--4644 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = TRUE)[] Underfull \hbox (badness 1199) in paragraph at lines 4675--4681 []\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 4686--4689 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [71] [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4862--4862 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 5115--5117 []\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 [77] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5528--5536 []\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 [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 1796) in paragraph at lines 6094--6102 []\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 : / / [92] [93] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6288--6288 []\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 6290--6290 []\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 6291--6291 []\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}[] [94] [95] Underfull \hbox (badness 1242) in paragraph at lines 6430--6434 \T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment. [96] Underfull \hbox (badness 1635) in paragraph at lines 6493--6496 []\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 6497--6500 []\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 [97] Underfull \hbox (badness 1308) in paragraph at lines 6540--6548 []\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 [98] [99] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6704--6704 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] Underfull \vbox (badness 10000) has occurred while \output is active [100] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6754--6756 []\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 : [101] Underfull \hbox (badness 1997) in paragraph at lines 6881--6886 []\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 , [102] Underfull \hbox (badness 10000) in paragraph at lines 6919--6922 []\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 6919--6922 \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 [103] [104] Underfull \hbox (badness 1406) in paragraph at lines 7101--7107 []\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 7101--7107 \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 7101--7107 \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 7101--7107 \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 7121--7123 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [105] Underfull \hbox (badness 3302) in paragraph at lines 7163--7170 []\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 7163--7170 \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 7163--7170 \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- [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [109] [110] Underfull \hbox (badness 1231) in paragraph at lines 7492--7498 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 7704--7706 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [114] [115] [116] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7849--7849 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [117] [118] [119] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 8209--8219 []\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 8209--8219 [][]\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 Overfull \hbox (4.63962pt too wide) in paragraph at lines 8241--8246 []\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") [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1629) in paragraph at lines 8730--8742 []\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 8730--8742 \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 = [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9178--9182 []\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 [135] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9269--9269 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9271--9271 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [136] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9297--9297 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9298--9298 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [137] [138] Underfull \hbox (badness 5403) in paragraph at lines 9435--9437 []\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 9454--9456 []\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 [139] [140] [141] Underfull \hbox (badness 1603) in paragraph at lines 9679--9682 []\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 [142] [143] [144] [145] [146] [147] [148] [149] [150] Underfull \hbox (badness 1917) in paragraph at lines 10292--10297 []\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 [151] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10347--10347 []\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 10348--10348 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [152] [153] Underfull \hbox (badness 1168) in paragraph at lines 10450--10455 \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 10489--10495 []\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 Underfull \hbox (badness 5403) in paragraph at lines 10496--10499 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [154] [155] Underfull \hbox (badness 2828) in paragraph at lines 10655--10660 [][][]$\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 10655--10660 \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 10655--10660 \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 : [156] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10686--10686 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [157] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10759--10759 []\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, ..[] [158] [159] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10906--10906 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [160] [161] [162] Underfull \hbox (badness 6396) in paragraph at lines 11103--11111 []\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 11112--11114 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 11329--11332 []\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 [166] [167] [168] [169] [170] [171] [172] [173] [174] Underfull \hbox (badness 5288) in paragraph at lines 12029--12031 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [175] Underfull \hbox (badness 3039) in paragraph at lines 12039--12044 []\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 Underfull \hbox (badness 10000) in paragraph at lines 12099--12101 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 12221--12225 []\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 12221--12225 \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 [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 12336--12338 []\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 [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13181--13181 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [191] [192] [193] [194] [195] [196] Underfull \hbox (badness 2221) in paragraph at lines 13635--13644 \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 13635--13644 \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 [197] [198] [199] [200] Underfull \hbox (badness 2253) in paragraph at lines 13896--13898 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [201] [202] Underfull \hbox (badness 2573) in paragraph at lines 14013--14015 []\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 = [203] [204] Underfull \hbox (badness 10000) in paragraph at lines 14172--14174 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [205] [206] Underfull \hbox (badness 10000) in paragraph at lines 14289--14293 [][][]\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 14300--14303 [][][]$\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 14321--14321 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [207] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14346--14346 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [208] Underfull \hbox (badness 10000) in paragraph at lines 14440--14443 [][][]\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 14450--14450 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [209] Underfull \hbox (badness 10000) in paragraph at lines 14516--14519 []\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 14533--14533 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14562--14562 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14586--14593 []\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 14586--14593 \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 14594--14598 []\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, [211] [212] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14758--14758 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14759--14759 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [214] [215] [216] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14991--14991 []\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 14994--14994 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [217] Underfull \hbox (badness 1168) in paragraph at lines 15078--15082 []\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 15078--15082 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [218] Underfull \hbox (badness 6944) in paragraph at lines 15176--15179 [][][]\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 , [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15201--15201 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 15339--15341 []\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 15359--15359 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15365--15365 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [222] Underfull \hbox (badness 2790) in paragraph at lines 15372--15375 []\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 15403--15410 []\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 [223] Underfull \hbox (badness 10000) in paragraph at lines 15478--15480 []\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 15478--15480 \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 15500--15505 []\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 15506--15508 []\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 = [224] Underfull \hbox (badness 10000) in paragraph at lines 15512--15516 []\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 15512--15516 \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 15517--15525 []\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 [225] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15625--15625 []\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 [226] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15647--15647 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16468--16468 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [239] Underfull \hbox (badness 2418) in paragraph at lines 16577--16581 \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 16584--16587 []\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 [240] Underfull \hbox (badness 2326) in paragraph at lines 16619--16626 [][][]\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 , [241] [242] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16869--16869 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [244] Underfull \hbox (badness 1867) in paragraph at lines 16894--16901 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17189--17189 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17218--17218 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17269--17269 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [250] [251] [252] [253] [254] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17636--17636 []\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))) [255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17701--17701 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [256] [257] [258] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17891--17891 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [259] [260] [261] [262] Underfull \hbox (badness 2285) in paragraph at lines 18225--18227 []\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 / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18233--18233 []\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.[] [263] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18263--18263 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [264] [265] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18397--18397 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18403--18403 []\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 18406--18406 []\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 18412--18412 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [266] [267] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18539--18539 []\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 18547--18547 []\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):[] [268] [269] [270] Underfull \hbox (badness 10000) in paragraph at lines 18752--18754 []\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 [271] [272] [273] [274] [275] Underfull \hbox (badness 10000) in paragraph at lines 19090--19096 Underfull \hbox (badness 10000) in paragraph at lines 19103--19105 []\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 _ [276] [277] [278] Underfull \hbox (badness 4699) in paragraph at lines 19335--19338 []\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 , [279] [280] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19463--19463 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [281] [282] [283] Underfull \hbox (badness 4739) in paragraph at lines 19598--19600 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19647--19647 []\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 19648--19648 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1975) in paragraph at lines 20224--20227 []\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 [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1077) in paragraph at lines 20622--20627 []\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 [299] Underfull \hbox (badness 10000) in paragraph at lines 20636--20643 [][][]$\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 / [300] Underfull \hbox (badness 10000) in paragraph at lines 20710--20714 []\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-tory [301] [302] Underfull \hbox (badness 10000) in paragraph at lines 20859--20863 []\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 20859--20863 [][]\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 20864--20871 []\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- [303] [304] Underfull \hbox (badness 10000) in paragraph at lines 20995--21002 [][][]\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 , [305] Underfull \hbox (badness 10000) in paragraph at lines 21116--21120 []\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 [306] Underfull \hbox (badness 5161) in paragraph at lines 21186--21191 []\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 21186--21191 \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 21186--21191 \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 21186--21191 \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 [307] [308] [309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21353--21353 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21357--21357 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [310] Underfull \hbox (badness 3343) in paragraph at lines 21418--21422 [][][]\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 [311] [312] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21559--21559 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21570--21570 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [313] [314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21681--21681 []\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 21684--21684 []\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 21729--21734 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [315] Underfull \hbox (badness 2564) in paragraph at lines 21820--21823 []\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 [316] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21850--21850 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [317] [318] Underfull \hbox (badness 1400) in paragraph at lines 22018--22022 [][][]\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 [319] [320] [321] Underfull \hbox (badness 2469) in paragraph at lines 22188--22194 []\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22188--22194 \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 22188--22194 \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, [322] [323] [324] [325] [326] [327] [328] [329] [330] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22826--22826 []\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 22827--22827 [] \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 22830--22830 []\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)[] [331] [332] Underfull \hbox (badness 1655) in paragraph at lines 22954--22958 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [333] [334] [335] [336] Underfull \hbox (badness 2277) in paragraph at lines 23203--23206 []\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. [337] [338] Underfull \hbox (badness 10000) in paragraph at lines 23332--23335 []\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, [339] [340] [341] [342] [343] [344] [345] Underfull \hbox (badness 1484) in paragraph at lines 23788--23796 []\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 23788--23796 \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 / [346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23866--23866 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [347] [348] [349] [350] [351] [352] [353] Underfull \hbox (badness 1448) in paragraph at lines 24377--24385 \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 = [354] [355] Underfull \hbox (badness 3849) in paragraph at lines 24492--24497 []\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 [356] Underfull \hbox (badness 7308) in paragraph at lines 24569--24575 []\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 24569--24575 \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 24569--24575 [][]\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 24579--24582 []\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 24579--24582 \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 [357] [358] Underfull \hbox (badness 10000) in paragraph at lines 24732--24734 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [359] [360] [361] Underfull \hbox (badness 6188) in paragraph at lines 24952--24955 []\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 [362] [363] [364] Underfull \hbox (badness 1521) in paragraph at lines 25137--25151 \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- [365] [366] [367] [368] [369] Underfull \hbox (badness 2197) in paragraph at lines 25448--25452 []\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 25448--25452 \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 25462--25466 []\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 25462--25466 \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 25504--25504 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25508--25508 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [371] Underfull \hbox (badness 10000) in paragraph at lines 25556--25562 []\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 25556--25562 \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 25569--25571 []\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% Overfull \hbox (4.38043pt too wide) in paragraph at lines 25620--25620 [] \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:[] [372] [373] [374] Underfull \hbox (badness 8189) in paragraph at lines 25815--25821 []\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 [][][] [375] [376] [377] Underfull \hbox (badness 1694) in paragraph at lines 26040--26043 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [378] [379] [380] [381] Underfull \hbox (badness 1603) in paragraph at lines 26287--26289 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [382] [383] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26414--26422 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [384] [385] Underfull \hbox (badness 3271) in paragraph at lines 26633--26636 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [386] [387] [388] Underfull \hbox (badness 3138) in paragraph at lines 26937--26943 []\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 26937--26943 \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 26937--26943 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 26950--26953 []\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 [389] Underfull \hbox (badness 1389) in paragraph at lines 26976--26978 []\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 26996--27002 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27011--27016 []\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 27029--27032 []\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 Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see [390] Underfull \hbox (badness 10000) in paragraph at lines 27053--27059 []\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 27053--27059 \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 27053--27059 \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 27053--27059 \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 27068--27075 []\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 27068--27075 \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 27068--27075 \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 27068--27075 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [391] [392] [393] [394] Underfull \vbox (badness 10000) has occurred while \output is active [395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27416--27416 []\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 27429--27433 []\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 27429--27433 \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)] = [396] [397] Underfull \hbox (badness 10000) in paragraph at lines 27576--27579 []\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 27576--27579 \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 [398] [399] [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27854--27860 [][][]\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 27854--27860 [][]\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 27876--27876 []\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 27888--27888 []\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 27901--27901 []\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 27905--27905 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [402] [403] [404] Underfull \hbox (badness 1360) in paragraph at lines 28071--28075 []\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 = [405] [406] [407] [408] [409] [410] Underfull \hbox (badness 1817) in paragraph at lines 28466--28470 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [411] Underfull \hbox (badness 1796) in paragraph at lines 28534--28537 []\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 [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 28738--28741 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29433--29433 [] \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))[] [425] [426] Underfull \vbox (badness 10000) has occurred while \output is active [427] [428] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29721--29721 []\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 29732--29732 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Underfull \vbox (badness 10000) has occurred while \output is active [429] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29738--29738 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29739--29739 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29744--29744 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [430] Underfull \hbox (badness 7415) in paragraph at lines 29827--29831 []\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 29848--29848 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29894--29894 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [432] Underfull \hbox (badness 3713) in paragraph at lines 30017--30028 []\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 [433] [434] Underfull \hbox (badness 1248) in paragraph at lines 30161--30168 \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 30161--30168 \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 / [435] [436] Underfull \hbox (badness 1533) in paragraph at lines 30279--30282 []\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 [437] [438] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30424--30424 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30442--30453 []\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 [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30586--30586 []\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 30588--30588 []\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 30589--30589 []\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 30590--30590 []\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 30591--30591 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] [441] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30598--30598 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [442] [443] [444] [445] [446] Underfull \hbox (badness 4048) in paragraph at lines 30945--30950 []\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 30945--30950 \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 30945--30950 \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 , [447] [448] [449] [450] [451] [452] [453] [454] Underfull \hbox (badness 2080) in paragraph at lines 31482--31492 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver -sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 31508--31508 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 7558) in paragraph at lines 32026--32030 []\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 32036--32038 []\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 5417) in paragraph at lines 32041--32044 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 32047--32049 []\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 32050--32054 []\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 . [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 10000) in paragraph at lines 32453--32457 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [468] [469] [470] [471] [472] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32809--32809 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32812--32812 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [473] [474] [475] [476] [477] [478] [479] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33252--33252 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [480] [481] [482] [483] [484] [485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33689--33689 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [486] [487] Underfull \hbox (badness 1158) in paragraph at lines 33793--33798 []\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 Underfull \hbox (badness 10000) in paragraph at lines 33820--33826 []\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 33820--33826 \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 [488] [489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33978--33978 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [490] [491] [492] Underfull \hbox (badness 8151) in paragraph at lines 34238--34241 []\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 . [493] [494] [495] [496] Underfull \hbox (badness 10000) in paragraph at lines 34453--34458 []\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 = [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] Overfull \hbox (66.78088pt too wide) in paragraph at lines 35442--35442 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [512] [513] [514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 35694--35694 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 35696--35696 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [515] Underfull \hbox (badness 4954) in paragraph at lines 35739--35745 [][][]\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 35739--35745 [][]\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 [516] [517] Overfull \hbox (20.58041pt too wide) in paragraph at lines 35850--35850 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [518] [519] [520] [521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36185--36185 []\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)[] [522] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36200--36200 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [523] [524] [525] Underfull \hbox (badness 10000) in paragraph at lines 36419--36421 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [526] [527] [528] Overfull \hbox (12.78088pt too wide) in paragraph at lines 36646--36646 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 36647--36647 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [529] [530] [531] [532] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36914--36914 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [533] Underfull \hbox (badness 6110) in paragraph at lines 37005--37015 []\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 37005--37015 \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 37005--37015 \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 37005--37015 \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 37005--37015 \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 Underfull \hbox (badness 10000) in paragraph at lines 37051--37057 []\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 37051--37057 \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 37051--37057 \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 [534] Underfull \hbox (badness 1460) in paragraph at lines 37063--37070 []\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 37063--37070 \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 37063--37070 \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 [535] [536] [537] Underfull \hbox (badness 1484) in paragraph at lines 37295--37299 []\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 [538] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37357--37357 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [539] [540] [541] [542] [543] [544] [545] [546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37937--37937 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [547] [548] [549] [550] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38185--38185 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38229--38229 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [551] [552] [553] [554] [555] [556] [557] Overfull \hbox (52.98038pt too wide) in paragraph at lines 38663--38663 []\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 38666--38666 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [558] Underfull \hbox (badness 10000) in paragraph at lines 38717--38724 []\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 38717--38724 \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 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 38770--38770 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [559] [560] [561] [562] [563] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39081--39081 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [564] [565] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39246--39246 []\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. Overfull \hbox (20.58041pt too wide) in paragraph at lines 39284--39284 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [567] Underfull \hbox (badness 2293) in paragraph at lines 39314--39320 []\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 39314--39320 \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 39333--39338 []\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 39333--39338 \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 [568] Underfull \hbox (badness 2452) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [569] [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39611--39615 []\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 Underfull \hbox (badness 1584) in paragraph at lines 39626--39629 []\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 [572] [573] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39758--39758 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39835--39835 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [575] [576] [577] Underfull \hbox (badness 1082) in paragraph at lines 39979--39982 []\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 [578] [579] [580] Underfull \hbox (badness 1038) in paragraph at lines 40170--40173 []\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 [581] [582] [583] [584] [585] Underfull \hbox (badness 1442) in paragraph at lines 40534--40538 \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 = [586] [587] [588] [589] Underfull \hbox (badness 4096) in paragraph at lines 40784--40787 []\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 , [590] Underfull \hbox (badness 7888) in paragraph at lines 40898--40902 []\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) > [591] [592] [593] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41052--41052 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 41054--41054 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 41056--41056 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/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 41069--41071 []\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 [594] Underfull \hbox (badness 10000) in paragraph at lines 41149--41152 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [595] [596] Underfull \hbox (badness 3872) in paragraph at lines 41267--41270 []\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 . [597] Underfull \hbox (badness 5475) in paragraph at lines 41333--41337 [][][]\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 : / / [598] [599] [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41754--41761 \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 41810--41819 []\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 41810--41819 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [604] Underfull \hbox (badness 1082) in paragraph at lines 41820--41832 \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 41893--41901 \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 [605] Underfull \hbox (badness 10000) in paragraph at lines 41902--41905 []\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 41956--41959 [][][]$\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 41960--41962 [][][]$\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 41969--41969 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [606] [607] [608] Underfull \hbox (badness 10000) in paragraph at lines 42190--42192 []\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 [609] [610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42312--42312 []\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 42314--42314 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [611] [612] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42415--42415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42417--42417 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [613] [614] [615] Underfull \hbox (badness 6542) in paragraph at lines 42691--42693 []\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 [616] [617] Overfull \hbox (30.78088pt too wide) in paragraph at lines 42810--42810 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [618] Underfull \hbox (badness 1708) in paragraph at lines 42878--42886 []\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 42878--42886 \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 [619] Underfull \hbox (badness 4859) in paragraph at lines 42908--42913 [][][]\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; [620] Underfull \hbox (badness 3895) in paragraph at lines 42970--42982 []\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 42970--42982 \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 , [621] [622] [623] [624] [625] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43292--43292 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [626] [627] [628] [629] [630] [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43760--43760 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [632] Overfull \hbox (25.98041pt too wide) in paragraph at lines 43769--43769 []\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 43835--43841 [][][]\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 , [633] Underfull \hbox (badness 3861) in paragraph at lines 43844--43849 [][][]\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 , [634] [635] Underfull \hbox (badness 1803) in paragraph at lines 43990--43993 []\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 43994--44001 []\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 [636] [637] [638] Underfull \hbox (badness 3668) in paragraph at lines 44209--44211 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [639] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44315--44315 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44390--44390 []\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[] [641] Overfull \hbox (90.78033pt too wide) in paragraph at lines 44398--44398 []\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 ...[] [642] Underfull \hbox (badness 6220) in paragraph at lines 44528--44533 []\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 44528--44533 \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, [643] Underfull \hbox (badness 10000) in paragraph at lines 44549--44554 []\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 44549--44554 \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 [644] Underfull \hbox (badness 2818) in paragraph at lines 44645--44651 []\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 [645] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44680--44680 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [646] [647] [648] [649] [650] [651] Underfull \hbox (badness 2846) in paragraph at lines 45137--45141 []\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 [652] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45177--45177 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 45198--45202 []\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 [653]) (./compiler-pkg.tex [654] Chapter 2. [655] 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 [656] [657] [658]) (./datasets-pkg.tex Chapter 3. [659] [660] [661] [662] [663] 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,[] [664] 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 [665] [666] [667] [668] 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)[] [669] 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") [670] [671] 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") [672] [673] [674] 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. [675] 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") [676] [677] [678] [679] [680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [681] [682] Underfull \hbox (badness 10000) in paragraph at lines 1547--1550 []\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 1547--1550 \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 [683] [684] [685] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1736--1739 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [686] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1830--1830 []\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 1838--1838 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [687] [688] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1954--1954 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [689] [690] [691] [692] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2158--2161 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [693] [694] [695] Overfull \vbox (4.29591pt too high) has occurred while \output is active [696] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2723--2726 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] Overfull \vbox (13.87083pt too high) has occurred while \output is active [702] Underfull \vbox (badness 2376) has occurred while \output is active [703] [704] Overfull \vbox (12.25539pt too high) has occurred while \output is active [705] [706] Overfull \vbox (17.12102pt too high) has occurred while \output is active [707] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3152--3152 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [708] [709] [710] [711] [712] [713] [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [715] [716] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3757--3760 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [717] Overfull \vbox (10.49593pt too high) has occurred while \output is active [718] Overfull \vbox (15.49593pt too high) has occurred while \output is active [719] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3966--3966 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4004--4006 []\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 4004--4006 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733]) (./grDevices-pkg.tex [734] Chapter 4. [735] [736] [737] [738] 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 [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\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 379--387 \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 [741] [742] Overfull \hbox (6.78088pt too wide) in paragraph at lines 516--516 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \hbox (badness 5175) in paragraph at lines 1189--1191 []\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 [753] [754] [755] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] Underfull \hbox (badness 1173) in paragraph at lines 1402--1405 []\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 [756] [757] [758] [759] [760] [761] [762] [763] Underfull \hbox (badness 1565) in paragraph at lines 1890--1895 []\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 1890--1895 \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 [764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1973--1973 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2014--2024 []\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 2014--2024 \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 , [765] [766] Underfull \hbox (badness 10000) in paragraph at lines 2126--2128 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [767] [768] Underfull \hbox (badness 6758) in paragraph at lines 2305--2308 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [769] [770] Underfull \hbox (badness 2326) in paragraph at lines 2423--2433 \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 2423--2433 \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 2423--2433 \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 2423--2433 \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 [771] [772] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2526--2526 []\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 [773] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2642--2642 []\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 2643--2643 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [774] [775] [776] [777] [778] Underfull \hbox (badness 10000) in paragraph at lines 2914--2915 Underfull \vbox (badness 10000) has occurred while \output is active [779] [780] [781] [782] [783] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3247--3247 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [784] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3331--3331 []\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 3332--3332 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 3488--3493 []\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 3488--3493 \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- [787] [788] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3562--3562 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3666--3666 []\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 3673--3673 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [790] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3729--3729 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [791] Underfull \hbox (badness 8170) in paragraph at lines 3758--3761 []\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 , [792] Underfull \hbox (badness 2189) in paragraph at lines 3819--3824 []\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 3857--3861 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [793] Underfull \vbox (badness 10000) has occurred while \output is active [794] Underfull \hbox (badness 5260) in paragraph at lines 3987--3990 []\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 [795] [796] [797] [798] [799] Underfull \hbox (badness 5939) in paragraph at lines 4320--4325 []\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 , [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 10000) in paragraph at lines 4724--4729 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [806] [807] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4839--4839 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [808] [809] Underfull \hbox (badness 1348) in paragraph at lines 5044--5047 []\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 [810] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5068--5068 []\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 5109--5115 []\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 [811] Underfull \hbox (badness 1112) in paragraph at lines 5142--5146 []\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" [812] Underfull \hbox (badness 1755) in paragraph at lines 5284--5286 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [813] [814] [815] Underfull \hbox (badness 7344) in paragraph at lines 5464--5466 []\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 5475--5479 [][][]\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 [816] [817] Underfull \hbox (badness 1552) in paragraph at lines 5602--5611 \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 5602--5611 \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 5602--5611 \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 5612--5614 []\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 5644--5650 \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 [818] Underfull \hbox (badness 10000) in paragraph at lines 5670--5677 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [819] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5771--5771 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\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 [824] [825] [826] [827] [828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6336--6336 []\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 6350--6353 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [829] [830] [831] [832] [833] [834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6685--6685 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 6955--6960 []\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 6955--6960 \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 6955--6960 \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 [839] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7061--7061 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [840] Underfull \hbox (badness 3590) in paragraph at lines 7100--7103 []\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 7100--7103 \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 7111--7111 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [841] Underfull \hbox (badness 1189) in paragraph at lines 7175--7177 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [842] Underfull \hbox (badness 10000) in paragraph at lines 7280--7282 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [843] Underfull \hbox (badness 10000) in paragraph at lines 7326--7333 []\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 7326--7333 \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 [844] Underfull \hbox (badness 5607) in paragraph at lines 7410--7414 []\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 [845] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7462--7462 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [846] [847] Underfull \hbox (badness 5637) in paragraph at lines 7594--7600 \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 7627--7630 []\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 / [848] [849] [850] Underfull \hbox (badness 1231) in paragraph at lines 7796--7798 []\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 [851] [852]) (./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 = [853] [854] [855] 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 [856] [857] [858] [859] 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 [860] [861] 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[] [862] 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 [863] [864] 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, ...)[] [865] [866] [867] 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 (106.98032pt too wide) in paragraph at lines 981--981 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = 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)[] [868] [869] [870] [871] 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"):[] [872] [873] [874] Underfull \hbox (badness 1024) in paragraph at lines 1431--1439 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1465--1467 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [875] [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535 []\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 1536--1536 []\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 1542--1542 []\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 1543--1543 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 1846--1852 [][][]\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 (42.18039pt too wide) in paragraph at lines 1878--1878 []\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 1894--1894 []\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 1903--1903 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [882] [883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1988--1988 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [884] [885] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2117--2117 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2122--2122 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [886] [887] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296 []\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 2297--2297 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [888] Underfull \hbox (badness 1430) in paragraph at lines 2328--2330 []\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 [889] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2421--2428 \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 [890] Underfull \hbox (badness 7273) in paragraph at lines 2503--2507 [][][]\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 [891] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2516--2516 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [892] [893] [894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2750--2750 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2787--2787 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [896] [897] Underfull \hbox (badness 1226) in paragraph at lines 2912--2916 \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 2965--2965 []\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 :[] [898] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2969--2969 []\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 3021--3024 [][][]\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 [899] [900] [901] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3226--3226 []\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 3231--3231 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 3373--3378 []\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 3373--3378 [][]\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 3373--3378 [][]\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 [904] [905] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3559--3559 []\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 3578--3578 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [907] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3582--3582 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3759--3759 [] \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 3760--3760 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3799--3799 [] \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 [911] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3851--3851 []\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 3859--3859 []\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 3861--3861 []\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 3869--3869 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [912] Underfull \hbox (badness 10000) in paragraph at lines 3932--3936 [][][]\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% [913] [914] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [915] [916] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4198--4198 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [917] Underfull \hbox (badness 3930) in paragraph at lines 4277--4279 []\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 [918] [919] [920] [921] [922] Underfull \hbox (badness 1286) in paragraph at lines 4588--4591 \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 4596--4601 []\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 [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693 []\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 4698--4698 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [925] Underfull \hbox (badness 1264) in paragraph at lines 4889--4902 \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 , [926] [927] Underfull \hbox (badness 10000) in paragraph at lines 5026--5032 []\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. [928] [929] Underfull \hbox (badness 10000) in paragraph at lines 5157--5160 [930 ] Underfull \hbox (badness 10000) in paragraph at lines 5218--5220 [931 ] [932] Underfull \hbox (badness 10000) in paragraph at lines 5408--5410 []\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 [933] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5464--5464 []\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 5465--5465 [] \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 [934] [935] [936] [937] [938] [939] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830 []\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 5831--5831 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [940]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5890 \aliasA{plot}{plot.default}{plot} [941] [942] [943] [944] [945] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [946] [947] [948] [949] [950] [951] Underfull \hbox (badness 10000) in paragraph at lines 6658--6660 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [952] [953] Underfull \hbox (badness 1028) in paragraph at lines 6752--6754 []\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 6795--6796 [][] [954 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6889--6889 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [955] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6920--6920 [] \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 [956] [957] Underfull \hbox (badness 10000) in paragraph at lines 7042--7044 []\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 7069--7069 [] \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 7075--7075 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [958] Underfull \hbox (badness 2600) in paragraph at lines 7135--7137 []\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 [959] [960] [961] [962] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [963] [964] [965] [966] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754 []\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 7758--7758 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [969] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7770--7770 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [970] [971] [972] [973] [974] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8119--8119 []\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 8122--8122 []\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 8126--8126 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [975] [976] [977] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8297--8297 []\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 8298--8298 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [978] [979] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8402--8402 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8413--8418 []\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 [980] Underfull \hbox (badness 1112) in paragraph at lines 8461--8465 []\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 [981] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8521--8521 []\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 8536--8536 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [982] [983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8858--8858 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [986] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8888--8890 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8920--8926 []\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 [987]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8968 \HeaderA{units}{Graphical Units}{units} [988] Underfull \hbox (badness 1205) in paragraph at lines 9033--9035 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [989] [990] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9152--9152 []\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)[] [991]) (./grid-pkg.tex [992] Chapter 6. [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \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 476--482 \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 [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\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- [1011] [1012] [1013] [1014] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\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 [1015] [1016] [1017] [1018] [1019] [1020] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1768--1768 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1021] [1022] [1023] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1982--1982 []\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 1983--1983 []\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 1984--1984 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1024] Underfull \hbox (badness 2961) in paragraph at lines 2019--2024 []\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 , [1025] Underfull \hbox (badness 1430) in paragraph at lines 2078--2083 []\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 2107--2110 []\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 [1026] [1027] [1028] Underfull \hbox (badness 2894) in paragraph at lines 2314--2321 []\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 [1029] [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2470--2470 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2482--2487 []\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- [1032] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2541--2541 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1033] [1034] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2693--2693 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1035] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1036] [1037] [1038] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2967--2967 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1039] [1040] [1041] [1042] [1043] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3282--3282 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1044] [1045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3412--3418 []\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 [1046] [1047] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3504--3504 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1048] [1049] [1050] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3712--3712 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3727--3727 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1051] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3748--3748 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \hbox (badness 1067) in paragraph at lines 4489--4492 []\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 [1064] Underfull \hbox (badness 1430) in paragraph at lines 4535--4540 []\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- [1065] [1066] [1067] Underfull \hbox (badness 7256) in paragraph at lines 4734--4736 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 10000) in paragraph at lines 5371--5373 []\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 [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] Underfull \hbox (badness 6859) in paragraph at lines 6059--6065 []\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 6059--6065 \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") [1088] [1089] [1090] [1091] [1092] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1093] Underfull \hbox (badness 1867) in paragraph at lines 6437--6439 []\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 [1094] Underfull \hbox (badness 10000) in paragraph at lines 6474--6480 [][][]\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 , [1095] [1096] Underfull \hbox (badness 1371) in paragraph at lines 6606--6609 []\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 [1097] Underfull \vbox (badness 10000) has occurred while \output is active [1098] [1099] [1100] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6810--6810 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1101]) (./methods-pkg.tex [1102] Chapter 7. [1103] [1104] 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 [1105] [1106] [1107] 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- [1108] [1109] 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[] [1110] 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 [1111] 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 [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] 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[] [1127] [1128] 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 [1129] [1130] [1131] 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 = [1132] [1133] 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 [1134] [1135] [1136] 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 [1137] 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))[] [1138] [1139] [1140] 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:[] [1141] [1142] [1143] [1144] [1145] [1146] [1147] 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 [1148] [1149] 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 [1150] 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 [] [1151] [1152] 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,...) { [1153] 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 [1154] [1155] [1156] 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 [1157] [1158] [1159] 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,[] [1160] 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) [1161] [1162] [1163] 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 , [1164] [1165] [1166] 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 [1167] [1168] [1169] [1170] 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[] [1171] 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 [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1174] [1175] 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 [1176] [1177] [1178] 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 [1179] [1180] [1181] [1182] [1183] [1184] 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 [1185] [1186] 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 [1187] 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 [1188] [1189] 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 [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] [1193]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1194] 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().[] [1195] [1196] 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")[] [1197]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 [1198] 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 , [1199] [1200] 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 [1201] [1202] 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 [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] 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 [1214] 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(), [1215] 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 =,[] [1216] [1217] [1218] [1219] 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[] [1220] [1221] [1222] 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")[] [1223] [1224] [1225] 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[] [1226] [1227] [1228] [1229] 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[] [1230] 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][] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] 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 [1241] [1242] [1243]) (./parallel-pkg.tex [1244] 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 [1245] 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 [1246] [1247] 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 [1248] [1249] [1250] 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 [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 1917) in paragraph at lines 770--779 []\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 770--779 \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 [1256] [1257] Overfull \hbox (60.78088pt too wide) in paragraph at lines 863--863 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1258] [1259] [1260] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1054--1054 []\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 1058--1058 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1261] Underfull \hbox (badness 5388) in paragraph at lines 1173--1178 []\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 [1262] Underfull \hbox (badness 10000) in paragraph at lines 1197--1205 []\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 1234--1234 []\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)[] [1263] [1264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1350--1350 [] \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 1364--1364 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1265] Underfull \hbox (badness 1577) in paragraph at lines 1393--1396 []\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 1440--1442 []\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 [1266] [1267]) (./splines-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] 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))[] [1277] 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 [1278] [1279] 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)))[] [1280] [1281] [1282]) (./stats-pkg.tex Chapter 10. [1283] 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[] [1284] [1285] [1286] [1287] [1288] 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[] [1289] 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) [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 1024) in paragraph at lines 882--884 []\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 [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 10000) in paragraph at lines 1544--1548 []\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 1544--1548 \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 1544--1548 \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 [1306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620 [] \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 1623--1623 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1307] [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1770--1770 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1309] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1782--1782 []\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 :[ ] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2800--2800 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1324] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3040--3040 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1328] [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 3251--3253 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1331] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3300--3300 []\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 3301--3301 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1332] [1333] [1334] [1335] [1336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3692--3692 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1337] [1338] [1339] [1340] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1341] [1342] [1343] [1344] [1345] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4260--4260 []\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 4261--4261 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1346] [1347] [1348] [1349] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4501--4501 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1350] [1351] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4676--4676 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1352] [1353] Underfull \hbox (badness 3989) in paragraph at lines 4770--4777 []\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 = [1354] [1355] [1356] [1357] [1358] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5155--5155 []\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 5157--5157 []\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))[] [1359] [1360] [1361] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5378--5378 []\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 5396--5396 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1362] Underfull \hbox (badness 2680) in paragraph at lines 5423--5425 []\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 [1363] [1364] [1365] Underfull \hbox (badness 1436) in paragraph at lines 5606--5611 []\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 5606--5611 \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 5606--5611 \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 , [1366] [1367] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5809--5809 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1368] [1369] [1370] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5976--5976 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1371] [1372] [1373] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6161--6161 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1374] [1375] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6269--6269 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1376] Underfull \hbox (badness 10000) in paragraph at lines 6336--6341 []\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 [1377] [1378] [1379] Underfull \hbox (badness 5954) in paragraph at lines 6532--6534 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1380] Underfull \hbox (badness 2503) in paragraph at lines 6614--6617 []\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 6618--6620 []\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 6621--6626 \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, [1381] Underfull \hbox (badness 7238) in paragraph at lines 6657--6660 [][][]\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 6692--6692 []\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 6707--6707 []\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):[] [1382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6722--6722 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1383] [1384] [1385] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6967--6967 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1386] [1387] [1388] Underfull \vbox (badness 10000) has occurred while \output is active [1389] [1390] [1391] [1392] Underfull \hbox (badness 10000) in paragraph at lines 7366--7370 \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 [1393] Underfull \hbox (badness 6493) in paragraph at lines 7465--7468 []\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 [1394] [1395] Underfull \hbox (badness 10000) in paragraph at lines 7602--7605 []\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 = [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 8014--8019 []\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 , ..., [1402] [1403] [1404] [1405] [1406] [1407] Underfull \hbox (badness 1210) in paragraph at lines 8369--8371 []\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 [1408] [1409] [1410] [1411] [1412] [1413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8832--8832 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1414] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8877--8877 []\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 8880--8880 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1415] [1416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9018--9018 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1417] [1418] [1419] [1420] [1421] [1422] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9445--9445 [] \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 9446--9446 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1423] [1424] [1425] Underfull \hbox (badness 7291) in paragraph at lines 9625--9627 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1426] [1427] [1428] [1429] [1430] [1431] [1432] Underfull \hbox (badness 6944) in paragraph at lines 10103--10109 [][][]\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); [1433] [1434] [1435] Underfull \hbox (badness 3758) in paragraph at lines 10317--10320 []\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 [1436] [1437] [1438] [1439] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10561--10561 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10587--10592 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] Underfull \hbox (badness 4132) in paragraph at lines 10626--10630 []\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 10680--10686 []\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- [1441] Underfull \hbox (badness 10000) in paragraph at lines 10731--10734 []\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 [1442] [1443] [1444] Underfull \hbox (badness 2142) in paragraph at lines 10948--10951 []\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 ^^@ [1445] Underfull \hbox (badness 1708) in paragraph at lines 11029--11033 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1446] Underfull \hbox (badness 10000) in paragraph at lines 11071--11077 [][][]\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 11109--11114 \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 (= [1447] [1448] Underfull \hbox (badness 2635) in paragraph at lines 11242--11245 \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 [1449] [1450] [1451] Underfull \hbox (badness 1694) in paragraph at lines 11425--11428 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11526--11526 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1453] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11559--11559 [] \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 11572--11576 []\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 [1454] [1455] [1456] [1457] [1458] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1459]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11909 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11969--11969 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1460] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12034--12039 []\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 12051--12053 []\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 [1461] [1462] [1463] [1464] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1465] [1466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1467] [1468] [1469] [1470] Underfull \hbox (badness 10000) in paragraph at lines 12649--12651 []\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 12672--12674 []\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 [1471] Underfull \hbox (badness 2753) in paragraph at lines 12741--12743 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1472] [1473] [1474] [1475] Underfull \hbox (badness 6910) in paragraph at lines 12979--12981 []\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 12985--12989 []\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 12985--12989 \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 [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13692--13692 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1486] Underfull \hbox (badness 4518) in paragraph at lines 13736--13741 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 13935--13939 []\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 , [1490] [1491] [1492] [1493] [1494] Underfull \hbox (badness 1163) in paragraph at lines 14269--14277 \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 , [1495] Underfull \hbox (badness 4518) in paragraph at lines 14389--14394 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1496] [1497] [1498] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14577--14577 []\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 14578--14578 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1499] [1500] [1501] [1502] [1503] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14921--14921 []\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 14922--14922 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1504] [1505] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15015--15015 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2726) in paragraph at lines 15421--15424 []\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 , [1512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15515--15515 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16141--16141 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1523] [1524] Underfull \hbox (badness 1490) in paragraph at lines 16279--16284 \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 [1525] Underfull \hbox (badness 1648) in paragraph at lines 16345--16347 []\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 16360--16369 \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 16360--16369 \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 [1526] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16430--16430 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16988--16988 []\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[] [1536] [1537] [1538] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17220--17220 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] Underfull \vbox (badness 10000) has occurred while \output is active [1550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17981--17981 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1551] [1552] [1553] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18144--18144 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18191--18191 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18238--18238 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] Underfull \hbox (badness 1248) in paragraph at lines 18736--18739 []\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 18749--18753 []\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 [1563] Underfull \hbox (badness 1478) in paragraph at lines 18757--18761 \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 Underfull \hbox (badness 2042) in paragraph at lines 18815--18817 []\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 [1564] [1565] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18921--18921 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1566] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18964--18964 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18982--18982 []\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 18985--18985 []\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 19005--19005 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 19008--19008 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1567] Underfull \hbox (badness 2564) in paragraph at lines 19043--19054 []\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 19043--19054 \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 [1568] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1569] [1570] [1571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19333--19333 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1572] [1573] Underfull \hbox (badness 1337) in paragraph at lines 19444--19447 []\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 [1574] [1575] [1576] [1577] [1578] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19763--19763 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1579] [1580] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19851--19851 [] \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 19853--19853 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19855--19855 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1581] Underfull \hbox (badness 10000) in paragraph at lines 19901--19907 []\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 19942--19946 []\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 [1582] [1583] [1584] [1585] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20195--20195 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20205--20208 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1586] Underfull \hbox (badness 1107) in paragraph at lines 20263--20265 []\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 [1587] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20318--20318 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20325--20325 []\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)[] [1589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20419--20419 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1590] [1591] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1592] Underfull \hbox (badness 7740) in paragraph at lines 20611--20613 []\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 [1593] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20659--20659 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1594] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20751--20751 [] \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 20756--20756 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21611--21611 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1608] Underfull \hbox (badness 6859) in paragraph at lines 21678--21685 [][][]\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 21689--21695 []\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 , [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22435--22435 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1621] [1622] [1623] [1624] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22719--22719 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22720--22720 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 23046--23052 []\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 [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] Underfull \hbox (badness 10000) in paragraph at lines 23602--23604 []\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 23602--23604 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23609--23610 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1639] [1640] [1641] Underfull \hbox (badness 1028) in paragraph at lines 23772--23775 []\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 [1642] Underfull \hbox (badness 10000) in paragraph at lines 23882--23885 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] Underfull \hbox (badness 7944) in paragraph at lines 23937--23939 []\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 = [1644] Underfull \hbox (badness 7944) in paragraph at lines 23999--24001 []\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 = [1645] [1646] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24101--24101 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1647] [1648] [1649] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24321--24321 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1650] [1651] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24425--24425 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24468--24474 \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 24489--24492 []\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] = [1652] Underfull \hbox (badness 2134) in paragraph at lines 24558--24562 [][][]\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 24571--24571 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1653] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24600--24600 []\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 24612--24612 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 6268) in paragraph at lines 25067--25072 [][]\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 , [1661] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25095--25095 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1662] [1663] [1664] Underfull \hbox (badness 1867) in paragraph at lines 25272--25274 []\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 25287--25291 []\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 25287--25291 \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 25323--25323 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1665] [1666] [1667] Underfull \hbox (badness 2495) in paragraph at lines 25513--25522 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1668] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25595--25595 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1669] Underfull \hbox (badness 1412) in paragraph at lines 25602--25604 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1670] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25689--25689 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25714--25714 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25717--25717 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1671] [1672] [1673] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25941--25941 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25945--25951 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1674] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25991--25991 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26012--26012 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1675] Underfull \hbox (badness 1019) in paragraph at lines 26074--26079 \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 [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26204--26204 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1678] [1679] [1680] [1681] [1682] [1683] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26584--26584 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1684] [1685] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26765--26765 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1686] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26771--26771 []\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 26780--26780 []\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 26781--26781 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1687] Underfull \hbox (badness 2922) in paragraph at lines 26850--26855 []\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 26887--26887 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1688] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26890--26890 [] \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 26899--26899 [] \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 26900--26900 [] \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 26904--26904 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1689] Underfull \hbox (badness 3240) in paragraph at lines 26958--26961 [][][]\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 26979--26979 [] \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 26982--26982 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1690] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27065--27065 [] \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 27069--27069 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1691] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27079--27079 [] \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 27084--27084 [] \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 27120--27126 []\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 [1692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27142--27142 []\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 27158--27158 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1693] [1694] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27272--27272 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1695] Underfull \hbox (badness 2922) in paragraph at lines 27334--27339 []\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 (69.18036pt too wide) in paragraph at lines 27372--27372 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1696] Underfull \hbox (badness 2922) in paragraph at lines 27421--27426 []\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 [1697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27452--27452 []\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 27486--27491 []\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 [1698] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27511--27511 []\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 27515--27515 []\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 27535--27535 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27545--27545 [] \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[] [1699] Underfull \hbox (badness 2922) in paragraph at lines 27580--27585 []\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 27602--27602 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1700] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27620--27620 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 27672--27677 []\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 [1701] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27700--27700 []\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 27703--27703 []\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 27706--27706 []\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 27709--27709 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 3396) in paragraph at lines 28631--28633 []\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 [1716] [1717] [1718] Underfull \hbox (badness 2237) in paragraph at lines 28808--28810 []\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 [1719] [1720] Underfull \hbox (badness 2591) in paragraph at lines 28972--28974 []\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 [1721] Underfull \hbox (badness 2237) in paragraph at lines 29018--29021 []\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 [1722] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29091--29091 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1723] [1724] Underfull \hbox (badness 3407) in paragraph at lines 29200--29204 []\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) [1725] [1726] Underfull \hbox (badness 1337) in paragraph at lines 29333--29337 []\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 [1727] [1728] [1729] [1730] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29591--29591 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29619--29619 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1731] Underfull \hbox (badness 1616) in paragraph at lines 29645--29648 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1732] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29724--29724 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1733] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29801--29801 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1734] [1735] Underfull \hbox (badness 2205) in paragraph at lines 29890--29895 []\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 [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30489--30489 []\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 30490--30490 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1745] [1746] [1747] [1748] [1749] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30790--30790 [] \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 30791--30791 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1750] [1751] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30917--30917 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30926--30926 []\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 [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 31143--31147 []\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 [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] Underfull \hbox (badness 1337) in paragraph at lines 31672--31676 []\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 31686--31688 []\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 [1764] [1765] [1766] Overfull \hbox (117.7803pt too wide) in paragraph at lines 31879--31879 []\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 31881--31881 []\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)[] [1767] [1768] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32040--32040 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1769] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32124--32124 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1770] Underfull \hbox (badness 6775) in paragraph at lines 32181--32186 []\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 [1771] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32244--32244 []\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 "")[] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] 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 [1776] 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[] [1777] [1778] [1779] [1780]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} [1781] [1782] [1783]) (./tcltk-pkg.tex [1784] Chapter 12. [1785] [1786] [1787] [1788] Overfull \hbox (36.7804pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1789] [1790] [1791] Underfull \vbox (badness 10000) has occurred while \output is active [1792] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\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 [1793] [1794] [1795] [1796] [1797] [1798] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1799] [1800] [1801] [1802] [1803] Underfull \hbox (badness 1189) in paragraph at lines 1406--1409 [][][]\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 [1804]) (./tools-pkg.tex Chapter 13. [1805] 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.[] [1806] 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 [1807] 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)[] [1808] 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 , [1809] 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 [1810] [1811] 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 [1812] [1813] [1814] [1815] [1816] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1817] [1818] 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")[] [1819] [1820] [1821] 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, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1150--1160 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1150--1160 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1822] 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 [1823] 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 [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1697--1697 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] 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--1712 []\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--1712 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1911 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] [1836] [1837] Underfull \hbox (badness 1142) in paragraph at lines 2179--2185 []\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 2213--2213 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2214--2214 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2241--2248 []\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 2241--2248 \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 2241--2248 \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 [1839] Underfull \hbox (badness 1342) in paragraph at lines 2293--2299 \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 [1840] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2369--2369 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2382--2388 []\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 2382--2388 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2424--2424 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2441--2441 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1842] [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1846] Underfull \hbox (badness 2486) in paragraph at lines 2770--2778 []\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 [1847] [1848] [1849] [1850] [1851] Underfull \hbox (badness 1072) in paragraph at lines 3150--3152 []\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 [1852] [1853] [1854] [1855] [1856] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3483--3483 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 4108) in paragraph at lines 3731--3738 []\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 [1861] [1862] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3831--3831 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3834--3834 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3851--3853 []\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 3868--3874 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1863] [1864] Underfull \hbox (badness 7832) in paragraph at lines 3990--3993 []\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 [1865] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4066--4066 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1866] Underfull \hbox (badness 1137) in paragraph at lines 4092--4094 []\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 [1867] [1868] [1869] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4277--4277 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1870] [1871] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4439--4439 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4450--4453 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1872] Underfull \hbox (badness 6859) in paragraph at lines 4466--4471 []\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 4474--4480 []\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 4474--4480 \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 [1873] [1874] [1875] [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4745--4748 []\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 4749--4759 \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 4784--4790 []\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 4784--4790 \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 ', [1877] Underfull \hbox (badness 1571) in paragraph at lines 4812--4816 []\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 4838--4843 \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 [1878] [1879] [1880]) (./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 ', [1881] [1882] [1883] [1884] 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[] [1885] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1886] 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 [1887] 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"))),[] [1888] [1889] Underfull \hbox (badness 1946) in paragraph at lines 626--630 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676 []\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 682--682 []\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 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684 []\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 685--685 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 719--725 []\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 719--725 \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- [1891] [1892] Underfull \hbox (badness 4505) in paragraph at lines 855--861 \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 [1893] [1894] [1895] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1896] Underfull \hbox (badness 1748) in paragraph at lines 1094--1102 []\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 1094--1102 \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 1094--1102 \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 1094--1102 \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 1106--1108 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1897] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1898] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1907] [1908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1909] [1910] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1911] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1912] [1913] [1914] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1915] [1916] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1917] Underfull \hbox (badness 1082) in paragraph at lines 2570--2574 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2575 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2606--2608 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1918] [1919] Underfull \hbox (badness 10000) in paragraph at lines 2694--2696 []\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 [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 2911--2913 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1923] [1924] [1925] [1926] Underfull \hbox (badness 1762) in paragraph at lines 3205--3208 []\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 = [1927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298 []\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 '[] [1928] Underfull \hbox (badness 2452) in paragraph at lines 3374--3377 []\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 [1929] [1930] [1931] [1932] [1933] [1934] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 3867--3871 []\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 3935--3943 []\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 [1937] Underfull \hbox (badness 1231) in paragraph at lines 4012--4024 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1938] Underfull \hbox (badness 10000) in paragraph at lines 4026--4031 []\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 4026--4031 \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 4026--4031 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1939] Underfull \hbox (badness 4660) in paragraph at lines 4146--4149 \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 4170--4172 []\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 [1940] [1941] [1942] Underfull \hbox (badness 1565) in paragraph at lines 4355--4359 []\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 [1943] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4438--4438 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1944] Underfull \hbox (badness 1931) in paragraph at lines 4473--4480 []\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) [1945] [1946] [1947] [1948] [1949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4797--4797 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4868 ...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.4868 ...mat Unordered and Ordered Lists}{format} [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1622) in paragraph at lines 5387--5391 []\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 [1959] [1960] [1961] [1962] [1963] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5709--5709 []\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 5721--5721 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1964] [1965] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5854--5854 [] \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 5855--5855 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1966] [1967] [1968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6065--6065 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1969] Underfull \hbox (badness 10000) in paragraph at lines 6149--6151 []\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 [1970] Underfull \hbox (badness 1502) in paragraph at lines 6198--6203 []\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 6198--6203 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1971] [1972] Underfull \hbox (badness 10000) in paragraph at lines 6371--6380 []\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 6371--6380 \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 [1973] Underfull \hbox (badness 2150) in paragraph at lines 6435--6438 []\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 6451--6454 []\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 [1974] [1975] Underfull \hbox (badness 3118) in paragraph at lines 6573--6575 []\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 [1976] [1977] Underfull \hbox (badness 5091) in paragraph at lines 6747--6749 []\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 [1978] Underfull \hbox (badness 5331) in paragraph at lines 6763--6769 []\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 6763--6769 \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 6763--6769 \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 6777--6784 []\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 6792--6802 \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 [1979] Underfull \hbox (badness 10000) in paragraph at lines 6835--6838 []\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 6835--6838 \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 6843--6846 []\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 [1980] Underfull \hbox (badness 2376) in paragraph at lines 6914--6921 []\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 6914--6921 \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 6914--6921 \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 6922--6925 []\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 [1981] Underfull \hbox (badness 1314) in paragraph at lines 7001--7008 []\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 7048--7051 []\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 7048--7051 \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 7081--7086 [][][]\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 , [1982] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7104--7104 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7140--7144 []\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 7154--7157 []\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 [1983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7201--7201 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1984] [1985] Underfull \hbox (badness 4132) in paragraph at lines 7325--7327 []\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 [1986] [1987] [1988] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7492--7492 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1989] [1990] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7635--7635 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1991] Underfull \hbox (badness 10000) in paragraph at lines 7675--7677 []\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 [1992] [1993] Underfull \hbox (badness 10000) in paragraph at lines 7863--7865 []\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 7868--7870 []\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 [1994] [1995] [1996] [1997] Underfull \hbox (badness 1859) in paragraph at lines 8096--8099 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1998] Underfull \hbox (badness 1655) in paragraph at lines 8190--8193 []\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 8201--8201 []\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 8209--8209 []\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):[] [1999] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8217--8217 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2000] Underfull \hbox (badness 1917) in paragraph at lines 8304--8306 []\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 , [2001] [2002] [2003] [2004] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8576--8576 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8577--8577 [] \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 8578--8578 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2005] Underfull \hbox (badness 10000) in paragraph at lines 8606--8608 []\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 8620--8622 []\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 8628--8633 []\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, [2006] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8674--8674 [] \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 8675--8675 [] \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[] [2007] [2008] Underfull \hbox (badness 10000) in paragraph at lines 8804--8809 []\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 8804--8809 [][]\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 8804--8809 \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 8811--8814 \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 [2009] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8927--8927 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8928--8928 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2010] [2011] [2012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/9 "S original, "),[] [2013] Underfull \hbox (badness 1789) in paragraph at lines 9232--9234 []\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 [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 5203) in paragraph at lines 9805--9808 []\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 [2023] [2024] Underfull \hbox (badness 1394) in paragraph at lines 10031--10038 \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 [2025] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10055--10055 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2026] [2027] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10216--10216 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2028] [2029] [2030] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10397--10397 []\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[] [2031] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10483--10483 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10486--10486 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10491--10491 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2032] Underfull \hbox (badness 2027) in paragraph at lines 10563--10566 []\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 [2033] [2034] [2035] [2036] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10835--10835 []\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 10836--10836 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10843--10848 []\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 10843--10848 \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 10843--10848 \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 [2037] [2038] [2039] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11076--11076 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2040] [2041] [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 \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 11355--11355 []\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 11360--11360 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2045] [2046] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11493--11493 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11494--11494 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2047] [2048] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11629--11629 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2049] Underfull \hbox (badness 1917) in paragraph at lines 11753--11756 []\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 11753--11756 \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 [2050] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11776--11776 []\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 '[] [2051] Underfull \hbox (badness 10000) in paragraph at lines 11839--11841 []\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 [2052] Underfull \hbox (badness 6725) in paragraph at lines 11889--11898 \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 11889--11898 \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 11889--11898 \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 11889--11898 \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 [2053] Underfull \hbox (badness 3646) in paragraph at lines 12015--12017 [][][]$\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 / [2054] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12053--12053 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2055] [2056] [2057] Underfull \hbox (badness 10000) in paragraph at lines 12234--12238 []\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 12265--12271 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2058] [2059] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12441--12441 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2060] Underfull \hbox (badness 1009) in paragraph at lines 12459--12471 []\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 12499--12501 []\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 [2061] Underfull \hbox (badness 1043) in paragraph at lines 12542--12547 []\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 [2062] [2063] [2064] [2065] Underfull \hbox (badness 1888) in paragraph at lines 12835--12838 []\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 12852--12855 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2066] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12898--12898 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2067] Underfull \hbox (badness 2158) in paragraph at lines 12953--12956 []\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 13001--13001 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2068] [2069] [2070] Underfull \hbox (badness 2302) in paragraph at lines 13158--13160 []\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 [2071] Underfull \hbox (badness 3333) in paragraph at lines 13265--13267 []\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- [2072] [2073] [2074] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13432--13432 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13456--13461 []\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 13465--13468 []\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 13465--13468 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2075] Underfull \hbox (badness 1442) in paragraph at lines 13492--13496 []\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 13524--13524 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2076] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13555--13555 []\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 13562--13562 []\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 13564--13564 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2077] [2078] Underfull \hbox (badness 10000) in paragraph at lines 13732--13734 []\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 [2079] [2080] [2081] Underfull \hbox (badness 6300) in paragraph at lines 13889--13896 []\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 13889--13896 \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 13889--13896 \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$"\T1/ptm/m/n/10 ) and [2082] [2083] Underfull \hbox (badness 2020) in paragraph at lines 14058--14074 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 14058--14074 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2084] [2085] Underfull \hbox (badness 5022) in paragraph at lines 14198--14202 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 14205--14208 [][][]$\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 14205--14208 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2086] [2087] [2088] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14369--14369 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2089] [2090] [2091] [2092] [2093] [2094] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14809--14809 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14815--14815 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14836--14838 []\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 14851--14855 \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 14865--14869 []\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 14871--14876 []\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 14871--14876 \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 14871--14876 \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 14877--14879 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2095] Underfull \hbox (badness 10000) in paragraph at lines 14907--14912 \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 14907--14912 \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 14928--14933 []\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 14936--14939 [][][]\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 , [2096] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14990--14990 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2097] [2098] [2099] Underfull \hbox (badness 10000) in paragraph at lines 15192--15195 [][][]\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 15192--15195 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2100] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15208--15208 []\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:[] [2101] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15275--15275 [] \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 15297--15297 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2102] [2103] Underfull \hbox (badness 1297) in paragraph at lines 15428--15430 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2104] Underfull \hbox (badness 4036) in paragraph at lines 15475--15477 []\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. [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15612--15612 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2107] Underfull \hbox (badness 1715) in paragraph at lines 15664--15667 []\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 15709--15711 []\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 = [2108] [2109] [2110]) [2111] [2112] (./KernSmooth-pkg.tex Chapter 15. [2113] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2114] [2115] [2116] [2117] [2118] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2119] [2120] [2121] [2122]) (./MASS-pkg.tex Chapter 16. [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] 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))[] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] 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"),[] [2157] [2158] [2159] [2160] 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 [2161] [2162] [2163] 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 , [2164] [2165] 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 [2166] [2167] [2168] 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, ...)[] [2169] 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")[] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] 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 [2182] [2183] [2184] [2185] [2186] [2187] [2188] 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", ...)[] [2189] [2190] [2191] 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, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] 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) [2206] 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") [2207] [2208]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} [2209] [2210] 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 [2211] [2212] [2213] [2214] 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)))[] [2215] 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"))[] [2216] [2217] [2218] [2219] [2220] [2221] 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"))[] [2222] 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 ) = [2223] 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)[] [2224] [2225] 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 [2226] [2227] 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")[] [2228] 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"), ...)[] [2229] [2230] [2231] [2232] [2233] [2234] 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 [2235] [2236] 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 [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254] [2255] [2256] 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, ...)[] [2257] 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), [2258] 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)[] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271]) (./Matrix-pkg.tex [2272] 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 [2273] 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 [2274] 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 [2275] 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 [2276] [2277] Underfull \hbox (badness 5147) in paragraph at lines 496--499 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2278] Underfull \hbox (badness 5119) in paragraph at lines 509--513 []\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 513--518 [][][]\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 543--543 []\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 545--545 []\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 554--554 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2279] [2280] Overfull \hbox (52.98038pt too wide) in paragraph at lines 668--668 []\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 669--669 []\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 670--670 []\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 683--683 [] \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 684--684 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 689--689 []\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 758--762 \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 / [2282] [2283] [2284] Overfull \hbox (72.78088pt too wide) in paragraph at lines 973--973 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2285] [2286] [2287]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) has been already used, duplicate ignored \relax l.1160 ...- '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.1160 ...- 'Matrix' S4 Generic and Methods}{chol} [2288pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} ] Underfull \hbox (badness 2285) in paragraph at lines 1249--1254 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the Overfull \hbox (31.3804pt too wide) in paragraph at lines 1295--1295 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2289] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1390--1390 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2290] Underfull \hbox (badness 2277) in paragraph at lines 1418--1421 []\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 [2291] Underfull \hbox (badness 1609) in paragraph at lines 1465--1469 []\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 1492--1492 []\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 1506--1506 []\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[] [2292] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1514--1514 []\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 1561--1568 []\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 1561--1568 \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 [2293] Underfull \hbox (badness 1783) in paragraph at lines 1596--1600 []\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 1612--1618 \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.1653 ... 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.1653 ... 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.1654 \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.1675 \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.1686 \aliasA{rowSums}{colSums}{rowSums} [2294] Underfull \hbox (badness 2922) in paragraph at lines 1740--1744 []\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 1740--1744 \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 1751--1754 [][][]\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 [2295] [2296] [2297] Underfull \hbox (badness 3547) in paragraph at lines 1905--1908 []\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 [2298] [2299] [2300] [2301] Underfull \hbox (badness 1484) in paragraph at lines 2267--2269 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2302] Underfull \hbox (badness 7379) in paragraph at lines 2363--2365 []\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 [2303] [2304] [2305] Underfull \hbox (badness 4846) in paragraph at lines 2639--2643 []\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 2644--2648 []\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 2651--2654 []\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 ; [2306] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2698--2698 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2707--2709 []\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 2711--2716 []\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 2711--2716 [][]\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 [2307] Underfull \hbox (badness 1097) in paragraph at lines 2734--2737 []\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 2747--2752 [][]\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 [2308] Underfull \hbox (badness 3646) in paragraph at lines 2986--2989 []\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 3018--3020 []\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 3021--3025 []\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 3030--3036 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2309] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 []\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 3047--3051 [][][]\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 [2310] [2311] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\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 3278--3280 [][][]\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) [2312] Underfull \hbox (badness 2469) in paragraph at lines 3398--3401 []\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 [2313] [2314] Underfull \hbox (badness 10000) in paragraph at lines 3563--3567 []\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 3563--3567 \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 , [2315] Underfull \hbox (badness 2285) in paragraph at lines 3613--3616 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2316] [2317] Underfull \hbox (badness 10000) in paragraph at lines 3760--3765 []\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 3760--3765 \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 3772--3775 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2318] Underfull \hbox (badness 10000) in paragraph at lines 3848--3850 []\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 [2319] [2320] [2321] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4058--4058 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4126--4130 []\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 [2322] Underfull \hbox (badness 10000) in paragraph at lines 4135--4138 []\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 4135--4138 \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 4140--4144 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2323] [2324] Underfull \hbox (badness 3158) in paragraph at lines 4323--4327 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2325] [2326] [2327] [2328] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4562--4562 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4565--4565 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4569--4569 []\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 4572--4572 []\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 4582--4582 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 4884--4889 []\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 , [2333] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4965--4965 []\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 4967--4967 [] \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 4971--4971 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2334] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4978--4978 [] \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 '[] [2335] [2336] Underfull \hbox (badness 4120) in paragraph at lines 5122--5125 []\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 5159--5159 []\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 5165--5165 [] \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 5166--5166 [] \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 5170--5170 []\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 5172--5172 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 []\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 5182--5182 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2338] Underfull \hbox (badness 1817) in paragraph at lines 5271--5280 []\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 5313--5315 []\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 5315--5318 []\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 5328--5331 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2339] Underfull \hbox (badness 4765) in paragraph at lines 5346--5349 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5406--5406 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2341] [2342] [2343] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5664--5664 []\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[] [2344] Underfull \hbox (badness 10000) in paragraph at lines 5747--5750 [][][]\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 5758--5758 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2345] Underfull \hbox (badness 1622) in paragraph at lines 5795--5800 []\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 5795--5800 \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 [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5856--5856 []\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 5857--5857 [] \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 5864--5864 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2347] Underfull \hbox (badness 1062) in paragraph at lines 5993--5996 []\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 [2348] Underfull \hbox (badness 6063) in paragraph at lines 6022--6025 []\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 [2349] Underfull \hbox (badness 2635) in paragraph at lines 6134--6139 []\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 6134--6139 \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 Underfull \hbox (badness 10000) in paragraph at lines 6142--6145 []\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., [2350] Underfull \hbox (badness 10000) in paragraph at lines 6252--6262 \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 6252--6262 [][]\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 [2351] Underfull \hbox (badness 3179) in paragraph at lines 6334--6337 []\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 [2352] Underfull \hbox (badness 10000) in paragraph at lines 6432--6435 []\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., [2353] Underfull \hbox (badness 10000) in paragraph at lines 6507--6510 []\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., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6523--6523 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2354] Underfull \hbox (badness 2443) in paragraph at lines 6562--6568 []\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 6562--6568 [][]\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 6583--6586 []\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 [2355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6653--6653 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2356] [2357] Underfull \hbox (badness 10000) in paragraph at lines 6794--6797 []\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 Underfull \hbox (badness 1490) in paragraph at lines 6816--6818 []\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) [2358] [2359] Underfull \hbox (badness 5036) in paragraph at lines 6896--6900 []\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 6896--6900 \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 [2360]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6995 \aliasA{det}{Matrix-class}{det} [2361] Underfull \hbox (badness 10000) in paragraph at lines 7098--7101 Underfull \hbox (badness 10000) in paragraph at lines 7108--7110 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2362]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7171 ...*\%}{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.7279 ...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.7379 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7477--7483 \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 [2363pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 ] Underfull \hbox (badness 10000) in paragraph at lines 7550--7553 []\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 7550--7553 \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 7553--7558 []\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 7553--7558 \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 7558--7562 []\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 7558--7562 \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 7568--7569 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2364] [2365] Underfull \hbox (badness 1009) in paragraph at lines 7704--7706 []\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 Underfull \hbox (badness 1062) in paragraph at lines 7749--7752 []\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 [2366] Underfull \hbox (badness 6063) in paragraph at lines 7783--7786 []\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 10000) in paragraph at lines 7839--7841 []\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 [2368] [2369] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7941--7941 [] \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 7981--7981 []\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 [2370] Underfull \hbox (badness 2635) in paragraph at lines 8046--8051 []\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 8046--8051 \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 8054--8057 []\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., [2371] Underfull \hbox (badness 3482) in paragraph at lines 8128--8134 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2372] Underfull \hbox (badness 1867) in paragraph at lines 8248--8250 []\T1/ptm/m/n/10 fast sim- [2373]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8288 \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.8288 \HeaderA{norm}{Matrix Norms}{norm} [2374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8375--8375 []\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 8376--8376 []\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 8377--8377 []\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 8490--8500 []\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 , [2375] Underfull \hbox (badness 3179) in paragraph at lines 8561--8564 []\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 [2376] Underfull \hbox (badness 10000) in paragraph at lines 8651--8654 []\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., [2377] Underfull \hbox (badness 10000) in paragraph at lines 8727--8730 []\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., [2378] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8743--8743 []\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 [2379] Underfull \hbox (badness 10000) in paragraph at lines 8853--8855 []\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 8855--8858 []\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 8861--8868 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2380] [2381] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8954--8954 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8957--8957 []\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 8959--8959 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8963--8963 []\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 8964--8964 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8989--8999 []\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 8989--8999 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2382] [2383]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9090 \aliasA{qr}{qr-methods}{qr} [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9163--9163 []\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 9174--9174 []\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 9178--9178 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9203--9203 []\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 [2385] Underfull \hbox (badness 10000) in paragraph at lines 9260--9266 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9277--9280 []\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 [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9376--9376 []\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 9392--9392 []\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 9398--9398 []\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 9399--9399 []\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.9418 ... the Reciprocal Condition Number}{rcond} [2388] [2389] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9531--9531 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2390] [2391] [2392] Underfull \hbox (badness 2351) in paragraph at lines 9722--9730 []\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 9722--9730 \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 [2393] [2394] Underfull \hbox (badness 1558) in paragraph at lines 9867--9870 []\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 [2395] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9929--9929 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9933--9933 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2396]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9995 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10092--10092 [] \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 10097--10097 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2397] Underfull \hbox (badness 1616) in paragraph at lines 10132--10144 []\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 10149--10152 []\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 10158--10165 []\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 10171--10181 []\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 10171--10181 \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 10198--10202 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10205--10207 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2398] Underfull \hbox (badness 10000) in paragraph at lines 10228--10229 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10234--10236 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10238--10239 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10246--10249 [][][]\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 10264--10264 []\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 10268--10268 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2399] Underfull \hbox (badness 10000) in paragraph at lines 10289--10292 []\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 10317--10319 []\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 10325--10328 []\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 10325--10328 \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 10336--10340 []\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 10336--10340 \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 [2400] Underfull \hbox (badness 1668) in paragraph at lines 10351--10356 [][][]\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 10372--10378 []\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- [2401] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10431--10431 [] \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 10432--10432 [] \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 10433--10433 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2402] [2403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10617--10617 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2404] Underfull \hbox (badness 1668) in paragraph at lines 10659--10664 [][][]\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 [2405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10756--10756 []\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 10760--10760 []\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 10761--10761 []\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 10766--10766 []\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 10769--10769 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10792--10792 []\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 10793--10793 []\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 10819--10819 []\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 10821--10821 [] \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 10823--10823 [] \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 [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 10968--10972 [][][]\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.11008 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2409] [2410] Underfull \hbox (badness 10000) in paragraph at lines 11138--11140 []\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 11166--11166 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2411] Underfull \hbox (badness 5036) in paragraph at lines 11194--11196 []\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 11328--11334 []\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 11328--11334 \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 , [2412] Underfull \hbox (badness 10000) in paragraph at lines 11401--11404 []\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 [2413] Underfull \hbox (badness 10000) in paragraph at lines 11419--11424 []\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 11434--11436 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2414] [2415] Underfull \hbox (badness 2698) in paragraph at lines 11559--11565 [][][]\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, [2416] Underfull \hbox (badness 10000) in paragraph at lines 11652--11654 []\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 11670--11675 []\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 11670--11675 \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 [2417] Underfull \hbox (badness 2591) in paragraph at lines 11678--11683 \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 11750--11752 []\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., [2418] [2419] Underfull \hbox (badness 6641) in paragraph at lines 11836--11839 []\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 11876--11880 []\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 11876--11880 \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 [2420] [2421] Underfull \hbox (badness 7649) in paragraph at lines 11983--11985 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2422] [2423] [2424] Underfull \hbox (badness 7362) in paragraph at lines 12184--12186 []\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 12222--12222 []\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 12223--12223 []\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)[] [2425] [2426] [2427] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12365--12365 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12378--12378 [] \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 12383--12383 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2428] Underfull \hbox (badness 6910) in paragraph at lines 12557--12559 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2429] [2430] [2431]) (./boot-pkg.tex [2432] Chapter 18. [2433] [2434] [2435] [2436] [2437] [2438] [2439] 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"), [2440] 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- [2441] [2442] [2443] 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 , [2444] 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 [2445] [2446] 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" [2447] 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 [2448] [2449] [2450] [2451] 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- [2452] [2453] [2454] [2455] [2456] 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), [2457] [2458] [2459] Underfull \vbox (badness 10000) has occurred while \output is active [2460] 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),[] [2461] 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. [2462] [2463] [2464] 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 [2465] 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 , [2466] [2467] 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 [2468] [2469] [2470] [2471] [2472] 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,[] [2473] [2474] [2475] 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 , [2476] 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)) [2477] [2478] [2479] 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 [2480] [2481] [2482] [2483] [2484] [2485] [2486] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2487] [2488] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2489] [2490] [2491] Underfull \hbox (badness 10000) in paragraph at lines 4190--4192 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2492] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2493] [2494] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2495] [2496] [2497] [2498] [2499] [2500] [2501] [2502] [2503] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2504] [2505] [2506] [2507] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2508] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2517] 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 [2518] 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 [2519] [2520] [2521] [2522] 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). [2523] [2524] 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[] [2525] [2526] [2527] 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 [2528] [2529] 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),[] [2530] [2531] [2532] [2533] [2534] [2535] [2536] [2537]) (./class-pkg.tex [2538] Chapter 19. [2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554]) (./cluster-pkg.tex Chapter 20. [2555] 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 [2556] [2557] 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]))[] [2558] [2559] Underfull \vbox (badness 10000) has occurred while \output is active [2560] [2561] 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, ...)[] [2562] [2563] 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)[] [2564] 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 [2565] [2566] 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 , [2567] 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 [2568] 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), ...)[] [2569] 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, [2570] [2571] 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 [2572] 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 [2573] 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."),[] [2574] [2575] 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 [2576] 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[] [2577] 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 [2578] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2579] [2580] 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 = [2581] 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, [2582] [2583] [2584] [2585] [2586] 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. [2587] [2588] 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 , [2589] 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 [2590] 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 , [2591] [2592] [2593] 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 ):[] [2594] 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"),[] [2595] [2596] [2597] 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):[] [2598] [2599] 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")[] [2600] [2601] [2602] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2603] Underfull \hbox (badness 10000) in paragraph at lines 3345--3348 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2604] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$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, ...)[] [2605] [2606] [2607] 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 [2608] 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 , [2609] 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 , [2610] [2611] [2612] 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 , [2613] 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 [2614] [2615] [2616] [2617] 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, ...)[] [2618] [2619] 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[] [2620] [2621] [2622] [2623] [2624] [2625] [2626] 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:[] [2627] 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:[] [2628]) (./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,[] [2629] 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 [2630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2631] [2632] [2633]) (./foreign-pkg.tex [2634] Chapter 22. [2635] 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 [2636] [2637] 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 , [2638] 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, [2639] [2640] [2641] 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,[] [2642] 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 [2643] 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 [2644] 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,[] [2645] 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="")[] [2646] [2647] 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])[] [2648] [2649] 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) [2650] 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))) [2651] [2652] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2653] [2654] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2655] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2656]) (./lattice-pkg.tex Chapter 23. [2657] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\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 / [2658] [2659] 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"),[] [2660] 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"),[] [2661] [2662] [2663] [2664] 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 [2665] [2666] [2667] [2668] 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. [2669] 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 [2670] [2671] 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 [2672] [2673] [2674] 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 , [2675] 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 , [2676] Underfull \vbox (badness 10000) has occurred while \output is active [2677] 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 [2678] 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 [2679] [2680] [2681] [2682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2683] 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 [2684] [2685] [2686] 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"),[] [2687] [2688] [2689] [2690] [2691] 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"),[] [2692] [2693] 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 [2694] Underfull \hbox (badness 6758) in paragraph at lines 2888--2892 []\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 2888--2892 \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 2894--2896 []\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 2946--2952 []\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 2946--2952 \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 2946--2952 \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 Underfull \hbox (badness 2486) in paragraph at lines 2970--2974 []\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 [2695] [2696] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3073--3073 [] \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 3074--3074 [] \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 3075--3075 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3086--3086 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2697] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3098--3098 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] Underfull \hbox (badness 2913) in paragraph at lines 3156--3163 []\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 3156--3163 \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 [2698] [2699] [2700] [2701]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3444 \aliasA{parallel}{B\_08\_splom}{parallel} [2702] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2703] [2704] [2705] [2706] [2707] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2708] Underfull \hbox (badness 2277) in paragraph at lines 3935--3939 []\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 3935--3939 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2709] [2710] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4065--4065 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4074--4078 []\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 Underfull \hbox (badness 3219) in paragraph at lines 4101--4103 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2711] Underfull \hbox (badness 1728) in paragraph at lines 4118--4122 \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 Underfull \hbox (badness 5161) in paragraph at lines 4183--4187 []\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 4183--4187 \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 [2712] [2713] Underfull \hbox (badness 1067) in paragraph at lines 4297--4307 []\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 4297--4307 \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 4297--4307 \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 4297--4307 \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 4297--4307 \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 [2714] Underfull \hbox (badness 1701) in paragraph at lines 4322--4325 []\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 4325--4327 []\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 [2715] [2716] [2717] [2718] [2719] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4729--4729 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 []\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 . [2722] [2723] Underfull \hbox (badness 1442) in paragraph at lines 5048--5051 []\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 [2724] [2725] [2726] [2727] [2728] [2729] Underfull \hbox (badness 3646) in paragraph at lines 5382--5385 [][][]\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 5412--5412 [] \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 5413--5413 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2730] Underfull \hbox (badness 10000) in paragraph at lines 5501--5504 []\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 5501--5504 \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 [2731] Underfull \hbox (badness 1635) in paragraph at lines 5527--5532 []\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 [2732] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5678--5678 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2733] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5692--5692 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5701--5701 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5707--5707 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5711--5711 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5727--5729 []\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 5738--5740 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2734] [2735] Underfull \hbox (badness 2538) in paragraph at lines 5863--5867 \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 5874--5881 []\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 5874--5881 \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 [2736] [2737] Underfull \hbox (badness 10000) in paragraph at lines 6027--6031 [][][]\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 , [2738] [2739] Underfull \hbox (badness 4242) in paragraph at lines 6174--6179 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2740] [2741] Underfull \hbox (badness 3601) in paragraph at lines 6290--6295 []\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 6290--6295 \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 [2742] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2743] [2744] Underfull \hbox (badness 1888) in paragraph at lines 6509--6516 \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 [2745] Underfull \hbox (badness 10000) in paragraph at lines 6566--6569 []\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 6566--6569 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 1320) in paragraph at lines 6972--6979 []\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 6972--6979 \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 [2752] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2753] Underfull \hbox (badness 10000) in paragraph at lines 7072--7076 []\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 7072--7076 \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 [2754] Underfull \hbox (badness 10000) in paragraph at lines 7177--7180 \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 [2755] [2756] Underfull \hbox (badness 2012) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2757] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2758] [2759] Underfull \hbox (badness 2644) in paragraph at lines 7530--7534 \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 7543--7546 []\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 [2760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613 [] \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 7623--7623 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7684--7684 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2762] [2763] [2764] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2765] Underfull \hbox (badness 1436) in paragraph at lines 7929--7935 []\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 [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 8487--8490 []\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 8487--8490 \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 [2774] [2775] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662 []\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 8663--8663 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2776] Underfull \hbox (badness 3118) in paragraph at lines 8694--8697 []\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 [2777] Underfull \hbox (badness 1515) in paragraph at lines 8770--8774 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2778] Underfull \hbox (badness 6316) in paragraph at lines 8876--8881 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2779] [2780] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2781] [2782] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2783] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185 []\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 9181--9185 \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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] Underfull \hbox (badness 7238) in paragraph at lines 9639--9643 []\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 9639--9643 \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 , [2791] [2792] [2793]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma} [2794] [2795] [2796] Underfull \hbox (badness 10000) in paragraph at lines 10032--10037 \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 10105--10105 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2797] [2798]) (./mgcv-pkg.tex Chapter 24. [2799] [2800] 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,[] [2801] 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. [2802] [2803] [2804] [2805] Underfull \hbox (badness 10000) in paragraph at lines 377--384 [][][]\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 377--384 [][]\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 377--384 [][]\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 , [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 420--420 []\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)+[] [2807] [2808] [2809] Underfull \hbox (badness 2922) in paragraph at lines 632--633 []\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 [2810] [2811] Underfull \hbox (badness 1406) in paragraph at lines 702--703 []\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 [2812] [2813] Underfull \hbox (badness 1158) in paragraph at lines 812--814 []\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 [2814] Underfull \hbox (badness 1259) in paragraph at lines 875--876 []\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). [2815] Underfull \vbox (badness 10000) has occurred while \output is active [2816] [2817] [2818] [2819] [2820] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224 []\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 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)[] [2821] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1254--1254 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1263--1263 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1265--1265 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2822] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2823] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1379--1379 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2824] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1390--1390 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1424--1424 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] [2833] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1930--1930 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2834] [2835] [2836] [2837] [2838] [2839] Underfull \hbox (badness 1052) in paragraph at lines 2318--2326 \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 2335--2335 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2347--2350 []\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 2360--2364 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2840] Underfull \hbox (badness 1043) in paragraph at lines 2386--2391 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2841] [2842] [2843] Underfull \hbox (badness 1043) in paragraph at lines 2551--2557 \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 [2844] Underfull \hbox (badness 10000) in paragraph at lines 2687--2693 [][][]\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 2687--2693 [][]\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 2687--2693 [][]\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 , [2845] [2846] Underfull \vbox (badness 10000) has occurred while \output is active [2847] Underfull \vbox (badness 10000) has occurred while \output is active [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3343--3343 [] \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 3346--3346 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] Underfull \hbox (badness 5189) in paragraph at lines 3821--3825 []\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 [2865] [2866] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3938--3938 []\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 [2867] [2868] [2869] Underfull \hbox (badness 1184) in paragraph at lines 4107--4111 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2870] [2871] [2872] [2873] [2874] [2875] [2876] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4553--4553 [] \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)+[] [2877] [2878] [2879] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4703--4703 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2880] [2881] Underfull \hbox (badness 1142) in paragraph at lines 4828--4832 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2882] Underfull \hbox (badness 10000) in paragraph at lines 4900--4909 []\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 [2883] [2884] Underfull \hbox (badness 5970) in paragraph at lines 5017--5023 [][][]\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 5017--5023 [][]\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 . [2885] Underfull \vbox (badness 10000) has occurred while \output is active [2886] [2887] [2888] [2889] Underfull \hbox (badness 1577) in paragraph at lines 5369--5372 []\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 5376--5377 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2890] [2891] [2892] [2893] [2894] [2895] [2896] Underfull \hbox (badness 6708) in paragraph at lines 5765--5766 []\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 [2897] [2898] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5814--5814 [] \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 5839--5839 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5868--5868 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2900] [2901] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5990--5990 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2902] [2903] [2904] [2905] [2906] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6327--6327 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2907] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6329--6329 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6350--6354 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2908] [2909] [2910] Underfull \vbox (badness 10000) has occurred while \output is active [2911] [2912] [2913] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6669--6669 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2914] [2915] [2916] [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] Underfull \vbox (badness 10000) has occurred while \output is active [2919] [2920] [2921] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7098--7098 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7125--7125 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] Underfull \hbox (badness 1242) in paragraph at lines 7668--7669 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2931] [2932] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7755--7755 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2933] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7818--7818 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] [2934] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7837--7837 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \hbox (badness 10000) in paragraph at lines 9057--9060 []\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 9057--9060 \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 9057--9060 \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 . [2954] Underfull \hbox (badness 10000) in paragraph at lines 9113--9116 []\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 9113--9116 \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 [2955] [2956] [2957] [2958] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9333--9333 []\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 9334--9334 [] \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 9337--9337 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2959] [2960] Underfull \hbox (badness 1629) in paragraph at lines 9495--9500 \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 [2961] [2962] Underfull \vbox (badness 10000) has occurred while \output is active [2963] [2964] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9706--9706 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2965] Underfull \hbox (badness 1062) in paragraph at lines 9743--9747 []\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 9743--9747 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2966] [2967] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9874--9874 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10147--10147 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [2972] Underfull \hbox (badness 1205) in paragraph at lines 10185--10187 []\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 10185--10187 \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 10191--10196 []\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 [2973] Underfull \hbox (badness 1205) in paragraph at lines 10275--10277 []\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 10275--10277 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2974] Underfull \hbox (badness 10000) in paragraph at lines 10344--10347 []\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 10344--10347 [][]\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, [2975] [2976] [2977] Underfull \hbox (badness 1253) in paragraph at lines 10474--10476 []\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, [2978] [2979] [2980] [2981] [2982] Underfull \hbox (badness 1946) in paragraph at lines 10727--10734 []\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 10727--10734 \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 10727--10734 \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 Underfull \hbox (badness 2846) in paragraph at lines 10735--10738 []\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 10735--10738 \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. [2983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10801--10801 []\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 10811--10811 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 10842--10845 []\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 , [2985] [2986] [2987] [2988] [2989] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11143--11143 []\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) [2990] [2991] [2992] [2993] [2994] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11474--11474 []\T1/pcr/m/n/9 dat <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(runif( n))) + (eps/del))[] [2995] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11513--11513 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~ s(times, k = 10), ~ 1, ~ 1),[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 11531--11531 []\T1/pcr/m/n/9 xSeq <- data.frame(cbind("accel" = rep(0, 1e3), "times" = seq( 2, 58, length.out = 1e3)))[] Underfull \vbox (badness 10000) has occurred while \output is active [2996] [2997] Underfull \hbox (badness 3861) in paragraph at lines 11628--11631 []\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 11637--11637 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [2998] Underfull \hbox (badness 10000) in paragraph at lines 11654--11658 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11694--11698 []\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- [2999] [3000] [3001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11838--11838 [] \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 11849--11854 []\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 [3002] Underfull \hbox (badness 1803) in paragraph at lines 11926--11930 \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 11938--11950 \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 [3003] Underfull \hbox (badness 2401) in paragraph at lines 11955--11959 \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 11955--11959 \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 , [3004] [3005] [3006] Underfull \hbox (badness 6876) in paragraph at lines 12150--12156 [][][]\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 [3007] Underfull \hbox (badness 10000) in paragraph at lines 12191--12192 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3008] [3009] Underfull \hbox (badness 10000) in paragraph at lines 12308--12309 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12362--12362 [] \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 12374--12374 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12386--12386 [] \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 12391--12391 [] \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 12397--12397 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3012] Underfull \hbox (badness 10000) in paragraph at lines 12467--12469 []\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 12467--12469 \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 [3013] [3014] Underfull \hbox (badness 10000) in paragraph at lines 12597--12598 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3015] [3016] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12678--12678 []\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 12679--12679 []\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[] [3017] [3018] Underfull \hbox (badness 10000) in paragraph at lines 12830--12831 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3019] [3020] [3021] [3022] [3023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13080--13080 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3024] Underfull \hbox (badness 10000) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 13300--13303 []\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 13300--13303 \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 13300--13303 \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" [3027] [3028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13384--13384 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3029] Underfull \hbox (badness 10000) in paragraph at lines 13429--13435 []\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 13429--13435 \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- [3030] [3031] [3032] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13643--13643 []\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 [3033] Underfull \vbox (badness 10000) has occurred while \output is active [3034] Underfull \hbox (badness 10000) in paragraph at lines 13746--13754 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13772--13773 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3035] [3036] [3037] [3038] [3039] Underfull \hbox (badness 3396) in paragraph at lines 14032--14035 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 14077--14079 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3040] [3041] [3042] [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 14358--14361 []\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 14358--14361 \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 Underfull \hbox (badness 10000) in paragraph at lines 14391--14395 [][][]\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 14391--14395 [][]\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 14391--14395 [][]\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 , [3046] [3047] [3048] [3049] [3050] Underfull \hbox (badness 2158) in paragraph at lines 14681--14681 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3051] [3052] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14760--14760 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3053] [3054] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14894--14894 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3055] [3056] Underfull \hbox (badness 4846) in paragraph at lines 15025--15028 []\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 [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16228--16228 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3077] [3078] [3079] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16438--16438 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16440--16440 []\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 16442--16442 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3080] Underfull \hbox (badness 10000) in paragraph at lines 16462--16463 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16462--16463 \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 [3081] [3082] [3083] [3084] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16650--16650 []\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 16651--16651 []\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 16663--16663 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3085] [3086] [3087]) (./nlme-pkg.tex [3088] Chapter 25. [3089] 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 [3090] 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 [3091] [3092] [3093] [3094] [3095] 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,[] [3096] [3097] 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 --------------------------- ---------------[] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] 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"),[] [3106] 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 [3107] [3108] [3109] [3110] [3111] [3112] [3113] 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 , [3114] 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 [3115] [3116] [3117] [3118] [3119] 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 , [3120] 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")[] [3121] 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 [3122] [3123] 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 , [3124] 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,[] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] 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 , [3133] [3134] [3135] [3136] [3137] [3138pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3139] [3140] [3141] [3142] [3143] [3144] 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 , [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] 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 , [3169] [3170] [3171] [3172] [3173] [3174] [3175] 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 , [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] 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 [3185] 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 , [3186] 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 , [3187] 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[] [3188] [3189] [3190] [3191] 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 , [3192] 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, [3193] 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 [3194] 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[] [3195] [3196] [3197] 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 , [3198] 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 [3199] [3200] [3201] 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 , [3202] [3203] [3204] 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 , [3205] [3206] [3207] 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 [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] 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 [3216] [3217] [3218] [3219] [3220] 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 [3221] 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} [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] 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") [3234] 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 [3235] [3236] [3237] [3238]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} [3239] 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 [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] 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 [3248] [3249] [3250] 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, [3251] 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 [3252] [3253] [3254] 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,[] [3255] [3256] 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[][][] [3257] 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[] [3258] [3259] [3260] [3261] 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)[] [3262] [3263] [3264] [3265] [3266] [3267] 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(*)) [3268] [3269] [3270] [3271] [3272] [3273] 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 , [3274] [3275] [3276] [3277] 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 , [3278] [3279] [3280] [3281] [3282] 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 [3283] [3284] 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 , [3285] 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 , [3286] [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] 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(*)) [3295] [3296] [3297] [3298] [3299] 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)[] [3300] 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 [3301] 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,[] [3302] 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 [3303] 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 [3304] 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 , [3305] 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 , [3306] [3307] [3308] [3309] 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 [3310] [3311] [3312] [3313] 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"),[] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322]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} [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] 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- [3333] 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)[] [3334] 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 [3335] [3336] 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, ...)[] [3337] [3338] [3339] [3340] [3341] 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 , [3342] 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, ...)[] [3343] [3344] [3345] [3346] [3347] [3348] [3349] 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 [3350] [3351] [3352] [3353] [3354] 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 [3355] 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 [3356] [3357] [3358] [3359] 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 , [3360] [3361] [3362] [3363] 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[] [3364] [3365] [3366] [3367] [3368] [3369] 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 , [3370] 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 [3371] 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 [3372] 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 [3373] 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 [3374] 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 , [3375] 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 [3376] [3377] 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 [3378] [3379] 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 [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388]) (./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} [3389] 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,[] [3390] [3391] [3392] 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,[] [3393] 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)[] [3394] [3395] 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,[] [3396]) (./rpart-pkg.tex Chapter 27. [3397] [3398] [3399] [3400] 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, ...)[] [3401] [3402] [3403] [3404] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\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 [3405] [3406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3407] [3408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3409] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3410] [3411] [3412] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\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 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3413] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\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 [3414] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\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 1288--1288 []\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 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3415] [3416] [3417] [3418] [3419] [3420] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\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 ', [3421] [3422] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3423] [3424] [3425]) (./spatial-pkg.tex [3426] Chapter 28. [3427] [3428] [3429] [3430] [3431] [3432] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3433] [3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445]) (./survival-pkg.tex [3446] Chapter 29. [3447] [3448] 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.[] [3449] [3450] 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 [3451] [3452]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} [3453] 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)[] [3454] 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)[] [3455] [3456] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3457] [3458] 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"),[] [3459] [3460] 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,[] [3461] [3462] [3463] 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[] [3464] [3465] 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) [3466] 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} [3467] 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, ...)[] [3468] [3469] [3470] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1572--1572 [] \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 1619--1619 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3471] [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 1935--1950 []\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 1935--1950 \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 1935--1950 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3476] Underfull \hbox (badness 1337) in paragraph at lines 2019--2023 [][][]\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 , [3477] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2074--2074 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2646--2646 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2673--2673 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3486] [3487] [3488] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2905--2905 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3489] [3490] [3491] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3492] [3493] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3246--3246 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3494] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3281--3281 [] \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 3295--3297 []\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 3306--3306 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3495] [3496] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3440--3440 [] \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 )))[] [3497] [3498] Overfull \hbox (467.89665pt too wide) in alignment at lines 3581--3581 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3499] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3500] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3703--3703 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3501] [3502] [3503] [3504] [3505] [3506] [3507] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4092--4092 [] \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 )))[] [3508] [3509] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4238--4238 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4243--4243 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4247--4247 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3510] Underfull \vbox (badness 1527) has occurred while \output is active [3511] [3512] [3513] [3514] [3515] [3516] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4664--4664 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3517] [3518] [3519] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4894--4894 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5020--5020 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5028--5028 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3522] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5114--5114 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5192--5192 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3524] Underfull \hbox (badness 1852) in paragraph at lines 5264--5266 []\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 [3525] [3526] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5389--5389 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3527] [3528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5491--5491 []\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 5492--5492 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3529] [3530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5656--5656 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5758--5758 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3532] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5779--5779 []\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 5781--5781 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3533] [3534] [3535] [3536] [3537] [3538] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6296--6296 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3539] [3540] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6476--6476 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6488--6491 \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 [3542] [3543] [3544] [3545] [3546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6796--6796 []\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 6797--6797 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3547] [3548] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6927--6927 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3549] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7001--7001 []\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.7005 ...ata from a soldering experiment}{solder} [3550] [3551] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7111--7111 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7475--7475 []\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 7476--7476 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3557] [3558] [3559] [3560] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7787--7787 [] \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 ),[] [3561] [3562] [3563] [3564] Underfull \hbox (badness 1253) in paragraph at lines 8076--8079 []\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 [3565] [3566] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3567] Underfull \hbox (badness 10000) in paragraph at lines 8328--8337 []\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 8328--8337 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3568] [3569] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8424--8424 [] \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 8442--8442 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8484--8490 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3570] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8536--8536 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3572] [3573] [3574] Underfull \hbox (badness 10000) in paragraph at lines 8847--8852 [][][]\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 , [3575] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8865--8865 [] \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 8866--8866 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3576] [3577] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9062--9062 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3578] [3579] Underfull \hbox (badness 3058) in paragraph at lines 9195--9200 []\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 9195--9200 \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 9195--9200 \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 9195--9200 \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 [3580] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9325--9325 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3581] [3582] [3583] [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9710--9710 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3586] Underfull \hbox (badness 1354) in paragraph at lines 9751--9755 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3587] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9797--9797 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3588] [3589] Underfull \hbox (badness 2035) in paragraph at lines 9961--9968 \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 9961--9968 \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 9961--9968 \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 [3590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10041--10041 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3591] [3592] [3593] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10198--10198 [] \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 )[] [3594] [3595] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10330--10330 [] \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 10333--10333 [] \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 )[] [3596] [3597] [3598] [3599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10643--10643 []\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 10644--10644 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10650--10650 [] \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 10652--10652 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3601] [3602] [3603] [3604] [3605] [3606] [3607] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11093--11093 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3608] [3609] [3610]) (./fullrefman.ind [3611] [3612] [3613] [3614] [3615] [3616] [3617] [3618] [3619] [3620] [3621] [3622] [3623] [3624] [3625] [3626] [3627] [3628] [3629] [3630] [3631] [3632] [3633] [3634] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2579--2581 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2581--2583 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 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paragraph at lines 5892--5894 []\T1/pcr/m/n/10 Arith,triangularMatrix,diagonalMatrix-method [3663] [3664] [3665] Overfull \hbox (32.8567pt too wide) in paragraph at lines 6385--6387 []\T1/pcr/m/n/10 aspell_write_personal_dictionary_file Overfull \hbox (46.01662pt too wide) in paragraph at lines 6548--6550 \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 , [3666] [3667] [3668] Overfull \hbox (26.8567pt too wide) in paragraph at lines 7193--7195 []\T1/pcr/m/n/10 cbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7195--7197 []\T1/pcr/m/n/10 cbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7197--7199 []\T1/pcr/m/n/10 cbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 7199--7201 []\T1/pcr/m/n/10 cbind2,ddiMatrix,atomicVector-method [3669] Overfull \hbox (32.8567pt too wide) in paragraph at lines 7203--7205 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\hbox (46.01662pt too wide) in paragraph at lines 18944--18946 \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 18947--18949 \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 18949--18951 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18951--18953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18953--18955 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18955--18957 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18957--18959 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18959--18961 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18961--18963 \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 18963--18965 \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 18967--18969 \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 18969--18971 \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 18971--18973 \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 18973--18975 \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 18975--18977 \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 18977--18979 \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 , [3735] [3736] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19326--19328 \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 19398--19400 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3737] [3738] [3739] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19868--19870 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19877--19879 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19879--19881 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19881--19883 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19883--19885 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19895--19897 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method [3740] Overfull \hbox (14.8567pt too wide) in paragraph at lines 19905--19907 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19920--19922 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19926--19928 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20046--20048 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3741] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20256--20258 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20258--20260 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20260--20262 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20262--20264 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method [3742] Overfull \hbox (32.8567pt too wide) in paragraph at lines 20266--20268 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20268--20270 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20270--20272 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20272--20274 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20274--20276 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20276--20278 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20278--20280 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20284--20286 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20288--20290 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20298--20300 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20302--20304 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20304--20306 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20306--20308 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20308--20310 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20310--20312 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20312--20314 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 20314--20316 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20343--20345 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20345--20347 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20347--20349 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20349--20351 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20353--20355 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20357--20359 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20361--20363 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20365--20367 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20369--20371 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20373--20375 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method [3743] Overfull \hbox (20.8567pt too wide) in paragraph at lines 20377--20379 []\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20381--20383 []\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20383--20385 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3744] [3745] [3746] [3747] Overfull \hbox (20.8567pt too wide) in paragraph at lines 21360--21362 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 21362--21364 []\T1/pcr/m/n/10 Schur,diagonalMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21366--21368 []\T1/pcr/m/n/10 Schur,generalMatrix,logical-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 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[3750] Overfull \hbox (20.8567pt too wide) in paragraph at lines 21780--21782 []\T1/pcr/m/n/10 show,MethodWithNextWithTrace-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 21790--21792 []\T1/pcr/m/n/10 show,refClassRepresentation-method [3751] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22036--22038 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22038--22040 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22041--22043 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22047--22048 []\T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22056--22058 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (5.3567pt too wide) in paragraph at lines 22060--22061 []\T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 22061--22063 \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 22064--22068 []\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 22069--22071 \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 , [3752] Overfull \hbox (46.01662pt too wide) in paragraph at lines 22117--22119 \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 22156--22158 []\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method 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wide) in paragraph at lines 22218--22220 []\T1/pcr/m/n/10 solve,dsCMatrix,denseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22220--22222 []\T1/pcr/m/n/10 solve,dsCMatrix,dsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22228--22230 []\T1/pcr/m/n/10 solve,dspMatrix,ddenseMatrix-method [3753] Overfull \hbox (20.8567pt too wide) in paragraph at lines 22234--22236 []\T1/pcr/m/n/10 solve,dsyMatrix,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22236--22238 []\T1/pcr/m/n/10 solve,dsyMatrix,denseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22242--22244 []\T1/pcr/m/n/10 solve,dtCMatrix,CsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22244--22246 []\T1/pcr/m/n/10 solve,dtCMatrix,dgeMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 22252--22254 []\T1/pcr/m/n/10 solve,dtpMatrix,ddenseMatrix-method Overfull \hbox (20.8567pt too wide) 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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 2435) in paragraph at lines 212--217 []\T1/ptm/m/n/10 when [][]\T1/pcr/m/n/10 capabilities[][][]("long.double") \T1/ ptm/m/n/10 is true, there are 10 such Underfull \hbox (badness 3009) in paragraph at lines 221--233 \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 363--366 [][][]\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 561--567 []\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] [12] [13] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [14] [15] Overfull \hbox (4.38043pt too wide) in paragraph at lines 903--903 []\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 921--921 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] Underfull \hbox (badness 10000) in paragraph at lines 1532--1538 Underfull \hbox (badness 10000) in paragraph at lines 1545--1547 []\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 1724--1724 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 1303) in paragraph at lines 1752--1755 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1871--1873 []\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 [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 2008--2008 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [32] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\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 2318--2318 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [37] [38] Underfull \hbox (badness 10000) in paragraph at lines 2446--2448 []\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 2449--2454 [][][]\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 2517--2519 []\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] Overfull \hbox (42.78088pt too wide) in paragraph at lines 2684--2684 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse1(substitute(what), back tick=FALSE), [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3353--3353 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3384--3384 []\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 3385--3385 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [52] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3392--3392 []\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 3393--3393 [] \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 3396--3396 []\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 3836--3838 []\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] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4077--4077 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [63] [64] [65] Underfull \hbox (badness 4927) in paragraph at lines 4335--4339 []\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 4335--4339 \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 [66] [67] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4419--4419 [] \T1/pcr/m/n/10 Xchk = any(nas %in% c("X11", "jpeg", "png", "tif f")))[] [68] Underfull \hbox (badness 4595) in paragraph at lines 4484--4487 []\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 4644--4644 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = TRUE)[] Underfull \hbox (badness 1199) in paragraph at lines 4675--4681 []\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 4686--4689 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [71] [72] [73] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4862--4862 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [74] [75] [76] Underfull \hbox (badness 2521) in paragraph at lines 5115--5117 []\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 [77] [78] [79] [80] [81] [82] Underfull \hbox (badness 10000) in paragraph at lines 5528--5536 []\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 [83] [84] [85] [86] [87] [88] [89] [90] [91] Underfull \hbox (badness 1796) in paragraph at lines 6094--6102 []\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 : / / [92] [93] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6288--6288 []\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 6290--6290 []\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 6291--6291 []\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}[] [94] [95] Underfull \hbox (badness 1242) in paragraph at lines 6430--6434 \T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment. [96] Underfull \hbox (badness 1635) in paragraph at lines 6493--6496 []\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 6497--6500 []\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 [97] Underfull \hbox (badness 1308) in paragraph at lines 6540--6548 []\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 [98] [99] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6704--6704 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] Underfull \vbox (badness 10000) has occurred while \output is active [100] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6754--6756 []\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 : [101] Underfull \hbox (badness 1997) in paragraph at lines 6881--6886 []\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 , [102] Underfull \hbox (badness 10000) in paragraph at lines 6919--6922 []\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 6919--6922 \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 [103] [104] Underfull \hbox (badness 1406) in paragraph at lines 7101--7107 []\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 7101--7107 \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 7101--7107 \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 7101--7107 \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 7121--7123 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [105] Underfull \hbox (badness 3302) in paragraph at lines 7163--7170 []\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 7163--7170 \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 7163--7170 \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- [106] [107] Underfull \vbox (badness 10000) has occurred while \output is active [108] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [109] [110] Underfull \hbox (badness 1231) in paragraph at lines 7492--7498 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 7704--7706 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [114] [115] [116] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7849--7849 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [117] [118] [119] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [120] [121] Underfull \hbox (badness 10000) in paragraph at lines 8209--8219 []\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 8209--8219 [][]\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 Overfull \hbox (4.63962pt too wide) in paragraph at lines 8241--8246 []\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") [122] [123] [124] [125] [126] [127] [128] Underfull \hbox (badness 1629) in paragraph at lines 8730--8742 []\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 8730--8742 \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 = [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 9178--9182 []\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 [135] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9269--9269 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9271--9271 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [136] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9297--9297 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9298--9298 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [137] [138] Underfull \hbox (badness 5403) in paragraph at lines 9435--9437 []\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 9454--9456 []\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 [139] [140] [141] Underfull \hbox (badness 1603) in paragraph at lines 9679--9682 []\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 [142] [143] [144] [145] [146] [147] [148] [149] [150] Underfull \hbox (badness 1917) in paragraph at lines 10292--10297 []\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 [151] Overfull \hbox (36.7804pt too wide) in paragraph at lines 10347--10347 []\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 10348--10348 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [152] [153] Underfull \hbox (badness 1168) in paragraph at lines 10450--10455 \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 10489--10495 []\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 Underfull \hbox (badness 5403) in paragraph at lines 10496--10499 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [154] [155] Underfull \hbox (badness 2828) in paragraph at lines 10655--10660 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10655--10660 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ Underfull \hbox (badness 10000) in paragraph at lines 10655--10660 \T1/pcr/m/n/10 754-[]2019$[][]\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 : [156] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10686--10686 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [157] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10759--10759 []\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, ..[] [158] [159] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10906--10906 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [160] [161] [162] Underfull \hbox (badness 6396) in paragraph at lines 11103--11111 []\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 11112--11114 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 11329--11332 []\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 [166] [167] [168] [169] [170] [171] [172] [173] [174] Underfull \hbox (badness 5288) in paragraph at lines 12029--12031 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [175] Underfull \hbox (badness 3039) in paragraph at lines 12039--12044 []\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 Underfull \hbox (badness 10000) in paragraph at lines 12099--12101 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [176] [177] Underfull \hbox (badness 4569) in paragraph at lines 12221--12225 []\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 12221--12225 \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 [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 12336--12338 []\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 [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13181--13181 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [191] [192] [193] [194] [195] [196] Underfull \hbox (badness 2221) in paragraph at lines 13635--13644 \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 13635--13644 \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 [197] [198] [199] [200] Underfull \hbox (badness 2253) in paragraph at lines 13896--13898 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [201] [202] Underfull \hbox (badness 2573) in paragraph at lines 14013--14015 []\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 = [203] [204] Underfull \hbox (badness 10000) in paragraph at lines 14172--14174 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [205] [206] Underfull \hbox (badness 10000) in paragraph at lines 14289--14293 [][][]\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 14300--14303 [][][]$\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 14321--14321 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [207] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14346--14346 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [208] Underfull \hbox (badness 10000) in paragraph at lines 14440--14443 [][][]\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 14450--14450 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [209] Underfull \hbox (badness 10000) in paragraph at lines 14516--14519 []\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 14533--14533 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14562--14562 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14586--14593 []\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 14586--14593 \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 14594--14598 []\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, [211] [212] [213] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14758--14758 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14759--14759 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [214] [215] [216] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14991--14991 []\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 14994--14994 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [217] Underfull \hbox (badness 1168) in paragraph at lines 15078--15082 []\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 15078--15082 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [218] Underfull \hbox (badness 6944) in paragraph at lines 15176--15179 [][][]\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 , [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15201--15201 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [220] [221] Underfull \hbox (badness 10000) in paragraph at lines 15339--15341 []\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 15359--15359 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15365--15365 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [222] Underfull \hbox (badness 2790) in paragraph at lines 15372--15375 []\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 15403--15410 []\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 [223] Underfull \hbox (badness 10000) in paragraph at lines 15478--15480 []\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 15478--15480 \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 15500--15505 []\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 15506--15508 []\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 = [224] Underfull \hbox (badness 10000) in paragraph at lines 15512--15516 []\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 15512--15516 \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 15517--15525 []\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 [225] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15625--15625 []\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 [226] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15647--15647 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16468--16468 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [239] Underfull \hbox (badness 2418) in paragraph at lines 16577--16581 \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 16584--16587 []\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 [240] Underfull \hbox (badness 2326) in paragraph at lines 16619--16626 [][][]\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 , [241] [242] [243] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16869--16869 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [244] Underfull \hbox (badness 1867) in paragraph at lines 16894--16901 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [245] [246] [247] [248] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17189--17189 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17218--17218 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [249] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17269--17269 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [250] [251] [252] [253] [254] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17636--17636 []\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))) [255] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17701--17701 []\T1/pcr/m/n/9 z <- gzcon(url("https://www.stats.ox.ac.uk/pub/datasets/csb/ch 12.dat.gz"))[] [256] [257] [258] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17891--17891 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [259] [260] [261] [262] Underfull \hbox (badness 2285) in paragraph at lines 18225--18227 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 18233--18233 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] [263] Overfull \hbox (24.78088pt too wide) in paragraph at lines 18263--18263 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [264] [265] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18397--18397 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18403--18403 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18406--18406 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18412--18412 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [266] [267] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18539--18539 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18547--18547 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [268] [269] [270] Underfull \hbox (badness 10000) in paragraph at lines 18752--18754 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [271] [272] [273] [274] [275] Underfull \hbox (badness 10000) in paragraph at lines 19090--19096 Underfull \hbox (badness 10000) in paragraph at lines 19103--19105 []\T1/ptm/m/n/10 Also avail-able at [][]$\T1/pcr/m/n/10 https : / / docs . orac le . com / cd / E19957-[]01 / 806-[]3568 / ncg _ [276] [277] [278] Underfull \hbox (badness 4699) in paragraph at lines 19335--19338 []\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 , [279] [280] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19463--19463 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [281] [282] [283] Underfull \hbox (badness 4739) in paragraph at lines 19598--19600 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19647--19647 []\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 19648--19648 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1975) in paragraph at lines 20224--20227 []\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 [293] [294] [295] [296] [297] [298] Underfull \hbox (badness 1077) in paragraph at lines 20622--20627 []\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 [299] Underfull \hbox (badness 10000) in paragraph at lines 20636--20643 [][][]$\T1/pcr/m/n/10 https : / / curl . se / docs / sslcerts . html$[][] \T1/p tm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / curl . se / docs / [300] Underfull \hbox (badness 10000) in paragraph at lines 20710--20714 []\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-tory [301] [302] Underfull \hbox (badness 10000) in paragraph at lines 20859--20863 []\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 20859--20863 [][]\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 20864--20871 []\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- [303] [304] Underfull \hbox (badness 10000) in paragraph at lines 20995--21002 [][][]\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 , [305] Underfull \hbox (badness 10000) in paragraph at lines 21116--21120 []\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 [306] Underfull \hbox (badness 5161) in paragraph at lines 21186--21191 []\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 21186--21191 \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 21186--21191 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 21186--21191 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [307] [308] [309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21353--21353 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 21357--21357 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [310] Underfull \hbox (badness 3343) in paragraph at lines 21418--21422 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [311] [312] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21559--21559 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21570--21570 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [313] [314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21681--21681 []\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 21684--21684 []\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 21729--21734 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [315] Underfull \hbox (badness 2564) in paragraph at lines 21820--21823 []\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 [316] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21850--21850 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [317] [318] Underfull \hbox (badness 1400) in paragraph at lines 22018--22022 [][][]\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 [319] [320] [321] Underfull \hbox (badness 2469) in paragraph at lines 22188--22194 []\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. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 22188--22194 \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 22188--22194 \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, [322] [323] [324] [325] [326] [327] [328] [329] [330] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22826--22826 []\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 22827--22827 [] \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 22830--22830 []\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)[] [331] [332] Underfull \hbox (badness 1655) in paragraph at lines 22954--22958 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [333] [334] [335] [336] Underfull \hbox (badness 2277) in paragraph at lines 23203--23206 []\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. [337] [338] Underfull \hbox (badness 10000) in paragraph at lines 23332--23335 []\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, [339] [340] [341] [342] [343] [344] [345] Underfull \hbox (badness 1484) in paragraph at lines 23788--23796 []\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 23788--23796 \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 / [346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23866--23866 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [347] [348] [349] [350] [351] [352] [353] Underfull \hbox (badness 1448) in paragraph at lines 24377--24385 \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 = [354] [355] Underfull \hbox (badness 3849) in paragraph at lines 24492--24497 []\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 [356] Underfull \hbox (badness 7308) in paragraph at lines 24569--24575 []\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 24569--24575 \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 24569--24575 [][]\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 24579--24582 []\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 24579--24582 \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 [357] [358] Underfull \hbox (badness 10000) in paragraph at lines 24732--24734 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [359] [360] [361] Underfull \hbox (badness 6188) in paragraph at lines 24952--24955 []\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 [362] [363] [364] Underfull \hbox (badness 1521) in paragraph at lines 25137--25151 \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- [365] [366] [367] [368] [369] Underfull \hbox (badness 2197) in paragraph at lines 25448--25452 []\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 25448--25452 \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 25462--25466 []\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 25462--25466 \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 25504--25504 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) [370] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25508--25508 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [371] Underfull \hbox (badness 10000) in paragraph at lines 25556--25562 []\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 25556--25562 \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 25569--25571 []\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% Overfull \hbox (4.38043pt too wide) in paragraph at lines 25620--25620 [] \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:[] [372] [373] [374] Underfull \hbox (badness 8189) in paragraph at lines 25815--25821 []\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 [][][] [375] [376] [377] Underfull \hbox (badness 1694) in paragraph at lines 26040--26043 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [378] [379] [380] [381] Underfull \hbox (badness 1603) in paragraph at lines 26287--26289 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [382] [383] Overfull \hbox (1.28088pt too wide) in paragraph at lines 26414--26422 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [384] [385] Underfull \hbox (badness 3271) in paragraph at lines 26633--26636 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [386] [387] [388] Underfull \hbox (badness 3138) in paragraph at lines 26937--26943 []\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 26937--26943 \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 26937--26943 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 1194) in paragraph at lines 26950--26953 []\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 [389] Underfull \hbox (badness 1389) in paragraph at lines 26976--26978 []\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 26996--27002 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 27011--27016 []\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 27029--27032 []\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 Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see [390] Underfull \hbox (badness 10000) in paragraph at lines 27053--27059 []\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 27053--27059 \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 27053--27059 \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 27053--27059 \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 27068--27075 []\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 27068--27075 \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 27068--27075 \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 27068--27075 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [391] [392] [393] [394] Underfull \vbox (badness 10000) has occurred while \output is active [395] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27416--27416 []\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 27429--27433 []\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 27429--27433 \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)] = [396] [397] Underfull \hbox (badness 10000) in paragraph at lines 27576--27579 []\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 27576--27579 \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 [398] [399] [400] [401] Underfull \hbox (badness 10000) in paragraph at lines 27854--27860 [][][]\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 27854--27860 [][]\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 27876--27876 []\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 27888--27888 []\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 27901--27901 []\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 27905--27905 []\T1/pcr/m/n/9 paste("The value is", val[valid], "-- good: empty!", recycle0= TRUE) # -> character(0)[] [402] [403] [404] Underfull \hbox (badness 1360) in paragraph at lines 28071--28075 []\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 = [405] [406] [407] [408] [409] [410] Underfull \hbox (badness 1817) in paragraph at lines 28466--28470 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [411] Underfull \hbox (badness 1796) in paragraph at lines 28534--28537 []\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 [412] [413] [414] Underfull \hbox (badness 10000) in paragraph at lines 28738--28741 []\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 [415] [416] [417] [418] [419] [420] [421] [422] [423] [424] Overfull \hbox (25.98041pt too wide) in paragraph at lines 29433--29433 [] \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))[] [425] [426] Underfull \vbox (badness 10000) has occurred while \output is active [427] [428] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29721--29721 []\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 29732--29732 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Underfull \vbox (badness 10000) has occurred while \output is active [429] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29738--29738 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29739--29739 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29744--29744 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [430] Underfull \hbox (badness 7415) in paragraph at lines 29827--29831 []\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 29848--29848 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [431] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29894--29894 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [432] Underfull \hbox (badness 3713) in paragraph at lines 30017--30028 []\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 [433] [434] Underfull \hbox (badness 1248) in paragraph at lines 30161--30168 \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 30161--30168 \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 / [435] [436] Underfull \hbox (badness 1533) in paragraph at lines 30279--30282 []\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 [437] [438] Overfull \hbox (42.78088pt too wide) in paragraph at lines 30424--30424 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 30442--30453 []\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 [439] [440] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30586--30586 []\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 30588--30588 []\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 30589--30589 []\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 30590--30590 []\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 30591--30591 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] [441] Overfull \hbox (15.18042pt too wide) in paragraph at lines 30598--30598 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [442] [443] [444] [445] [446] Underfull \hbox (badness 4048) in paragraph at lines 30945--30950 []\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 30945--30950 \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 30945--30950 \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 , [447] [448] [449] [450] [451] [452] [453] [454] Underfull \hbox (badness 2080) in paragraph at lines 31482--31492 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 infoRDS\T1/ptm/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 list with el-e-ments \T1/pcr/m/n/10 version \T1/ptm/m/n/10 (ver -sion num-ber, cur-rently 2 or 3), Overfull \hbox (4.38043pt too wide) in paragraph at lines 31508--31508 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [455] [456] [457] [458] [459] [460] [461] Underfull \hbox (badness 7558) in paragraph at lines 32026--32030 []\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 32036--32038 []\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 5417) in paragraph at lines 32041--32044 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 32047--32049 []\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 32050--32054 []\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 . [462] [463] [464] [465] [466] [467] Underfull \hbox (badness 10000) in paragraph at lines 32453--32457 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [468] [469] [470] [471] [472] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32809--32809 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32812--32812 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [473] [474] [475] [476] [477] [478] [479] Overfull \hbox (54.78088pt too wide) in paragraph at lines 33252--33252 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [480] [481] [482] [483] [484] [485] Overfull \hbox (12.78088pt too wide) in paragraph at lines 33689--33689 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [486] [487] Underfull \hbox (badness 1158) in paragraph at lines 33793--33798 []\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 Underfull \hbox (badness 10000) in paragraph at lines 33820--33826 []\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 33820--33826 \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 [488] [489] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33978--33978 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [490] [491] [492] Underfull \hbox (badness 8151) in paragraph at lines 34238--34241 []\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 . [493] [494] [495] [496] Underfull \hbox (badness 10000) in paragraph at lines 34453--34458 []\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 = [497] [498] [499] [500] [501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] Overfull \hbox (66.78088pt too wide) in paragraph at lines 35442--35442 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [512] [513] [514] Overfull \hbox (6.78088pt too wide) in paragraph at lines 35694--35694 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 35696--35696 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [515] Underfull \hbox (badness 4954) in paragraph at lines 35739--35745 [][][]\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 35739--35745 [][]\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 [516] [517] Overfull \hbox (20.58041pt too wide) in paragraph at lines 35850--35850 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [518] [519] [520] [521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36185--36185 []\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)[] [522] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36200--36200 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [523] [524] [525] Underfull \hbox (badness 10000) in paragraph at lines 36419--36421 [][][]$\T1/pcr/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / [526] [527] [528] Overfull \hbox (12.78088pt too wide) in paragraph at lines 36646--36646 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 36647--36647 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [529] [530] [531] [532] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36914--36914 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [533] Underfull \hbox (badness 6110) in paragraph at lines 37005--37015 []\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 37005--37015 \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 37005--37015 \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 37005--37015 \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 37005--37015 \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 Underfull \hbox (badness 10000) in paragraph at lines 37051--37057 []\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 37051--37057 \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 37051--37057 \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 [534] Underfull \hbox (badness 1460) in paragraph at lines 37063--37070 []\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 37063--37070 \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 37063--37070 \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 [535] [536] [537] Underfull \hbox (badness 1484) in paragraph at lines 37295--37299 []\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 [538] Overfull \hbox (60.78088pt too wide) in paragraph at lines 37357--37357 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [539] [540] [541] [542] [543] [544] [545] [546] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37937--37937 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [547] [548] [549] [550] Overfull \hbox (6.78088pt too wide) in paragraph at lines 38185--38185 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38229--38229 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [551] [552] [553] [554] [555] [556] [557] Overfull \hbox (52.98038pt too wide) in paragraph at lines 38663--38663 []\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 38666--38666 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [558] Underfull \hbox (badness 10000) in paragraph at lines 38717--38724 []\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 38717--38724 \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 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 38770--38770 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [559] [560] [561] [562] [563] Overfull \hbox (31.3804pt too wide) in paragraph at lines 39081--39081 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [564] [565] [566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 39246--39246 []\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. Overfull \hbox (20.58041pt too wide) in paragraph at lines 39284--39284 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [567] Underfull \hbox (badness 2293) in paragraph at lines 39314--39320 []\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 39314--39320 \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 39333--39338 []\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 39333--39338 \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 [568] Underfull \hbox (badness 2452) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 39423--39426 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [569] [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39611--39615 []\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 Underfull \hbox (badness 1584) in paragraph at lines 39626--39629 []\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 [572] [573] Overfull \hbox (25.98041pt too wide) in paragraph at lines 39758--39758 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [574] Overfull \hbox (20.58041pt too wide) in paragraph at lines 39835--39835 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [575] [576] [577] Underfull \hbox (badness 1082) in paragraph at lines 39979--39982 []\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 [578] [579] [580] Underfull \hbox (badness 1038) in paragraph at lines 40170--40173 []\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 [581] [582] [583] [584] [585] Underfull \hbox (badness 1442) in paragraph at lines 40534--40538 \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 = [586] [587] [588] [589] Underfull \hbox (badness 4096) in paragraph at lines 40784--40787 []\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 , [590] Underfull \hbox (badness 7888) in paragraph at lines 40898--40902 []\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) > [591] [592] [593] Overfull \hbox (63.78036pt too wide) in paragraph at lines 41052--41052 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 41054--41054 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 41056--41056 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/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 41069--41071 []\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 [594] Underfull \hbox (badness 10000) in paragraph at lines 41149--41152 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [595] [596] Underfull \hbox (badness 3872) in paragraph at lines 41267--41270 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [597] Underfull \hbox (badness 5475) in paragraph at lines 41333--41337 [][][]\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 \ [][]$\T1/pcr/m/n/10 https : / / [598] [599] [600] [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41754--41761 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 41810--41819 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 41810--41819 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, [604] Underfull \hbox (badness 1082) in paragraph at lines 41820--41832 \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' in that di-rec-tory states the ver-sion. That op-tion is Underfull \hbox (badness 1337) in paragraph at lines 41893--41901 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or [605] Underfull \hbox (badness 10000) in paragraph at lines 41902--41905 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of Underfull \hbox (badness 3460) in paragraph at lines 41956--41959 [][][]$\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 41960--41962 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 41969--41969 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [606] [607] [608] Underfull \hbox (badness 10000) in paragraph at lines 42190--42192 []\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 [609] [610] Overfull \hbox (15.18042pt too wide) in paragraph at lines 42312--42312 []\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 42314--42314 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] [611] [612] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42415--42415 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 42417--42417 [] \T1/pcr/m/n/10 getOption("deparse .max.lines", -1L)))[] [613] [614] [615] Underfull \hbox (badness 6542) in paragraph at lines 42691--42693 []\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 [616] [617] Overfull \hbox (30.78088pt too wide) in paragraph at lines 42810--42810 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [618] Underfull \hbox (badness 1708) in paragraph at lines 42878--42886 []\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 42878--42886 \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 [619] Underfull \hbox (badness 4859) in paragraph at lines 42908--42913 [][][]\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; [620] Underfull \hbox (badness 3895) in paragraph at lines 42970--42982 []\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 42970--42982 \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 , [621] [622] [623] [624] [625] Overfull \hbox (9.78043pt too wide) in paragraph at lines 43292--43292 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [626] [627] [628] [629] [630] [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43760--43760 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [632] Overfull \hbox (25.98041pt too wide) in paragraph at lines 43769--43769 []\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 43835--43841 [][][]\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 , [633] Underfull \hbox (badness 3861) in paragraph at lines 43844--43849 [][][]\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 , [634] [635] Underfull \hbox (badness 1803) in paragraph at lines 43990--43993 []\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 43994--44001 []\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 [636] [637] [638] Underfull \hbox (badness 3668) in paragraph at lines 44209--44211 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [639] Overfull \hbox (36.78088pt too wide) in paragraph at lines 44315--44315 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [640] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44390--44390 []\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[] [641] Overfull \hbox (90.78033pt too wide) in paragraph at lines 44398--44398 []\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 ...[] [642] Underfull \hbox (badness 6220) in paragraph at lines 44528--44533 []\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 44528--44533 \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, [643] Underfull \hbox (badness 10000) in paragraph at lines 44549--44554 []\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 44549--44554 \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 [644] Underfull \hbox (badness 2818) in paragraph at lines 44645--44651 []\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 [645] Overfull \hbox (15.18042pt too wide) in paragraph at lines 44680--44680 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [646] [647] [648] [649] [650] [651] Underfull \hbox (badness 2846) in paragraph at lines 45137--45141 []\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 [652] Overfull \hbox (4.38043pt too wide) in paragraph at lines 45177--45177 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 45198--45202 []\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 [653]) (./compiler-pkg.tex [654] Chapter 2. [655] 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 [656] [657] [658]) (./datasets-pkg.tex Chapter 3. [659] [660] [661] [662] [663] 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,[] [664] 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 [665] [666] [667] [668] 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)[] [669] 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") [670] [671] 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") [672] [673] [674] 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. [675] 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") [676] [677] [678] [679] [680] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [681] [682] Underfull \hbox (badness 10000) in paragraph at lines 1547--1550 []\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 1547--1550 \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 [683] [684] [685] Overfull \hbox (48.81013pt too wide) in paragraph at lines 1736--1739 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [686] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1830--1830 []\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 1838--1838 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [687] [688] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1954--1954 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1955--1955 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [689] [690] [691] [692] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2158--2161 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [693] [694] [695] Overfull \vbox (4.29591pt too high) has occurred while \output is active [696] [697] [698] [699] [700] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2723--2726 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [701] Overfull \vbox (13.87083pt too high) has occurred while \output is active [702] Underfull \vbox (badness 2376) has occurred while \output is active [703] [704] Overfull \vbox (12.25539pt too high) has occurred while \output is active [705] [706] Overfull \vbox (17.12102pt too high) has occurred while \output is active [707] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3152--3152 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [708] [709] [710] [711] [712] [713] [714] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3609--3609 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [715] [716] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3757--3760 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [717] Overfull \vbox (10.49593pt too high) has occurred while \output is active [718] Overfull \vbox (15.49593pt too high) has occurred while \output is active [719] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3966--3966 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 4004--4006 []\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 4004--4006 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732] [733]) (./grDevices-pkg.tex [734] Chapter 4. [735] [736] [737] [738] 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 [739] [740] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\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 379--387 \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 [741] [742] Overfull \hbox (6.78088pt too wide) in paragraph at lines 516--516 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] Underfull \hbox (badness 5175) in paragraph at lines 1189--1191 []\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 [753] [754] [755] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] Underfull \hbox (badness 1173) in paragraph at lines 1402--1405 []\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 [756] [757] [758] [759] [760] [761] [762] [763] Underfull \hbox (badness 1565) in paragraph at lines 1890--1895 []\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 1890--1895 \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 [764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1973--1973 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 2014--2024 []\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 2014--2024 \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 , [765] [766] Underfull \hbox (badness 10000) in paragraph at lines 2126--2128 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [767] [768] Underfull \hbox (badness 6758) in paragraph at lines 2305--2308 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [769] [770] Underfull \hbox (badness 2326) in paragraph at lines 2423--2433 \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 2423--2433 \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 2423--2433 \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 2423--2433 \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 [771] [772] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2526--2526 []\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 [773] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2642--2642 []\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 2643--2643 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha, re v = FALSE)[] [774] [775] [776] [777] [778] Underfull \hbox (badness 10000) in paragraph at lines 2914--2915 Underfull \vbox (badness 10000) has occurred while \output is active [779] [780] [781] [782] [783] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3247--3247 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [784] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3331--3331 []\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 3332--3332 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [785] [786] Underfull \hbox (badness 10000) in paragraph at lines 3488--3493 []\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 3488--3493 \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- [787] [788] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3562--3562 []\T1/pcr/m/n/10 palette.colors(n = NULL, palette = "Okabe-Ito", alpha, recycl e = FALSE)[] [789] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3666--3666 []\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 3673--3673 [] \T1/pcr/m/n/9 matplot(x, type = "l", lwd = 4, lty = 1, col = 1:8, ylab = "", main=main)[] [790] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3729--3729 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) [791] Underfull \hbox (badness 8170) in paragraph at lines 3758--3761 []\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 , [792] Underfull \hbox (badness 2189) in paragraph at lines 3819--3824 []\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 3857--3861 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [793] Underfull \vbox (badness 10000) has occurred while \output is active [794] Underfull \hbox (badness 5260) in paragraph at lines 3987--3990 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [795] [796] [797] [798] [799] Underfull \hbox (badness 5939) in paragraph at lines 4320--4325 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 10000) in paragraph at lines 4724--4729 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / [806] [807] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4839--4839 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [808] [809] Underfull \hbox (badness 1348) in paragraph at lines 5044--5047 []\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 [810] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5068--5068 []\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 5109--5115 []\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 [811] Underfull \hbox (badness 1112) in paragraph at lines 5142--5146 []\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" [812] Underfull \hbox (badness 1755) in paragraph at lines 5284--5286 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [813] [814] [815] Underfull \hbox (badness 7344) in paragraph at lines 5464--5466 []\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 5475--5479 [][][]\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 [816] [817] Underfull \hbox (badness 1552) in paragraph at lines 5602--5611 \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 5602--5611 \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 5602--5611 \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 5612--5614 []\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 5644--5650 \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 [818] Underfull \hbox (badness 10000) in paragraph at lines 5670--5677 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [819] [820] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5771--5771 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5883--5883 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [822] [823] Underfull \hbox (badness 10000) in paragraph at lines 5969--5971 []\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 [824] [825] [826] [827] [828] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6336--6336 []\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 6350--6353 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [829] [830] [831] [832] [833] [834] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6685--6685 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6692--6692 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [835] [836] [837] [838] Underfull \hbox (badness 10000) in paragraph at lines 6955--6960 []\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 6955--6960 \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 6955--6960 \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 [839] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7061--7061 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [840] Underfull \hbox (badness 3590) in paragraph at lines 7100--7103 []\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 7100--7103 \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 7111--7111 [] \T1/pcr/m/n/10 fonts, family, xpos, ypos, title, type, antialias, symbol family)[] [841] Underfull \hbox (badness 1189) in paragraph at lines 7175--7177 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [842] Underfull \hbox (badness 10000) in paragraph at lines 7280--7282 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [843] Underfull \hbox (badness 10000) in paragraph at lines 7326--7333 []\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 7326--7333 \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 [844] Underfull \hbox (badness 5607) in paragraph at lines 7410--7414 []\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 [845] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7462--7462 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [846] [847] Underfull \hbox (badness 5637) in paragraph at lines 7594--7600 \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 7627--7630 []\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 / [848] [849] [850] Underfull \hbox (badness 1231) in paragraph at lines 7796--7798 []\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 [851] [852]) (./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 = [853] [854] [855] 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 [856] [857] [858] [859] 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 [860] [861] 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[] [862] 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 [863] [864] 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, ...)[] [865] [866] [867] 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 (106.98032pt too wide) in paragraph at lines 981--981 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = 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)[] [868] [869] [870] [871] 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"):[] [872] [873] [874] Underfull \hbox (badness 1024) in paragraph at lines 1431--1439 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1465--1467 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [875] [876] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1535--1535 []\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 1536--1536 []\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 1542--1542 []\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 1543--1543 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [877] [878] [879] [880] [881] Underfull \hbox (badness 10000) in paragraph at lines 1846--1852 [][][]\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 (42.18039pt too wide) in paragraph at lines 1878--1878 []\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 1894--1894 []\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 1903--1903 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [882] [883] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1988--1988 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [884] [885] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2117--2117 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2122--2122 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [886] [887] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2296--2296 []\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 2297--2297 [] \T1/pcr/m/n/10 ann = par("ann"), xaxt = par("xaxt"), frame.plot = T RUE, log = "",[] [888] Underfull \hbox (badness 1430) in paragraph at lines 2328--2330 []\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 [889] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2409--2409 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2421--2428 \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 [890] Underfull \hbox (badness 7273) in paragraph at lines 2503--2507 [][][]\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 [891] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2516--2516 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [892] [893] [894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2750--2750 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [895] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2787--2787 [] \T1/pcr/m/n/10 density = NULL, angle = 45, col = "lightgray", border = NULL,[] [896] [897] Underfull \hbox (badness 1226) in paragraph at lines 2912--2916 \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 2965--2965 []\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 :[] [898] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2969--2969 []\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 3021--3024 [][][]\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 [899] [900] [901] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3226--3226 []\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 3231--3231 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [902] [903] Underfull \hbox (badness 10000) in paragraph at lines 3373--3378 []\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 3373--3378 [][]\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 3373--3378 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [904] [905] [906] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3559--3559 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3578--3578 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] [907] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3582--3582 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [908] [909] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3759--3759 [] \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 3760--3760 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [910] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3799--3799 [] \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 [911] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3851--3851 []\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 3859--3859 []\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 3861--3861 []\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 3869--3869 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [912] Underfull \hbox (badness 10000) in paragraph at lines 3932--3936 [][][]\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% [913] [914] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4044--4044 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [915] [916] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4198--4198 []\T1/pcr/m/n/9 nd <- length(dv <- seq(as.Date("1959-02-21"), by = "weeks", le ngth.out = 100))[] [917] Underfull \hbox (badness 3930) in paragraph at lines 4277--4279 []\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 [918] [919] [920] [921] [922] Underfull \hbox (badness 1286) in paragraph at lines 4588--4591 \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 4596--4601 []\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 [923] [924] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4693--4693 []\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 4698--4698 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [925] Underfull \hbox (badness 1264) in paragraph at lines 4889--4902 \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 , [926] [927] Underfull \hbox (badness 10000) in paragraph at lines 5026--5032 []\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. [928] [929] Underfull \hbox (badness 10000) in paragraph at lines 5157--5160 [930 ] Underfull \hbox (badness 10000) in paragraph at lines 5218--5220 [931 ] [932] Underfull \hbox (badness 10000) in paragraph at lines 5408--5410 []\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 [933] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5464--5464 []\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 5465--5465 [] \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 [934] [935] [936] [937] [938] [939] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5830--5830 []\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 5831--5831 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] [940]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot }) has been already used, duplicate ignored \relax l.5890 \aliasA{plot}{plot.default}{plot} [941] [942] [943] [944] [945] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6222--6222 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6228--6228 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [946] [947] [948] [949] [950] [951] Underfull \hbox (badness 10000) in paragraph at lines 6658--6660 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [952] [953] Underfull \hbox (badness 1028) in paragraph at lines 6752--6754 []\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 6795--6796 [][] [954 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6889--6889 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [955] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6920--6920 [] \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 [956] [957] Underfull \hbox (badness 10000) in paragraph at lines 7042--7044 []\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 7069--7069 [] \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 7075--7075 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [958] Underfull \hbox (badness 2600) in paragraph at lines 7135--7137 []\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 [959] [960] [961] [962] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7367--7367 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [963] [964] [965] [966] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7754--7754 []\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 7758--7758 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [969] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7770--7770 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [970] [971] [972] [973] [974] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8119--8119 []\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 8122--8122 []\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 8126--8126 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [975] [976] [977] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8297--8297 []\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 8298--8298 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [978] [979] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8402--8402 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8413--8418 []\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 [980] Underfull \hbox (badness 1112) in paragraph at lines 8461--8465 []\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 [981] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8521--8521 []\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 8536--8536 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [982] [983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [984] [985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8858--8858 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [986] Underfull \hbox (badness 10000) in paragraph at lines 8886--8888 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8888--8890 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8920--8926 []\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 [987]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8968 \HeaderA{units}{Graphical Units}{units} [988] Underfull \hbox (badness 1205) in paragraph at lines 9033--9035 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [989] [990] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9152--9152 []\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)[] [991]) (./grid-pkg.tex [992] Chapter 6. [993] [994] [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \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 476--482 \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 [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\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- [1011] [1012] [1013] [1014] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\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 [1015] [1016] [1017] [1018] [1019] [1020] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1768--1768 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1021] [1022] [1023] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1982--1982 []\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 1983--1983 []\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 1984--1984 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1024] Underfull \hbox (badness 2961) in paragraph at lines 2019--2024 []\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 , [1025] Underfull \hbox (badness 1430) in paragraph at lines 2078--2083 []\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 2107--2110 []\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 [1026] [1027] [1028] Underfull \hbox (badness 2894) in paragraph at lines 2314--2321 []\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 [1029] [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2470--2470 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2482--2487 []\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- [1032] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2541--2541 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1033] [1034] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2693--2693 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] [1035] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1036] [1037] [1038] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2967--2967 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1039] [1040] [1041] [1042] [1043] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3282--3282 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1044] [1045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3378--3378 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] Underfull \hbox (badness 2799) in paragraph at lines 3412--3418 []\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 [1046] [1047] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3504--3504 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3511--3511 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1048] [1049] [1050] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3712--3712 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3727--3727 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1051] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3748--3748 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] Underfull \hbox (badness 1067) in paragraph at lines 4489--4492 []\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 [1064] Underfull \hbox (badness 1430) in paragraph at lines 4535--4540 []\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- [1065] [1066] [1067] Underfull \hbox (badness 7256) in paragraph at lines 4734--4736 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] Underfull \hbox (badness 10000) in paragraph at lines 5371--5373 []\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 [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] Underfull \hbox (badness 6859) in paragraph at lines 6059--6065 []\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 6059--6065 \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") [1088] [1089] [1090] [1091] [1092] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6337--6337 []\T1/pcr/m/n/9 unitType(min(unit(1, "in"), unit(1, "npc") + unit(1, "mm")), r ecurse=TRUE)[] [1093] Underfull \hbox (badness 1867) in paragraph at lines 6437--6439 []\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 [1094] Underfull \hbox (badness 10000) in paragraph at lines 6474--6480 [][][]\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 , [1095] [1096] Underfull \hbox (badness 1371) in paragraph at lines 6606--6609 []\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 [1097] Underfull \vbox (badness 10000) has occurred while \output is active [1098] [1099] [1100] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6810--6810 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1101]) (./methods-pkg.tex [1102] Chapter 7. [1103] [1104] 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 [1105] [1106] [1107] 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- [1108] [1109] 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[] [1110] 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 [1111] 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 [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] 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[] [1127] [1128] 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 [1129] [1130] [1131] 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 = [1132] [1133] 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 [1134] [1135] [1136] 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 [1137] 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))[] [1138] [1139] [1140] 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:[] [1141] [1142] [1143] [1144] [1145] [1146] [1147] 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 [1148] [1149] 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 [1150] 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 [] [1151] [1152] 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,...) { [1153] 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 [1154] [1155] [1156] 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 [1157] [1158] [1159] 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,[] [1160] 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) [1161] [1162] [1163] 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 , [1164] [1165] [1166] 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 [1167] [1168] [1169] [1170] 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[] [1171] 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 [1172] [1173] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1174] [1175] 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 [1176] [1177] [1178] 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 [1179] [1180] [1181] [1182] [1183] [1184] 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 [1185] [1186] 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 [1187] 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 [1188] [1189] 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 [1190] Underfull \vbox (badness 10000) has occurred while \output is active [1191] [1192] [1193]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1194] 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().[] [1195] [1196] 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")[] [1197]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 [1198] 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 , [1199] [1200] 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 [1201] [1202] 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 [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] 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 [1214] 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(), [1215] 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 =,[] [1216] [1217] [1218] [1219] 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[] [1220] [1221] [1222] 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")[] [1223] [1224] [1225] 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[] [1226] [1227] [1228] [1229] 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[] [1230] 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][] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239] [1240] 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 [1241] [1242] [1243]) (./parallel-pkg.tex [1244] 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 [1245] 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 [1246] [1247] 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 [1248] [1249] [1250] 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 [1251] [1252] [1253] [1254] [1255] Underfull \hbox (badness 1917) in paragraph at lines 770--779 []\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 770--779 \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 [1256] [1257] Overfull \hbox (60.78088pt too wide) in paragraph at lines 863--863 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1258] [1259] [1260] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1054--1054 []\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 1058--1058 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1261] Underfull \hbox (badness 5388) in paragraph at lines 1173--1178 []\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 [1262] Underfull \hbox (badness 10000) in paragraph at lines 1197--1205 []\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 1234--1234 []\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)[] [1263] [1264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1350--1350 [] \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 1364--1364 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1265] Underfull \hbox (badness 1577) in paragraph at lines 1393--1396 []\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 1440--1442 []\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 [1266] [1267]) (./splines-pkg.tex [1268] 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 [1269] [1270] [1271] [1272] [1273] [1274] [1275] [1276] 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))[] [1277] 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 [1278] [1279] 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)))[] [1280] [1281] [1282]) (./stats-pkg.tex Chapter 10. [1283] 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[] [1284] [1285] [1286] [1287] [1288] 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[] [1289] 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) [1290] [1291] [1292] [1293] [1294] [1295] Underfull \hbox (badness 1024) in paragraph at lines 882--884 []\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 [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] [1305] Underfull \hbox (badness 10000) in paragraph at lines 1544--1548 []\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 1544--1548 \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 1544--1548 \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 [1306] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1620--1620 [] \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 1623--1623 [] \T1/pcr/m/n/10 yleft, yright, rule = 1, f = 0, ties = mean, na.rm = TRUE)[] [1307] [1308] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1770--1770 [] \T1/pcr/m/n/9 approx(xn, yn, xout=xout, method=M, rule=R, n a.rm=na.)$y),[] [1309] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1782--1782 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$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 :[ ] [1310] [1311] [1312] [1313] [1314] [1315] [1316] [1317] [1318] [1319] [1320] [1321] [1322] [1323] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2800--2800 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1324] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3040--3040 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1328] [1329] [1330] Underfull \hbox (badness 10000) in paragraph at lines 3251--3253 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1331] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3300--3300 []\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 3301--3301 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1332] [1333] [1334] [1335] [1336] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3692--3692 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1337] [1338] [1339] [1340] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3971--3971 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1341] [1342] [1343] [1344] [1345] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4260--4260 []\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 4261--4261 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1346] [1347] [1348] [1349] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4501--4501 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1350] [1351] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4676--4676 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1352] [1353] Underfull \hbox (badness 3989) in paragraph at lines 4770--4777 []\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 = [1354] [1355] [1356] [1357] [1358] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5155--5155 []\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 5157--5157 []\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))[] [1359] [1360] [1361] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5378--5378 []\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 5396--5396 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) [1362] Underfull \hbox (badness 2680) in paragraph at lines 5423--5425 []\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 [1363] [1364] [1365] Underfull \hbox (badness 1436) in paragraph at lines 5606--5611 []\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 5606--5611 \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 5606--5611 \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 , [1366] [1367] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5809--5809 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1368] [1369] [1370] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5976--5976 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1371] [1372] [1373] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6161--6161 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1374] [1375] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6269--6269 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1376] Underfull \hbox (badness 10000) in paragraph at lines 6336--6341 []\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 [1377] [1378] [1379] Underfull \hbox (badness 5954) in paragraph at lines 6532--6534 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1380] Underfull \hbox (badness 2503) in paragraph at lines 6614--6617 []\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 6618--6620 []\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 6621--6626 \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, [1381] Underfull \hbox (badness 7238) in paragraph at lines 6657--6660 [][][]\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 6692--6692 []\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 6707--6707 []\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):[] [1382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6722--6722 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1383] [1384] [1385] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6967--6967 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] Underfull \vbox (badness 10000) has occurred while \output is active [1386] [1387] [1388] Underfull \vbox (badness 10000) has occurred while \output is active [1389] [1390] [1391] [1392] Underfull \hbox (badness 10000) in paragraph at lines 7366--7370 \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 [1393] Underfull \hbox (badness 6493) in paragraph at lines 7465--7468 []\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 [1394] [1395] Underfull \hbox (badness 10000) in paragraph at lines 7602--7605 []\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 = [1396] [1397] [1398] [1399] [1400] [1401] Underfull \hbox (badness 10000) in paragraph at lines 8014--8019 []\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 , ..., [1402] [1403] [1404] [1405] [1406] [1407] Underfull \hbox (badness 1210) in paragraph at lines 8369--8371 []\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 [1408] [1409] [1410] [1411] [1412] [1413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8832--8832 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] [1414] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8877--8877 []\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 8880--8880 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1415] [1416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9018--9018 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1417] [1418] [1419] [1420] [1421] [1422] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9445--9445 [] \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 9446--9446 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1423] [1424] [1425] Underfull \hbox (badness 7291) in paragraph at lines 9625--9627 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1426] [1427] [1428] [1429] [1430] [1431] [1432] Underfull \hbox (badness 6944) in paragraph at lines 10103--10109 [][][]\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); [1433] [1434] [1435] Underfull \hbox (badness 3758) in paragraph at lines 10317--10320 []\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 [1436] [1437] [1438] [1439] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10561--10561 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10587--10592 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1440] Underfull \hbox (badness 4132) in paragraph at lines 10626--10630 []\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 10680--10686 []\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- [1441] Underfull \hbox (badness 10000) in paragraph at lines 10731--10734 []\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 [1442] [1443] [1444] Underfull \hbox (badness 2142) in paragraph at lines 10948--10951 []\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 ^^@ [1445] Underfull \hbox (badness 1708) in paragraph at lines 11029--11033 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1446] Underfull \hbox (badness 10000) in paragraph at lines 11071--11077 [][][]\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 11109--11114 \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 (= [1447] [1448] Underfull \hbox (badness 2635) in paragraph at lines 11242--11245 \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 [1449] [1450] [1451] Underfull \hbox (badness 1694) in paragraph at lines 11425--11428 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1452] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11526--11526 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1453] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11559--11559 [] \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 11572--11576 []\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 [1454] [1455] [1456] [1457] [1458] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11894--11894 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1459]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11909 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11969--11969 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1460] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11981--11981 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 12034--12039 []\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 12051--12053 []\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 [1461] [1462] [1463] [1464] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12305--12305 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12306--12306 [] \T1/pcr/m/n/10 trace.label = deparse1(substitute(trace.fact or)),[] [1465] [1466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1467] [1468] [1469] [1470] Underfull \hbox (badness 10000) in paragraph at lines 12649--12651 []\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 12672--12674 []\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 [1471] Underfull \hbox (badness 2753) in paragraph at lines 12741--12743 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1472] [1473] [1474] [1475] Underfull \hbox (badness 6910) in paragraph at lines 12979--12981 []\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 12985--12989 []\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 12985--12989 \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 [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13692--13692 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1486] Underfull \hbox (badness 4518) in paragraph at lines 13736--13741 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1487] [1488] [1489] Underfull \hbox (badness 10000) in paragraph at lines 13935--13939 []\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 , [1490] [1491] [1492] [1493] [1494] Underfull \hbox (badness 1163) in paragraph at lines 14269--14277 \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 , [1495] Underfull \hbox (badness 4518) in paragraph at lines 14389--14394 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1496] [1497] [1498] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14577--14577 []\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 14578--14578 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1499] [1500] [1501] [1502] [1503] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14921--14921 []\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 14922--14922 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1504] [1505] Overfull \hbox (18.78088pt too wide) in paragraph at lines 15015--15015 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1506] [1507] [1508] [1509] [1510] [1511] Underfull \hbox (badness 2726) in paragraph at lines 15421--15424 []\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 , [1512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15515--15515 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1513] [1514] [1515] [1516] [1517] [1518] [1519] [1520] [1521] [1522] Overfull \hbox (31.3804pt too wide) in paragraph at lines 16141--16141 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1523] [1524] Underfull \hbox (badness 1490) in paragraph at lines 16279--16284 \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 [1525] Underfull \hbox (badness 1648) in paragraph at lines 16345--16347 []\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 16360--16369 \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 16360--16369 \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 [1526] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16430--16430 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16988--16988 []\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[] [1536] [1537] [1538] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17220--17220 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1539] [1540] [1541] [1542] [1543] [1544] [1545] [1546] [1547] [1548] Underfull \vbox (badness 10000) has occurred while \output is active [1549] Underfull \vbox (badness 10000) has occurred while \output is active [1550] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17981--17981 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1551] [1552] [1553] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18144--18144 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18191--18191 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1554] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18238--18238 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1555] [1556] [1557] [1558] [1559] [1560] [1561] [1562] Underfull \hbox (badness 1248) in paragraph at lines 18736--18739 []\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 18749--18753 []\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 [1563] Underfull \hbox (badness 1478) in paragraph at lines 18757--18761 \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 Underfull \hbox (badness 2042) in paragraph at lines 18815--18817 []\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 [1564] [1565] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18921--18921 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1566] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18964--18964 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18982--18982 []\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 18985--18985 []\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 19005--19005 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 19008--19008 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1567] Underfull \hbox (badness 2564) in paragraph at lines 19043--19054 []\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 19043--19054 \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 [1568] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19106--19106 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1569] [1570] [1571] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19333--19333 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1572] [1573] Underfull \hbox (badness 1337) in paragraph at lines 19444--19447 []\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 [1574] [1575] [1576] [1577] [1578] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19763--19763 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1579] [1580] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19851--19851 [] \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 19853--19853 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19855--19855 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1581] Underfull \hbox (badness 10000) in paragraph at lines 19901--19907 []\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 19942--19946 []\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 [1582] [1583] [1584] [1585] Overfull \hbox (0.78088pt too wide) in paragraph at lines 20195--20195 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 1194) in paragraph at lines 20205--20208 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1586] Underfull \hbox (badness 1107) in paragraph at lines 20263--20265 []\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 [1587] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20318--20318 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20325--20325 []\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)[] [1589] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20419--20419 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1590] [1591] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1592] Underfull \hbox (badness 7740) in paragraph at lines 20611--20613 []\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 [1593] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20659--20659 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1594] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20751--20751 [] \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 20756--20756 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] [1603] [1604] [1605] [1606] [1607] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21611--21611 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1608] Underfull \hbox (badness 6859) in paragraph at lines 21678--21685 [][][]\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 21689--21695 []\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 , [1609] [1610] [1611] [1612] [1613] [1614] [1615] [1616] [1617] [1618] [1619] [1620] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22435--22435 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1621] [1622] [1623] [1624] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22719--22719 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22720--22720 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1626] [1627] [1628] [1629] [1630] Underfull \hbox (badness 1337) in paragraph at lines 23046--23052 []\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 [1631] [1632] [1633] [1634] [1635] [1636] [1637] [1638] Underfull \hbox (badness 10000) in paragraph at lines 23602--23604 []\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 23602--23604 \T1/ptm/m/n/10 SAS Blog. [][]$\T1/pcr/m/n/10 https : / / blogs . sas . com / co ntent / iml / 2017 / 05 / 24 / Underfull \hbox (badness 10000) in paragraph at lines 23609--23610 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . or g / wiki / Quantile # Estimating _ [1639] [1640] [1641] Underfull \hbox (badness 1028) in paragraph at lines 23772--23775 []\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 [1642] Underfull \hbox (badness 10000) in paragraph at lines 23882--23885 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1643] Underfull \hbox (badness 7944) in paragraph at lines 23937--23939 []\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 = [1644] Underfull \hbox (badness 7944) in paragraph at lines 23999--24001 []\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 = [1645] [1646] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24101--24101 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1647] [1648] [1649] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24321--24321 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1650] [1651] Overfull \hbox (60.78088pt too wide) in paragraph at lines 24425--24425 [] \T1/pcr/m/n/10 na.action = c("+Big_alternate", "-Big_alternate", "na. omit", "fail"),[] Underfull \hbox (badness 1033) in paragraph at lines 24468--24474 \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 24489--24492 []\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] = [1652] Underfull \hbox (badness 2134) in paragraph at lines 24558--24562 [][][]\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 24571--24571 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1653] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24600--24600 []\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 24612--24612 []\T1/pcr/m/n/9 matplot(y = cbind(x15, rT15), type = "b", ylim = c(1,9), pch=1 :5, xlab = NA,[] [1654] [1655] [1656] [1657] [1658] [1659] [1660] Underfull \hbox (badness 6268) in paragraph at lines 25067--25072 [][]\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 , [1661] Overfull \hbox (58.38037pt too wide) in paragraph at lines 25095--25095 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1662] [1663] [1664] Underfull \hbox (badness 1867) in paragraph at lines 25272--25274 []\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 25287--25291 []\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 25287--25291 \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 25323--25323 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1665] [1666] [1667] Underfull \hbox (badness 2495) in paragraph at lines 25513--25522 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1668] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25595--25595 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] [1669] Underfull \hbox (badness 1412) in paragraph at lines 25602--25604 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1670] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25689--25689 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25714--25714 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25717--25717 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1671] [1672] [1673] Overfull \hbox (6.78088pt too wide) in paragraph at lines 25941--25941 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / t ol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25945--25951 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1674] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25991--25991 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26012--26012 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1675] Underfull \hbox (badness 1019) in paragraph at lines 26074--26079 \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 [1676] [1677] Overfull \hbox (0.78088pt too wide) in paragraph at lines 26204--26204 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1678] [1679] [1680] [1681] [1682] [1683] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26584--26584 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1684] [1685] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26765--26765 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] [1686] Overfull \hbox (52.98038pt too wide) in paragraph at lines 26771--26771 []\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 26780--26780 []\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 26781--26781 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] [1687] Underfull \hbox (badness 2922) in paragraph at lines 26850--26855 []\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 26887--26887 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] [1688] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26890--26890 [] \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 26899--26899 [] \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 26900--26900 [] \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 26904--26904 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1689] Underfull \hbox (badness 3240) in paragraph at lines 26958--26961 [][][]\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 26979--26979 [] \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 26982--26982 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1690] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27065--27065 [] \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 27069--27069 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] [1691] Overfull \hbox (58.38037pt too wide) in paragraph at lines 27079--27079 [] \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 27084--27084 [] \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 27120--27126 []\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 [1692] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27142--27142 []\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 27158--27158 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1693] [1694] Overfull \hbox (30.78088pt too wide) in paragraph at lines 27272--27272 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1695] Underfull \hbox (badness 2922) in paragraph at lines 27334--27339 []\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 (69.18036pt too wide) in paragraph at lines 27372--27372 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1696] Underfull \hbox (badness 2922) in paragraph at lines 27421--27426 []\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 [1697] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27452--27452 []\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 27486--27491 []\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 [1698] Overfull \hbox (25.98041pt too wide) in paragraph at lines 27511--27511 []\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 27515--27515 []\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 27535--27535 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27545--27545 [] \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[] [1699] Underfull \hbox (badness 2922) in paragraph at lines 27580--27585 []\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 27602--27602 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] [1700] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27620--27620 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] Underfull \hbox (badness 6493) in paragraph at lines 27672--27677 []\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 [1701] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27700--27700 []\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 27703--27703 []\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 27706--27706 []\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 27709--27709 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] Underfull \hbox (badness 3396) in paragraph at lines 28631--28633 []\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 [1716] [1717] [1718] Underfull \hbox (badness 2237) in paragraph at lines 28808--28810 []\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 [1719] [1720] Underfull \hbox (badness 2591) in paragraph at lines 28972--28974 []\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 [1721] Underfull \hbox (badness 2237) in paragraph at lines 29018--29021 []\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 [1722] Overfull \hbox (48.78088pt too wide) in paragraph at lines 29091--29091 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1723] [1724] Underfull \hbox (badness 3407) in paragraph at lines 29200--29204 []\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) [1725] [1726] Underfull \hbox (badness 1337) in paragraph at lines 29333--29337 []\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 [1727] [1728] [1729] [1730] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29591--29591 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29619--29619 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1731] Underfull \hbox (badness 1616) in paragraph at lines 29645--29648 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1732] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29724--29724 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1733] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29801--29801 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1734] [1735] Underfull \hbox (badness 2205) in paragraph at lines 29890--29895 []\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 [1736] [1737] [1738] [1739] [1740] [1741] [1742] [1743] [1744] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30489--30489 []\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 30490--30490 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1745] [1746] [1747] [1748] [1749] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30790--30790 [] \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 30791--30791 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1750] [1751] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30917--30917 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30926--30926 []\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 [1752] [1753] [1754] Underfull \hbox (badness 1337) in paragraph at lines 31143--31147 []\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 [1755] [1756] [1757] [1758] [1759] [1760] [1761] [1762] [1763] Underfull \hbox (badness 1337) in paragraph at lines 31672--31676 []\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 31686--31688 []\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 [1764] [1765] [1766] Overfull \hbox (117.7803pt too wide) in paragraph at lines 31879--31879 []\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 31881--31881 []\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)[] [1767] [1768] Overfull \hbox (138.78088pt too wide) in paragraph at lines 32040--32040 [] \T1/pcr/m/n/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.eps = getOption("ts.eps"), ...)[] [1769] Overfull \hbox (0.78088pt too wide) in paragraph at lines 32124--32124 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1770] Underfull \hbox (badness 6775) in paragraph at lines 32181--32186 []\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 [1771] Overfull \hbox (47.58038pt too wide) in paragraph at lines 32244--32244 []\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 "")[] [1772]) (./stats4-pkg.tex Chapter 11. [1773] [1774] [1775] 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 [1776] 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[] [1777] [1778] [1779] [1780]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} [1781] [1782] [1783]) (./tcltk-pkg.tex [1784] Chapter 12. [1785] [1786] [1787] [1788] Overfull \hbox (36.7804pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all.names = TRUE) # .Tcl.args put a ca llback ref in here[] [1789] [1790] [1791] Underfull \vbox (badness 10000) has occurred while \output is active [1792] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\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 [1793] [1794] [1795] [1796] [1797] [1798] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1077--1077 []\T1/pcr/m/n/9 eval.txt <- function() eval(str2lang(tclvalue(tkget(txt.w, "0. 0", "end"))))[] [1799] [1800] [1801] [1802] [1803] Underfull \hbox (badness 1189) in paragraph at lines 1406--1409 [][][]\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 [1804]) (./tools-pkg.tex Chapter 13. [1805] 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.[] [1806] 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 [1807] 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)[] [1808] 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 , [1809] 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 [1810] [1811] 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 [1812] [1813] [1814] [1815] [1816] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1817] [1818] 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")[] [1819] [1820] [1821] 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, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1150--1160 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1150--1160 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1822] 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 [1823] 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 [1824] [1825] 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 [1826] [1827] [1828] [1829] [1830] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1697--1697 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] 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--1712 []\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--1712 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1831] [1832] [1833]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1911 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1834] [1835] [1836] [1837] Underfull \hbox (badness 1142) in paragraph at lines 2179--2185 []\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 2213--2213 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2214--2214 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2241--2248 []\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 2241--2248 \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 2241--2248 \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 [1839] Underfull \hbox (badness 1342) in paragraph at lines 2293--2299 \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 [1840] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2369--2369 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2382--2388 []\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 2382--2388 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1841] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2415--2415 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2424--2424 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2441--2441 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1842] [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2725--2725 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1846] Underfull \hbox (badness 2486) in paragraph at lines 2770--2778 []\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 [1847] [1848] [1849] [1850] [1851] Underfull \hbox (badness 1072) in paragraph at lines 3150--3152 []\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 [1852] [1853] [1854] [1855] [1856] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3483--3483 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1857] [1858] [1859] [1860] Underfull \hbox (badness 4108) in paragraph at lines 3731--3738 []\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 [1861] [1862] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3831--3831 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3834--3834 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3851--3853 []\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 3868--3874 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1863] [1864] Underfull \hbox (badness 7832) in paragraph at lines 3990--3993 []\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 [1865] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4066--4066 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1866] Underfull \hbox (badness 1137) in paragraph at lines 4092--4094 []\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 [1867] [1868] [1869] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4277--4277 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1870] [1871] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4439--4439 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4450--4453 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1872] Underfull \hbox (badness 6859) in paragraph at lines 4466--4471 []\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 4474--4480 []\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 4474--4480 \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 [1873] [1874] [1875] [1876] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4732--4732 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4733--4733 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4745--4748 []\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 4749--4759 \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 4784--4790 []\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 4784--4790 \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 ', [1877] Underfull \hbox (badness 1571) in paragraph at lines 4812--4816 []\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 4838--4843 \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 [1878] [1879] [1880]) (./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 ', [1881] [1882] [1883] [1884] 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[] [1885] Overfull \hbox (24.05087pt too wide) in paragraph at lines 378--383 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1886] 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 [1887] 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"))),[] [1888] [1889] Underfull \hbox (badness 1946) in paragraph at lines 626--630 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1890] Overfull \hbox (0.78088pt too wide) in paragraph at lines 676--676 []\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 682--682 []\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 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 684--684 []\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 685--685 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 719--725 []\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 719--725 \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- [1891] [1892] Underfull \hbox (badness 4505) in paragraph at lines 855--861 \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 [1893] [1894] [1895] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1029--1029 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1896] Underfull \hbox (badness 1748) in paragraph at lines 1094--1102 []\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 1094--1102 \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 1094--1102 \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 1094--1102 \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 1106--1108 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1897] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1898] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1297--1297 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1899] [1900] [1901] [1902] [1903] [1904] [1905] [1906] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1799--1799 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1834--1834 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1907] [1908] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1980--1980 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1909] [1910] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2132--2132 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1911] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2184--2184 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1912] [1913] [1914] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2353--2353 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2376--2376 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1915] [1916] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2496--2496 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1917] Underfull \hbox (badness 1082) in paragraph at lines 2570--2574 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2575 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2606--2608 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1918] [1919] Underfull \hbox (badness 10000) in paragraph at lines 2694--2696 []\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 [1920] [1921] [1922] Underfull \hbox (badness 10000) in paragraph at lines 2911--2913 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1923] [1924] [1925] [1926] Underfull \hbox (badness 1762) in paragraph at lines 3205--3208 []\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 = [1927] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3298--3298 []\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 '[] [1928] Underfull \hbox (badness 2452) in paragraph at lines 3374--3377 []\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 [1929] [1930] [1931] [1932] [1933] [1934] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3783--3783 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1935] [1936] Underfull \hbox (badness 10000) in paragraph at lines 3867--3871 []\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 3935--3943 []\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 [1937] Underfull \hbox (badness 1231) in paragraph at lines 4012--4024 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able [1938] Underfull \hbox (badness 10000) in paragraph at lines 4026--4031 []\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 4026--4031 \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 4026--4031 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1939] Underfull \hbox (badness 4660) in paragraph at lines 4146--4149 \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 4170--4172 []\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 [1940] [1941] [1942] Underfull \hbox (badness 1565) in paragraph at lines 4355--4359 []\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 [1943] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4438--4438 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1944] Underfull \hbox (badness 1931) in paragraph at lines 4473--4480 []\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) [1945] [1946] [1947] [1948] [1949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4797--4797 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4868 ...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.4868 ...mat Unordered and Ordered Lists}{format} [1951] [1952] [1953] [1954] [1955] [1956] [1957] [1958] Underfull \hbox (badness 1622) in paragraph at lines 5387--5391 []\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 [1959] [1960] [1961] [1962] [1963] Overfull \hbox (96.78088pt too wide) in paragraph at lines 5709--5709 []\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 5721--5721 []\T1/pcr/m/n/10 tail(x, n = 6L, keepnums = TRUE, addrownums, ...) # exported as tail.matrix()[] [1964] [1965] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5854--5854 [] \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 5855--5855 [] \T1/pcr/m/n/9 ## --- because [i,j]-indexing of data frames *also* drops "other" attributes ..[] [1966] [1967] [1968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6065--6065 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1969] Underfull \hbox (badness 10000) in paragraph at lines 6149--6151 []\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 [1970] Underfull \hbox (badness 1502) in paragraph at lines 6198--6203 []\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 6198--6203 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1971] [1972] Underfull \hbox (badness 10000) in paragraph at lines 6371--6380 []\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 6371--6380 \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 [1973] Underfull \hbox (badness 2150) in paragraph at lines 6435--6438 []\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 6451--6454 []\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 [1974] [1975] Underfull \hbox (badness 3118) in paragraph at lines 6573--6575 []\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 [1976] [1977] Underfull \hbox (badness 5091) in paragraph at lines 6747--6749 []\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 [1978] Underfull \hbox (badness 5331) in paragraph at lines 6763--6769 []\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 6763--6769 \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 6763--6769 \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 6777--6784 []\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 6792--6802 \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 [1979] Underfull \hbox (badness 10000) in paragraph at lines 6835--6838 []\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 6835--6838 \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 6843--6846 []\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 [1980] Underfull \hbox (badness 2376) in paragraph at lines 6914--6921 []\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 6914--6921 \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 6914--6921 \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 6922--6925 []\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 [1981] Underfull \hbox (badness 1314) in paragraph at lines 7001--7008 []\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 7048--7051 []\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 7048--7051 \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 7081--7086 [][][]\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 , [1982] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7104--7104 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 7140--7144 []\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 7154--7157 []\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 [1983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7201--7201 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1984] [1985] Underfull \hbox (badness 4132) in paragraph at lines 7325--7327 []\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 [1986] [1987] [1988] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7492--7492 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1989] [1990] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7635--7635 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1991] Underfull \hbox (badness 10000) in paragraph at lines 7675--7677 []\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 [1992] [1993] Underfull \hbox (badness 10000) in paragraph at lines 7863--7865 []\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 7868--7870 []\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 [1994] [1995] [1996] [1997] Underfull \hbox (badness 1859) in paragraph at lines 8096--8099 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1998] Underfull \hbox (badness 1655) in paragraph at lines 8190--8193 []\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 8201--8201 []\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 8209--8209 []\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):[] [1999] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8217--8217 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [2000] Underfull \hbox (badness 1917) in paragraph at lines 8304--8306 []\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 , [2001] [2002] [2003] [2004] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8576--8576 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8577--8577 [] \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 8578--8578 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [2005] Underfull \hbox (badness 10000) in paragraph at lines 8606--8608 []\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 8620--8622 []\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 8628--8633 []\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, [2006] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8674--8674 [] \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 8675--8675 [] \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[] [2007] [2008] Underfull \hbox (badness 10000) in paragraph at lines 8804--8809 []\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 8804--8809 [][]\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 8804--8809 \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 8811--8814 \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 [2009] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8927--8927 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8928--8928 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [2010] [2011] [2012] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9101--9101 [] \T1/pcr/m/n/9 "S original, "),[] [2013] Underfull \hbox (badness 1789) in paragraph at lines 9232--9234 []\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 [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] Underfull \hbox (badness 5203) in paragraph at lines 9805--9808 []\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 [2023] [2024] Underfull \hbox (badness 1394) in paragraph at lines 10031--10038 \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 [2025] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10055--10055 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2026] [2027] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10216--10216 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2028] [2029] [2030] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10397--10397 []\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[] [2031] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10483--10483 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10486--10486 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10491--10491 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2032] Underfull \hbox (badness 2027) in paragraph at lines 10563--10566 []\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 [2033] [2034] [2035] [2036] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10835--10835 []\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 10836--10836 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] Underfull \hbox (badness 10000) in paragraph at lines 10843--10848 []\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 10843--10848 \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 10843--10848 \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 [2037] [2038] [2039] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11076--11076 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2040] [2041] [2042] [2043] [2044] Underfull \hbox (badness 10000) in paragraph at lines 11337--11341 \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 11355--11355 []\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 11360--11360 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2045] [2046] Overfull \hbox (18.78088pt too wide) in paragraph at lines 11493--11493 []\T1/pcr/m/n/10 4. | \-base:::tryCatchOne(expr, names, parentenv, handler s[[1L]])[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 11494--11494 []\T1/pcr/m/n/10 5. | \-base:::doTryCatch(return(expr), name, parentenv, handler)[] [2047] [2048] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11629--11629 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2049] Underfull \hbox (badness 1917) in paragraph at lines 11753--11756 []\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 11753--11756 \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 [2050] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11776--11776 []\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 '[] [2051] Underfull \hbox (badness 10000) in paragraph at lines 11839--11841 []\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 [2052] Underfull \hbox (badness 6725) in paragraph at lines 11889--11898 \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 11889--11898 \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 11889--11898 \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 11889--11898 \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 [2053] Underfull \hbox (badness 3646) in paragraph at lines 12015--12017 [][][]$\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 / [2054] Overfull \hbox (30.78088pt too wide) in paragraph at lines 12053--12053 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2055] [2056] [2057] Underfull \hbox (badness 10000) in paragraph at lines 12234--12238 []\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 12265--12271 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2058] [2059] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12441--12441 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [2060] Underfull \hbox (badness 1009) in paragraph at lines 12459--12471 []\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 12499--12501 []\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 [2061] Underfull \hbox (badness 1043) in paragraph at lines 12542--12547 []\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 [2062] [2063] [2064] [2065] Underfull \hbox (badness 1888) in paragraph at lines 12835--12838 []\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 12852--12855 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2066] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12898--12898 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] [2067] Underfull \hbox (badness 2158) in paragraph at lines 12953--12956 []\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 13001--13001 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2068] [2069] [2070] Underfull \hbox (badness 2302) in paragraph at lines 13158--13160 []\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 [2071] Underfull \hbox (badness 3333) in paragraph at lines 13265--13267 []\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- [2072] [2073] [2074] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13432--13432 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13456--13461 []\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 13465--13468 []\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 13465--13468 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2075] Underfull \hbox (badness 1442) in paragraph at lines 13492--13496 []\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 13524--13524 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2076] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13555--13555 []\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 13562--13562 []\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 13564--13564 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2077] [2078] Underfull \hbox (badness 10000) in paragraph at lines 13732--13734 []\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 [2079] [2080] [2081] Underfull \hbox (badness 6300) in paragraph at lines 13889--13896 []\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 13889--13896 \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 13889--13896 \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$"\T1/ptm/m/n/10 ) and [2082] [2083] Underfull \hbox (badness 2020) in paragraph at lines 14058--14074 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 14058--14074 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2084] [2085] Underfull \hbox (badness 5022) in paragraph at lines 14198--14202 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 14205--14208 [][][]$\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 14205--14208 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ 92 _ [2086] [2087] [2088] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14369--14369 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2089] [2090] [2091] [2092] [2093] [2094] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14809--14809 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14815--14815 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14836--14838 []\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 14851--14855 \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 14865--14869 []\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 14871--14876 []\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 14871--14876 \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 14871--14876 \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 14877--14879 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2095] Underfull \hbox (badness 10000) in paragraph at lines 14907--14912 \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 14907--14912 \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 14928--14933 []\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 14936--14939 [][][]\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 , [2096] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14990--14990 []\T1/pcr/m/n/9 ## Not run: url.show("https://www.stats.ox.ac.uk/pub/datasets/ csb/ch3a.txt") [2097] [2098] [2099] Underfull \hbox (badness 10000) in paragraph at lines 15192--15195 [][][]\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 15192--15195 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2100] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15208--15208 []\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:[] [2101] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15275--15275 [] \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 15297--15297 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2102] [2103] Underfull \hbox (badness 1297) in paragraph at lines 15428--15430 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2104] Underfull \hbox (badness 4036) in paragraph at lines 15475--15477 []\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. [2105] [2106] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15612--15612 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2107] Underfull \hbox (badness 1715) in paragraph at lines 15664--15667 []\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 15709--15711 []\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 = [2108] [2109] [2110]) [2111] [2112] (./KernSmooth-pkg.tex Chapter 15. [2113] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2114] [2115] [2116] [2117] [2118] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2119] [2120] [2121] [2122]) (./MASS-pkg.tex Chapter 16. [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] [2132] [2133] 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))[] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] 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"),[] [2157] [2158] [2159] [2160] 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 [2161] [2162] [2163] 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 , [2164] [2165] 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 [2166] [2167] [2168] 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, ...)[] [2169] 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")[] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] [2180] [2181] 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 [2182] [2183] [2184] [2185] [2186] [2187] [2188] 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", ...)[] [2189] [2190] [2191] 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, [2192] [2193] [2194] [2195] [2196] [2197] [2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] 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) [2206] 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") [2207] [2208]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} [2209] [2210] 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 [2211] [2212] [2213] [2214] 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)))[] [2215] 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"))[] [2216] [2217] [2218] [2219] [2220] [2221] 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"))[] [2222] 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 ) = [2223] 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)[] [2224] [2225] 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 [2226] [2227] 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")[] [2228] 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"), ...)[] [2229] [2230] [2231] [2232] [2233] [2234] 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 [2235] [2236] 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 [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245] [2246] [2247] [2248] [2249] [2250] [2251] [2252] [2253] [2254] [2255] [2256] 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, ...)[] [2257] 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), [2258] 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)[] [2259] [2260] [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] [2270] [2271]) (./Matrix-pkg.tex [2272] 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 [2273] 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 [2274] 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 [2275] 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 [2276] [2277] Underfull \hbox (badness 5147) in paragraph at lines 496--499 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2278] Underfull \hbox (badness 5119) in paragraph at lines 509--513 []\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 513--518 [][][]\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 543--543 []\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 545--545 []\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 554--554 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2279] [2280] Overfull \hbox (52.98038pt too wide) in paragraph at lines 668--668 []\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 669--669 []\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 670--670 []\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 683--683 [] \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 684--684 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] [2281] Overfull \hbox (4.38043pt too wide) in paragraph at lines 689--689 []\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 758--762 \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 / [2282] [2283] [2284] Overfull \hbox (72.78088pt too wide) in paragraph at lines 973--973 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2285] [2286] [2287]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) has been already used, duplicate ignored \relax l.1160 ...- '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.1160 ...- 'Matrix' S4 Generic and Methods}{chol} [2288pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} pdfTeX warning (ext4): destination with the same identifier ( name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1231 \end{Value} ] Underfull \hbox (badness 2285) in paragraph at lines 1249--1254 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the Overfull \hbox (31.3804pt too wide) in paragraph at lines 1295--1295 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2289] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1390--1390 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) [2290] Underfull \hbox (badness 2277) in paragraph at lines 1418--1421 []\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 [2291] Underfull \hbox (badness 1609) in paragraph at lines 1465--1469 []\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 1492--1492 []\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 1506--1506 []\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[] [2292] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1514--1514 []\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 1561--1568 []\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 1561--1568 \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 [2293] Underfull \hbox (badness 1783) in paragraph at lines 1596--1600 []\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 1612--1618 \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.1653 ... 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.1653 ... 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.1654 \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.1675 \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.1686 \aliasA{rowSums}{colSums}{rowSums} [2294] Underfull \hbox (badness 2922) in paragraph at lines 1740--1744 []\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 1740--1744 \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 1751--1754 [][][]\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 [2295] [2296] [2297] Underfull \hbox (badness 3547) in paragraph at lines 1905--1908 []\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 [2298] [2299] [2300] [2301] Underfull \hbox (badness 1484) in paragraph at lines 2267--2269 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2302] Underfull \hbox (badness 7379) in paragraph at lines 2363--2365 []\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 [2303] [2304] [2305] Underfull \hbox (badness 4846) in paragraph at lines 2639--2643 []\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 2644--2648 []\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 2651--2654 []\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 ; [2306] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2698--2698 [] \T1/pcr/m/n/10 .trDiagonal(n, x = 1, uplo = "U", unitri=TRUE, kind)[] Underfull \hbox (badness 2689) in paragraph at lines 2707--2709 []\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 2711--2716 []\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 2711--2716 [][]\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 [2307] Underfull \hbox (badness 1097) in paragraph at lines 2734--2737 []\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 2747--2752 [][]\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 [2308] Underfull \hbox (badness 3646) in paragraph at lines 2986--2989 []\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 3018--3020 []\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 3021--3025 []\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 3030--3036 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2309] Underfull \hbox (badness 10000) in paragraph at lines 3037--3041 []\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 3047--3051 [][][]\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 [2310] [2311] Underfull \hbox (badness 10000) in paragraph at lines 3231--3233 []\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 3278--3280 [][][]\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) [2312] Underfull \hbox (badness 2469) in paragraph at lines 3398--3401 []\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 [2313] [2314] Underfull \hbox (badness 10000) in paragraph at lines 3563--3567 []\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 3563--3567 \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 , [2315] Underfull \hbox (badness 2285) in paragraph at lines 3613--3616 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2316] [2317] Underfull \hbox (badness 10000) in paragraph at lines 3760--3765 []\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 3760--3765 \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 3772--3775 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2318] Underfull \hbox (badness 10000) in paragraph at lines 3848--3850 []\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 [2319] [2320] [2321] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4058--4058 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4126--4130 []\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 [2322] Underfull \hbox (badness 10000) in paragraph at lines 4135--4138 []\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 4135--4138 \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 4140--4144 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2323] [2324] Underfull \hbox (badness 3158) in paragraph at lines 4323--4327 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2325] [2326] [2327] [2328] Overfull \hbox (90.78033pt too wide) in paragraph at lines 4562--4562 [] \T1/pcr/m/n/9 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB /Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4565--4565 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4569--4569 []\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 4572--4572 []\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 4582--4582 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2329] [2330] [2331] [2332] Underfull \hbox (badness 10000) in paragraph at lines 4884--4889 []\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 , [2333] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4965--4965 []\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 4967--4967 [] \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 4971--4971 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2334] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4978--4978 [] \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 '[] [2335] [2336] Underfull \hbox (badness 4120) in paragraph at lines 5122--5125 []\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 5159--5159 []\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 5165--5165 [] \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 5166--5166 [] \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 5170--5170 []\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 5172--5172 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2337] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5179--5179 []\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 5182--5182 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2338] Underfull \hbox (badness 1817) in paragraph at lines 5271--5280 []\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 5313--5315 []\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 5315--5318 []\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 5328--5331 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2339] Underfull \hbox (badness 4765) in paragraph at lines 5346--5349 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2340] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5406--5406 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2341] [2342] [2343] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5664--5664 []\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[] [2344] Underfull \hbox (badness 10000) in paragraph at lines 5747--5750 [][][]\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 5758--5758 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2345] Underfull \hbox (badness 1622) in paragraph at lines 5795--5800 []\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 5795--5800 \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 [2346] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5856--5856 []\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 5857--5857 [] \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 5864--5864 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2347] Underfull \hbox (badness 1062) in paragraph at lines 5993--5996 []\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 [2348] Underfull \hbox (badness 6063) in paragraph at lines 6022--6025 []\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 [2349] Underfull \hbox (badness 2635) in paragraph at lines 6134--6139 []\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 6134--6139 \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 Underfull \hbox (badness 10000) in paragraph at lines 6142--6145 []\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., [2350] Underfull \hbox (badness 10000) in paragraph at lines 6252--6262 \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 6252--6262 [][]\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 [2351] Underfull \hbox (badness 3179) in paragraph at lines 6334--6337 []\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 [2352] Underfull \hbox (badness 10000) in paragraph at lines 6432--6435 []\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., [2353] Underfull \hbox (badness 10000) in paragraph at lines 6507--6510 []\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., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6523--6523 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2354] Underfull \hbox (badness 2443) in paragraph at lines 6562--6568 []\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 6562--6568 [][]\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 6583--6586 []\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 [2355] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6653--6653 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2356] [2357] Underfull \hbox (badness 10000) in paragraph at lines 6794--6797 []\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 Underfull \hbox (badness 1490) in paragraph at lines 6816--6818 []\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) [2358] [2359] Underfull \hbox (badness 5036) in paragraph at lines 6896--6900 []\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 6896--6900 \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 [2360]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6995 \aliasA{det}{Matrix-class}{det} [2361] Underfull \hbox (badness 10000) in paragraph at lines 7098--7101 Underfull \hbox (badness 10000) in paragraph at lines 7108--7110 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2362]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \relax l.7171 ...*\%}{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.7279 ...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.7379 ...tcrossprod}{matrix-products}{tcrossprod} Underfull \hbox (badness 1881) in paragraph at lines 7477--7483 \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 [2363pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tc rossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7535 ] Underfull \hbox (badness 10000) in paragraph at lines 7550--7553 []\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 7550--7553 \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 7553--7558 []\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 7553--7558 \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 7558--7562 []\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 7558--7562 \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 7568--7569 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2364] [2365] Underfull \hbox (badness 1009) in paragraph at lines 7704--7706 []\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 Underfull \hbox (badness 1062) in paragraph at lines 7749--7752 []\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 [2366] Underfull \hbox (badness 6063) in paragraph at lines 7783--7786 []\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 10000) in paragraph at lines 7839--7841 []\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 [2368] [2369] Overfull \hbox (85.38034pt too wide) in paragraph at lines 7941--7941 [] \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 7981--7981 []\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 [2370] Underfull \hbox (badness 2635) in paragraph at lines 8046--8051 []\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 8046--8051 \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 8054--8057 []\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., [2371] Underfull \hbox (badness 3482) in paragraph at lines 8128--8134 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2372] Underfull \hbox (badness 1867) in paragraph at lines 8248--8250 []\T1/ptm/m/n/10 fast sim- [2373]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8288 \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.8288 \HeaderA{norm}{Matrix Norms}{norm} [2374] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8375--8375 []\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 8376--8376 []\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 8377--8377 []\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 8490--8500 []\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 , [2375] Underfull \hbox (badness 3179) in paragraph at lines 8561--8564 []\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 [2376] Underfull \hbox (badness 10000) in paragraph at lines 8651--8654 []\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., [2377] Underfull \hbox (badness 10000) in paragraph at lines 8727--8730 []\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., [2378] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8743--8743 []\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 [2379] Underfull \hbox (badness 10000) in paragraph at lines 8853--8855 []\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 8855--8858 []\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 8861--8868 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2380] [2381] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8954--8954 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8957--8957 []\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 8959--8959 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8963--8963 []\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 8964--8964 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8989--8999 []\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 8989--8999 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2382] [2383]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.9090 \aliasA{qr}{qr-methods}{qr} [2384] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9163--9163 []\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 9174--9174 []\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 9178--9178 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9195--9195 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9203--9203 []\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 [2385] Underfull \hbox (badness 10000) in paragraph at lines 9260--9266 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9277--9280 []\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 [2386] [2387] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9376--9376 []\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 9392--9392 []\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 9398--9398 []\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 9399--9399 []\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.9418 ... the Reciprocal Condition Number}{rcond} [2388] [2389] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9531--9531 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2390] [2391] [2392] Underfull \hbox (badness 2351) in paragraph at lines 9722--9730 []\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 9722--9730 \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 [2393] [2394] Underfull \hbox (badness 1558) in paragraph at lines 9867--9870 []\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 [2395] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9929--9929 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9933--9933 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2396]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9995 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 10092--10092 [] \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 10097--10097 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2397] Underfull \hbox (badness 1616) in paragraph at lines 10132--10144 []\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 10149--10152 []\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 10158--10165 []\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 10171--10181 []\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 10171--10181 \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 10198--10202 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10205--10207 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines [2398] Underfull \hbox (badness 10000) in paragraph at lines 10228--10229 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10234--10236 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10238--10239 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10246--10249 [][][]\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 10264--10264 []\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 10268--10268 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2399] Underfull \hbox (badness 10000) in paragraph at lines 10289--10292 []\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 10317--10319 []\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 10325--10328 []\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 10325--10328 \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 10336--10340 []\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 10336--10340 \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 [2400] Underfull \hbox (badness 1668) in paragraph at lines 10351--10356 [][][]\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 10372--10378 []\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- [2401] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10431--10431 [] \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 10432--10432 [] \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 10433--10433 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2402] [2403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10617--10617 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] [2404] Underfull \hbox (badness 1668) in paragraph at lines 10659--10664 [][][]\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 [2405] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10756--10756 []\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 10760--10760 []\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 10761--10761 []\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 10766--10766 []\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 10769--10769 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2406] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10792--10792 []\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 10793--10793 []\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 10819--10819 []\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 10821--10821 [] \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 10823--10823 [] \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 [2407] [2408] Underfull \hbox (badness 10000) in paragraph at lines 10968--10972 [][][]\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.11008 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2409] [2410] Underfull \hbox (badness 10000) in paragraph at lines 11138--11140 []\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 11166--11166 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] [2411] Underfull \hbox (badness 5036) in paragraph at lines 11194--11196 []\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 11328--11334 []\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 11328--11334 \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 , [2412] Underfull \hbox (badness 10000) in paragraph at lines 11401--11404 []\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 [2413] Underfull \hbox (badness 10000) in paragraph at lines 11419--11424 []\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 11434--11436 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2414] [2415] Underfull \hbox (badness 2698) in paragraph at lines 11559--11565 [][][]\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, [2416] Underfull \hbox (badness 10000) in paragraph at lines 11652--11654 []\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 11670--11675 []\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 11670--11675 \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 [2417] Underfull \hbox (badness 2591) in paragraph at lines 11678--11683 \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 11750--11752 []\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., [2418] [2419] Underfull \hbox (badness 6641) in paragraph at lines 11836--11839 []\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 11876--11880 []\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 11876--11880 \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 [2420] [2421] Underfull \hbox (badness 7649) in paragraph at lines 11983--11985 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2422] [2423] [2424] Underfull \hbox (badness 7362) in paragraph at lines 12184--12186 []\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 12222--12222 []\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 12223--12223 []\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)[] [2425] [2426] [2427] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12365--12365 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12378--12378 [] \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 12383--12383 [] \T1/pcr/m/n/9 sapply(rho, function(x) c(2* determinant(update(C2, nWC, 1/ x))$modulus))[] [2428] Underfull \hbox (badness 6910) in paragraph at lines 12557--12559 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2429] [2430] [2431]) (./boot-pkg.tex [2432] Chapter 18. [2433] [2434] [2435] [2436] [2437] [2438] [2439] 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"), [2440] 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- [2441] [2442] [2443] 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 , [2444] 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 [2445] [2446] 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" [2447] 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 [2448] [2449] [2450] [2451] 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- [2452] [2453] [2454] [2455] [2456] 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), [2457] [2458] [2459] Underfull \vbox (badness 10000) has occurred while \output is active [2460] 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),[] [2461] 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. [2462] [2463] [2464] 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 [2465] 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 , [2466] [2467] 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 [2468] [2469] [2470] [2471] [2472] 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,[] [2473] [2474] [2475] 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 , [2476] 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)) [2477] [2478] [2479] 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 [2480] [2481] [2482] [2483] [2484] [2485] [2486] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3838--3838 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2487] [2488] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3977--3977 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2489] [2490] [2491] Underfull \hbox (badness 10000) in paragraph at lines 4190--4192 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2492] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4259--4259 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2493] [2494] Underfull \hbox (badness 10000) in paragraph at lines 4362--4364 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4371--4375 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2495] [2496] [2497] [2498] [2499] [2500] [2501] [2502] [2503] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2504] [2505] [2506] [2507] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2508] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5317--5317 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5866--5866 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2517] 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 [2518] 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 [2519] [2520] [2521] [2522] 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). [2523] [2524] 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[] [2525] [2526] [2527] 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 [2528] [2529] 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),[] [2530] [2531] [2532] [2533] [2534] [2535] [2536] [2537]) (./class-pkg.tex [2538] Chapter 19. [2539] [2540] [2541] [2542] [2543] [2544] [2545] [2546] [2547] [2548] [2549] [2550] [2551] [2552] [2553] [2554]) (./cluster-pkg.tex Chapter 20. [2555] 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 [2556] [2557] 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]))[] [2558] [2559] Underfull \vbox (badness 10000) has occurred while \output is active [2560] [2561] 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, ...)[] [2562] [2563] 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)[] [2564] 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 [2565] [2566] 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 , [2567] 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 [2568] 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), ...)[] [2569] 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, [2570] [2571] 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 [2572] 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 [2573] 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."),[] [2574] [2575] 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 [2576] 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[] [2577] 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 [2578] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1636--1636 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2579] [2580] 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 = [2581] 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, [2582] [2583] [2584] [2585] [2586] 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. [2587] [2588] 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 , [2589] 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 [2590] 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 , [2591] [2592] [2593] 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 ):[] [2594] 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"),[] [2595] [2596] [2597] 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):[] [2598] [2599] 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")[] [2600] [2601] [2602] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3277--3277 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3278--3278 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2603] Underfull \hbox (badness 10000) in paragraph at lines 3345--3348 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2604] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3395--3395 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$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, ...)[] [2605] [2606] [2607] 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 [2608] 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 , [2609] 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 , [2610] [2611] [2612] 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 , [2613] 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 [2614] [2615] [2616] [2617] 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, ...)[] [2618] [2619] 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[] [2620] [2621] [2622] [2623] [2624] [2625] [2626] 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:[] [2627] 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:[] [2628]) (./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,[] [2629] 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 [2630] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2631] [2632] [2633]) (./foreign-pkg.tex [2634] Chapter 22. [2635] 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 [2636] [2637] 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 , [2638] 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, [2639] [2640] [2641] 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,[] [2642] 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 [2643] 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 [2644] 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,[] [2645] 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="")[] [2646] [2647] 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])[] [2648] [2649] 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) [2650] 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))) [2651] [2652] Underfull \hbox (badness 10000) in paragraph at lines 1076--1077 [][][]$\T1/pcr/m/n/10 https : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1112--1112 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2653] [2654] Underfull \hbox (badness 10000) in paragraph at lines 1270--1276 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2655] Underfull \hbox (badness 2088) in paragraph at lines 1296--1299 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2656]) (./lattice-pkg.tex Chapter 23. [2657] Underfull \hbox (badness 2073) in paragraph at lines 117--121 \T1/ptm/m/n/10 pro-vide a holis-tic in-tro-duc-tion to the Trel-lis paradigm: [ ][]$\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 / [2658] [2659] 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"),[] [2660] 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"),[] [2661] [2662] [2663] [2664] 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 [2665] [2666] [2667] [2668] 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. [2669] 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 [2670] [2671] 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 [2672] [2673] [2674] 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 , [2675] 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 , [2676] Underfull \vbox (badness 10000) has occurred while \output is active [2677] 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 [2678] 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 [2679] [2680] [2681] [2682] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2683] 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 [2684] [2685] [2686] 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"),[] [2687] [2688] [2689] [2690] [2691] 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"),[] [2692] [2693] 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 [2694] Underfull \hbox (badness 6758) in paragraph at lines 2888--2892 []\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 2888--2892 \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 2894--2896 []\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 2946--2952 []\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 2946--2952 \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 2946--2952 \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 Underfull \hbox (badness 2486) in paragraph at lines 2970--2974 []\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 [2695] [2696] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3073--3073 [] \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 3074--3074 [] \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 3075--3075 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3086--3086 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] [2697] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3098--3098 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] Underfull \hbox (badness 2913) in paragraph at lines 3156--3163 []\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 3156--3163 \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 [2698] [2699] [2700] [2701]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3444 \aliasA{parallel}{B\_08\_splom}{parallel} [2702] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3486--3486 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3509--3509 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2703] [2704] [2705] [2706] [2707] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3845--3845 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2708] Underfull \hbox (badness 2277) in paragraph at lines 3935--3939 []\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 3935--3939 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2709] [2710] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4065--4065 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) Underfull \hbox (badness 1173) in paragraph at lines 4074--4078 []\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 Underfull \hbox (badness 3219) in paragraph at lines 4101--4103 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2711] Underfull \hbox (badness 1728) in paragraph at lines 4118--4122 \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 Underfull \hbox (badness 5161) in paragraph at lines 4183--4187 []\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 4183--4187 \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 [2712] [2713] Underfull \hbox (badness 1067) in paragraph at lines 4297--4307 []\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 4297--4307 \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 4297--4307 \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 4297--4307 \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 4297--4307 \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 [2714] Underfull \hbox (badness 1701) in paragraph at lines 4322--4325 []\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 4325--4327 []\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 [2715] [2716] [2717] [2718] [2719] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4729--4729 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 []\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 . [2722] [2723] Underfull \hbox (badness 1442) in paragraph at lines 5048--5051 []\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 [2724] [2725] [2726] [2727] [2728] [2729] Underfull \hbox (badness 3646) in paragraph at lines 5382--5385 [][][]\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 5412--5412 [] \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 5413--5413 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2730] Underfull \hbox (badness 10000) in paragraph at lines 5501--5504 []\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 5501--5504 \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 [2731] Underfull \hbox (badness 1635) in paragraph at lines 5527--5532 []\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 [2732] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5678--5678 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2733] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5692--5692 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5693--5693 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5696--5696 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5699--5699 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5701--5701 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5707--5707 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5708--5708 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5709--5709 [] \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi ch.panel",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5710--5710 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5711--5711 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5727--5729 []\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 5738--5740 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2734] [2735] Underfull \hbox (badness 2538) in paragraph at lines 5863--5867 \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 5874--5881 []\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 5874--5881 \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 [2736] [2737] Underfull \hbox (badness 10000) in paragraph at lines 6027--6031 [][][]\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 , [2738] [2739] Underfull \hbox (badness 4242) in paragraph at lines 6174--6179 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2740] [2741] Underfull \hbox (badness 3601) in paragraph at lines 6290--6295 []\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 6290--6295 \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 [2742] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6377--6377 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2743] [2744] Underfull \hbox (badness 1888) in paragraph at lines 6509--6516 \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 [2745] Underfull \hbox (badness 10000) in paragraph at lines 6566--6569 []\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 6566--6569 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 1320) in paragraph at lines 6972--6979 []\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 6972--6979 \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 [2752] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7042--7042 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2753] Underfull \hbox (badness 10000) in paragraph at lines 7072--7076 []\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 7072--7076 \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 [2754] Underfull \hbox (badness 10000) in paragraph at lines 7177--7180 \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 [2755] [2756] Underfull \hbox (badness 2012) in paragraph at lines 7343--7346 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2757] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7389--7389 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2758] [2759] Underfull \hbox (badness 2644) in paragraph at lines 7530--7534 \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 7543--7546 []\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 [2760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7613--7613 [] \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 7623--7623 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2761] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7684--7684 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7689--7689 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2762] [2763] [2764] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7874--7874 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2765] Underfull \hbox (badness 1436) in paragraph at lines 7929--7935 []\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 [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 8487--8490 []\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 8487--8490 \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 [2774] [2775] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8662--8662 []\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 8663--8663 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8675--8675 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2776] Underfull \hbox (badness 3118) in paragraph at lines 8694--8697 []\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 [2777] Underfull \hbox (badness 1515) in paragraph at lines 8770--8774 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2778] Underfull \hbox (badness 6316) in paragraph at lines 8876--8881 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2779] [2780] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8983--8983 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2781] [2782] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9122--9122 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2783] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9181--9185 []\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 9181--9185 \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 [2784] [2785] [2786] [2787] [2788] [2789] [2790] Underfull \hbox (badness 7238) in paragraph at lines 9639--9643 []\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 9639--9643 \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 , [2791] [2792] [2793]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9870 \aliasA{melanoma}{H\_melanoma}{melanoma} [2794] [2795] [2796] Underfull \hbox (badness 10000) in paragraph at lines 10032--10037 \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 10105--10105 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2797] [2798]) (./mgcv-pkg.tex Chapter 24. [2799] [2800] 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,[] [2801] 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. [2802] [2803] [2804] [2805] Underfull \hbox (badness 10000) in paragraph at lines 377--384 [][][]\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 377--384 [][]\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 377--384 [][]\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 , [2806] Overfull \hbox (4.38043pt too wide) in paragraph at lines 420--420 []\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)+[] [2807] [2808] [2809] Underfull \hbox (badness 2922) in paragraph at lines 632--633 []\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 [2810] [2811] Underfull \hbox (badness 1406) in paragraph at lines 702--703 []\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 [2812] [2813] Underfull \hbox (badness 1158) in paragraph at lines 812--814 []\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 [2814] Underfull \hbox (badness 1259) in paragraph at lines 875--876 []\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). [2815] Underfull \vbox (badness 10000) has occurred while \output is active [2816] [2817] [2818] [2819] [2820] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1224--1224 []\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 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)[] [2821] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1242--1242 [] \T1/pcr/m/n/9 plot(b$y[oy],rs[oy,ii[1]],ylim=c(-3,3),type="l",ylab="scor e residuals",[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1254--1254 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1263--1263 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in d]),type="l",[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1265--1265 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Underfull \vbox (badness 10000) has occurred while \output is active [2822] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] [2823] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1379--1379 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2824] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1390--1390 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1424--1424 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] [2833] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1930--1930 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2834] [2835] [2836] [2837] [2838] [2839] Underfull \hbox (badness 1052) in paragraph at lines 2318--2326 \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 2335--2335 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2347--2350 []\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 2360--2364 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2840] Underfull \hbox (badness 1043) in paragraph at lines 2386--2391 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2841] [2842] [2843] Underfull \hbox (badness 1043) in paragraph at lines 2551--2557 \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 [2844] Underfull \hbox (badness 10000) in paragraph at lines 2687--2693 [][][]\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 2687--2693 [][]\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 2687--2693 [][]\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 , [2845] [2846] Underfull \vbox (badness 10000) has occurred while \output is active [2847] Underfull \vbox (badness 10000) has occurred while \output is active [2848] [2849] [2850] [2851] [2852] [2853] [2854] [2855] [2856] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3343--3343 [] \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 3346--3346 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2857] [2858] [2859] [2860] [2861] [2862] [2863] [2864] Underfull \hbox (badness 5189) in paragraph at lines 3821--3825 []\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 [2865] [2866] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3938--3938 []\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 [2867] [2868] [2869] Underfull \hbox (badness 1184) in paragraph at lines 4107--4111 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2870] [2871] [2872] [2873] [2874] [2875] [2876] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4553--4553 [] \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)+[] [2877] [2878] [2879] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4703--4703 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2880] [2881] Underfull \hbox (badness 1142) in paragraph at lines 4828--4832 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2882] Underfull \hbox (badness 10000) in paragraph at lines 4900--4909 []\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 [2883] [2884] Underfull \hbox (badness 5970) in paragraph at lines 5017--5023 [][][]\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 5017--5023 [][]\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 . [2885] Underfull \vbox (badness 10000) has occurred while \output is active [2886] [2887] [2888] [2889] Underfull \hbox (badness 1577) in paragraph at lines 5369--5372 []\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 5376--5377 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2890] [2891] [2892] [2893] [2894] [2895] [2896] Underfull \hbox (badness 6708) in paragraph at lines 5765--5766 []\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 [2897] [2898] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5814--5814 [] \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 5839--5839 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] [2899] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5868--5868 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] [2900] [2901] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5990--5990 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2902] [2903] [2904] [2905] [2906] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6327--6327 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, [2907] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6329--6329 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 6350--6354 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2908] [2909] [2910] Underfull \vbox (badness 10000) has occurred while \output is active [2911] [2912] [2913] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6669--6669 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2914] [2915] [2916] [2917] Underfull \vbox (badness 10000) has occurred while \output is active [2918] Underfull \vbox (badness 10000) has occurred while \output is active [2919] [2920] [2921] Overfull \hbox (52.98038pt too wide) in paragraph at lines 7098--7098 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 7125--7125 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2922] [2923] [2924] [2925] [2926] [2927] [2928] [2929] [2930] Underfull \hbox (badness 1242) in paragraph at lines 7668--7669 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2931] [2932] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7755--7755 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2933] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7818--7818 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] [2934] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7837--7837 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943] [2944] [2945] [2946] [2947] [2948] [2949] [2950] [2951] [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] Underfull \hbox (badness 10000) in paragraph at lines 9057--9060 []\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 9057--9060 \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 9057--9060 \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 . [2954] Underfull \hbox (badness 10000) in paragraph at lines 9113--9116 []\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 9113--9116 \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 [2955] [2956] [2957] [2958] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9333--9333 []\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 9334--9334 [] \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 9337--9337 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2959] [2960] Underfull \hbox (badness 1629) in paragraph at lines 9495--9500 \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 [2961] [2962] Underfull \vbox (badness 10000) has occurred while \output is active [2963] [2964] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9706--9706 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2965] Underfull \hbox (badness 1062) in paragraph at lines 9743--9747 []\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 9743--9747 \T1/ptm/m/n/10 are ex-cluded. To avoid sup-ply-ing co-vari-ate val-ues for ex-c luded terms, [2966] [2967] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9874--9874 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2968] [2969] [2970] Underfull \vbox (badness 10000) has occurred while \output is active [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10147--10147 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] Underfull \vbox (badness 10000) has occurred while \output is active [2972] Underfull \hbox (badness 1205) in paragraph at lines 10185--10187 []\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 10185--10187 \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 10191--10196 []\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 [2973] Underfull \hbox (badness 1205) in paragraph at lines 10275--10277 []\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 10275--10277 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2974] Underfull \hbox (badness 10000) in paragraph at lines 10344--10347 []\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 10344--10347 [][]\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, [2975] [2976] [2977] Underfull \hbox (badness 1253) in paragraph at lines 10474--10476 []\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, [2978] [2979] [2980] [2981] [2982] Underfull \hbox (badness 1946) in paragraph at lines 10727--10734 []\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 10727--10734 \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 10727--10734 \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 Underfull \hbox (badness 2846) in paragraph at lines 10735--10738 []\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 10735--10738 \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. [2983] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10801--10801 []\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 10811--10811 []\T1/pcr/m/n/9 ## The effect of the new factor levels (or any interaction inv olving them)[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 10842--10845 []\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 , [2985] [2986] [2987] [2988] [2989] Overfull \hbox (36.78088pt too wide) in paragraph at lines 11143--11143 []\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) [2990] [2991] [2992] [2993] [2994] Overfull \hbox (31.3804pt too wide) in paragraph at lines 11474--11474 []\T1/pcr/m/n/9 dat <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(runif( n))) + (eps/del))[] [2995] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11513--11513 [] \T1/pcr/m/n/9 true <- mu + (del * sigma) * sinh((1/del) * asinh(qnorm(qq)) + (eps/del))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11527--11527 []\T1/pcr/m/n/9 b <- gam(list(accel~s(times, k=20, bs = "ad"), ~ s(times, k = 10), ~ 1, ~ 1),[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 11531--11531 []\T1/pcr/m/n/9 xSeq <- data.frame(cbind("accel" = rep(0, 1e3), "times" = seq( 2, 58, length.out = 1e3)))[] Underfull \vbox (badness 10000) has occurred while \output is active [2996] [2997] Underfull \hbox (badness 3861) in paragraph at lines 11628--11631 []\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 11637--11637 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE,[] [2998] Underfull \hbox (badness 10000) in paragraph at lines 11654--11658 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11694--11698 []\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- [2999] [3000] [3001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11838--11838 [] \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 11849--11854 []\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 [3002] Underfull \hbox (badness 1803) in paragraph at lines 11926--11930 \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 11938--11950 \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 [3003] Underfull \hbox (badness 2401) in paragraph at lines 11955--11959 \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 11955--11959 \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 , [3004] [3005] [3006] Underfull \hbox (badness 6876) in paragraph at lines 12150--12156 [][][]\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 [3007] Underfull \hbox (badness 10000) in paragraph at lines 12191--12192 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3008] [3009] Underfull \hbox (badness 10000) in paragraph at lines 12308--12309 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3010] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12362--12362 [] \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 12374--12374 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] [3011] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12386--12386 [] \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 12391--12391 [] \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 12397--12397 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12398--12398 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [3012] Underfull \hbox (badness 10000) in paragraph at lines 12467--12469 []\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 12467--12469 \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 [3013] [3014] Underfull \hbox (badness 10000) in paragraph at lines 12597--12598 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3015] [3016] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12678--12678 []\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 12679--12679 []\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[] [3017] [3018] Underfull \hbox (badness 10000) in paragraph at lines 12830--12831 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3019] [3020] [3021] [3022] [3023] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13080--13080 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [3024] Underfull \hbox (badness 10000) in paragraph at lines 13141--13143 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3025] [3026] Underfull \hbox (badness 10000) in paragraph at lines 13300--13303 []\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 13300--13303 \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 13300--13303 \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" [3027] [3028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13384--13384 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [3029] Underfull \hbox (badness 10000) in paragraph at lines 13429--13435 []\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 13429--13435 \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- [3030] [3031] [3032] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13643--13643 []\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 [3033] Underfull \vbox (badness 10000) has occurred while \output is active [3034] Underfull \hbox (badness 10000) in paragraph at lines 13746--13754 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13772--13773 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3035] [3036] [3037] [3038] [3039] Underfull \hbox (badness 3396) in paragraph at lines 14032--14035 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 14077--14079 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3040] [3041] [3042] [3043] [3044] [3045] Underfull \hbox (badness 10000) in paragraph at lines 14358--14361 []\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 14358--14361 \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 Underfull \hbox (badness 10000) in paragraph at lines 14391--14395 [][][]\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 14391--14395 [][]\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 14391--14395 [][]\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 , [3046] [3047] [3048] [3049] [3050] Underfull \hbox (badness 2158) in paragraph at lines 14681--14681 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3051] [3052] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14760--14760 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3053] [3054] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14894--14894 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3055] [3056] Underfull \hbox (badness 4846) in paragraph at lines 15025--15028 []\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 [3057] [3058] [3059] [3060] [3061] [3062] [3063] [3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Overfull \hbox (24.78088pt too wide) in paragraph at lines 16228--16228 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3077] [3078] [3079] Overfull \hbox (54.78088pt too wide) in paragraph at lines 16438--16438 []\T1/pcr/m/n/10 XWXd(X,w,k,ks,ts,dt,v,qc,nthreads=1,drop=NULL,ar.stop=-1,ar.r ow=-1,ar.w=-1, Overfull \hbox (48.78088pt too wide) in paragraph at lines 16440--16440 []\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 16442--16442 []\T1/pcr/m/n/10 diagXVXd(X,V,k,ks,ts,dt,v,qc,drop=NULL,nthreads=1,lt=NULL,rt= NULL)[] [3080] Underfull \hbox (badness 10000) in paragraph at lines 16462--16463 []\T1/ptm/m/n/10 Negative to ig-nore. Oth-er-wise sum rows Underfull \hbox (badness 1668) in paragraph at lines 16462--16463 \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 [3081] [3082] [3083] [3084] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16650--16650 []\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 16651--16651 []\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 16663--16663 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3085] [3086] [3087]) (./nlme-pkg.tex [3088] Chapter 25. [3089] 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 [3090] 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 [3091] [3092] [3093] [3094] [3095] 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,[] [3096] [3097] 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 --------------------------- ---------------[] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] 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"),[] [3106] 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 [3107] [3108] [3109] [3110] [3111] [3112] [3113] 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 , [3114] 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 [3115] [3116] [3117] [3118] [3119] 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 , [3120] 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")[] [3121] 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 [3122] [3123] 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 , [3124] 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,[] [3125] [3126] [3127] [3128] [3129] [3130] [3131] [3132] 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 , [3133] [3134] [3135] [3136] [3137] [3138pdfTeX warning (ext4): destination with the same identifier (name{Rfn.corMatrix.corCompSymm}) has been already used, d uplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.3193 ...trix(cs1, covariate = 1:4, corr = FALSE) ] [3139] [3140] [3141] [3142] [3143] [3144] 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 , [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] [3166] [3167] [3168] 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 , [3169] [3170] [3171] [3172] [3173] [3174] [3175] 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 , [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] 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 [3185] 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 , [3186] 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 , [3187] 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[] [3188] [3189] [3190] [3191] 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 , [3192] 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, [3193] 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 [3194] 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[] [3195] [3196] [3197] 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 , [3198] 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 [3199] [3200] [3201] 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 , [3202] [3203] [3204] 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 , [3205] [3206] [3207] 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 [3208] [3209] [3210] [3211] [3212] [3213] [3214] [3215] 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 [3216] [3217] [3218] [3219] [3220] 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 [3221] 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} [3222] [3223] [3224] [3225] [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] 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") [3234] 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 [3235] [3236] [3237] [3238]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} [3239] 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 [3240] [3241] [3242] [3243] [3244] [3245] [3246] [3247] 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 [3248] [3249] [3250] 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, [3251] 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 [3252] [3253] [3254] 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,[] [3255] [3256] 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[][][] [3257] 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[] [3258] [3259] [3260] [3261] 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)[] [3262] [3263] [3264] [3265] [3266] [3267] 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(*)) [3268] [3269] [3270] [3271] [3272] [3273] 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 , [3274] [3275] [3276] [3277] 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 , [3278] [3279] [3280] [3281] [3282] 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 [3283] [3284] 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 , [3285] 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 , [3286] [3287] [3288] [3289] [3290] [3291] [3292] [3293] [3294] 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(*)) [3295] [3296] [3297] [3298] [3299] 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)[] [3300] 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 [3301] 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,[] [3302] 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 [3303] 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 [3304] 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 , [3305] 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 , [3306] [3307] [3308] [3309] 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 [3310] [3311] [3312] [3313] 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"),[] [3314] [3315] [3316] [3317] [3318] [3319] [3320] [3321] [3322]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} [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] 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- [3333] 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)[] [3334] 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 [3335] [3336] 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, ...)[] [3337] [3338] [3339] [3340] [3341] 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 , [3342] 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, ...)[] [3343] [3344] [3345] [3346] [3347] [3348] [3349] 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 [3350] [3351] [3352] [3353] [3354] 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 [3355] 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 [3356] [3357] [3358] [3359] 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 , [3360] [3361] [3362] [3363] 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[] [3364] [3365] [3366] [3367] [3368] [3369] 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 , [3370] 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 [3371] 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 [3372] 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 [3373] 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 [3374] 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 , [3375] 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 [3376] [3377] 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 [3378] [3379] 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 [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388]) (./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} [3389] 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,[] [3390] [3391] [3392] 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,[] [3393] 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)[] [3394] [3395] 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,[] [3396]) (./rpart-pkg.tex Chapter 27. [3397] [3398] [3399] [3400] 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, ...)[] [3401] [3402] [3403] [3404] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\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 [3405] [3406] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3407] [3408] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3409] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3410] [3411] [3412] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\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 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3413] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\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 [3414] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\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 1288--1288 []\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 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3415] [3416] [3417] [3418] [3419] [3420] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\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 ', [3421] [3422] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3423] [3424] [3425]) (./spatial-pkg.tex [3426] Chapter 28. [3427] [3428] [3429] [3430] [3431] [3432] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3433] [3434] [3435] [3436] [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445]) (./survival-pkg.tex [3446] Chapter 29. [3447] [3448] 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.[] [3449] [3450] 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 [3451] [3452]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} [3453] 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)[] [3454] 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)[] [3455] [3456] Overfull \vbox (3.85637pt too high) has occurred while \output is active [3457] [3458] 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"),[] [3459] [3460] 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,[] [3461] [3462] [3463] 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[] [3464] [3465] 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) [3466] 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} [3467] 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, ...)[] [3468] [3469] [3470] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1572--1572 [] \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 1619--1619 []\T1/pcr/m/n/10 cox.zph(fit, transform="km", terms=TRUE, singledf=FALSE, glob al=TRUE) [3471] [3472] [3473] [3474] [3475] Underfull \hbox (badness 10000) in paragraph at lines 1935--1950 []\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 1935--1950 \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 1935--1950 \T1/ptm/m/n/10 cial terms, e.g., \T1/pcr/m/n/10 survival::coxph(survival:Surv(t ime,status) ~ age + [3476] Underfull \hbox (badness 1337) in paragraph at lines 2019--2023 [][][]\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 , [3477] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2074--2074 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2646--2646 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2673--2673 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3486] [3487] [3488] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2905--2905 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3489] [3490] [3491] Overfull \vbox (31.18587pt too high) has occurred while \output is active [3492] [3493] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3246--3246 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3494] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3281--3281 [] \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 3295--3297 []\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 3306--3306 [] \T1/pcr/m/n/10 conf.type = c("log", "log-log", "plain", "logit", "ar csin"),[] [3495] [3496] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3440--3440 [] \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 )))[] [3497] [3498] Overfull \hbox (467.89665pt too wide) in alignment at lines 3581--3581 [] [] Underfull \vbox (badness 10000) has occurred while \output is active [3499] Overfull \vbox (8.56093pt too high) has occurred while \output is active [3500] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3703--3703 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3501] [3502] [3503] [3504] [3505] [3506] [3507] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4092--4092 [] \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 )))[] [3508] [3509] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4238--4238 []\T1/pcr/m/n/9 tdata <- data.frame(x= lung$age, y = 10*log(lung$age-35) + rno rm(228, 0, 2))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4243--4243 []\T1/pcr/m/n/9 knots <- unlist(attributes(fit1$model[[2]])[c(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Boundary.knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 , \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 knots\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4247--4247 []\T1/pcr/m/n/9 unname(coef(fit1)[-1] - coef(fit1)[1]) # differences: yhat[2: 4] - yhat[1][] [3510] Underfull \vbox (badness 1527) has occurred while \output is active [3511] [3512] [3513] [3514] [3515] [3516] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4664--4664 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3517] [3518] [3519] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4894--4894 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3520] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5020--5020 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5028--5028 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3522] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5114--5114 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3523] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5192--5192 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars"), expand=FALSE , ...)[] [3524] Underfull \hbox (badness 1852) in paragraph at lines 5264--5266 []\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 [3525] [3526] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5389--5389 []\T1/pcr/m/n/10 pseudo(fit, times, type, addNA=TRUE, data.frame=FALSE, minus1 =FALSE, ...) [3527] [3528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5491--5491 []\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 5492--5492 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3529] [3530] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5656--5656 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5758--5758 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] [3532] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5779--5779 []\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 5781--5781 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3533] [3534] [3535] [3536] [3537] [3538] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6296--6296 [] \T1/pcr/m/n/10 collapse=FALSE, weighted= (type %in% c("dfbeta", "dfbe tas")), ...)[] [3539] [3540] [3541] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6476--6476 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 6488--6491 \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 [3542] [3543] [3544] [3545] [3546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6796--6796 []\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 6797--6797 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), lung)[] [3547] [3548] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6927--6927 []\T1/pcr/m/n/10 rttright(formula, data, weights, subset, na.action, times, id , timefix = TRUE) [3549] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7001--7001 []\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.7005 ...ata from a soldering experiment}{solder} [3550] [3551] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7111--7111 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3552] [3553] [3554] [3555] [3556] Overfull \hbox (42.78088pt too wide) in paragraph at lines 7475--7475 []\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 7476--7476 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3557] [3558] [3559] [3560] Overfull \hbox (54.78088pt too wide) in paragraph at lines 7787--7787 [] \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 ),[] [3561] [3562] [3563] [3564] Underfull \hbox (badness 1253) in paragraph at lines 8076--8079 []\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 [3565] [3566] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8206--8206 []\T1/pcr/m/n/10 survcheck(formula, data, subset, na.action, id, istate, istat e0="(s0)", [3567] Underfull \hbox (badness 10000) in paragraph at lines 8328--8337 []\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 8328--8337 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3568] [3569] Overfull \hbox (36.7804pt too wide) in paragraph at lines 8424--8424 [] \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 8442--8442 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 8484--8490 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3570] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8536--8536 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3572] [3573] [3574] Underfull \hbox (badness 10000) in paragraph at lines 8847--8852 [][][]\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 , [3575] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8865--8865 [] \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 8866--8866 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3576] [3577] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9062--9062 [] \T1/pcr/m/n/10 stype=1, ctype=1, id, cluster, robust, istate, timefi x=TRUE,[] [3578] [3579] Underfull \hbox (badness 3058) in paragraph at lines 9195--9200 []\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 9195--9200 \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 9195--9200 \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 9195--9200 \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 [3580] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9325--9325 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3581] [3582] [3583] [3584] [3585] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9710--9710 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3586] Underfull \hbox (badness 1354) in paragraph at lines 9751--9755 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3587] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9797--9797 []\T1/pcr/m/n/10 survConcordance(formula, data, weights, subset, na.action) # use concordance [3588] [3589] Underfull \hbox (badness 2035) in paragraph at lines 9961--9968 \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 9961--9968 \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 9961--9968 \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 [3590] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10041--10041 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3591] [3592] [3593] Overfull \hbox (31.3804pt too wide) in paragraph at lines 10198--10198 [] \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 )[] [3594] [3595] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10330--10330 [] \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 10333--10333 [] \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 )[] [3596] [3597] [3598] [3599] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10643--10643 []\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 10644--10644 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3600] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10650--10650 [] \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 10652--10652 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3601] [3602] [3603] [3604] [3605] [3606] [3607] Overfull \hbox (12.78088pt too wide) in paragraph at lines 11093--11093 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3608] [3609] [3610]) (./fullrefman.ind [3611] [3612] [3613] [3614] [3615] [3616] [3617] [3618] [3619] [3620] [3621] [3622] [3623] [3624] [3625] [3626] [3627] [3628] [3629] [3630] [3631] [3632] [3633] [3634] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2579--2581 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2581--2583 []| \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 2583--2585 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , [3635] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2585--2587 []| \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 2587--2589 []| \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 2589--2591 []| \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 2591--2593 []| \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 2593--2595 []| \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 2595--2597 []| \T1/pcr/m/n/10 smooth.construct.re.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.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2599--2601 []| \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 2601--2603 []| \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 2603--2605 []| \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 2605--2607 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3636] [3637] [3638] [3639] [3640] [3641] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3213--3215 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3215--3217 []| \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 3217--3219 []| \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 3219--3221 []| \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 3221--3223 []| \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 3223--3225 []| \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 3225--3227 []| \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 3227--3229 []| \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 3229--3231 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 3231--3233 []| \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 3233--3235 []| \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 3235--3237 []| \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 3237--3239 []| \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 3239--3241 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3642] Overfull \hbox (19.3567pt too wide) in paragraph at lines 3394--3396 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] Overfull \hbox (62.8567pt too wide) in paragraph at lines 4494--4496 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at 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cbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7237--7239 []\T1/pcr/m/n/10 cbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7239--7241 []\T1/pcr/m/n/10 cbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 7241--7243 []\T1/pcr/m/n/10 cbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 7243--7245 []\T1/pcr/m/n/10 cbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 7245--7247 []\T1/pcr/m/n/10 cbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 7247--7249 []\T1/pcr/m/n/10 cbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 7249--7251 []\T1/pcr/m/n/10 cbind2,sparseMatrix,sparseMatrix-method [3670] Overfull \hbox (10.01662pt too wide) in paragraph at lines 7499--7501 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3671] [3672] [3673] Overfull \hbox (50.8567pt too wide) in paragraph at lines 7998--8000 []\T1/pcr/m/n/10 coerce,atomicVector,dsparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8000--8002 []\T1/pcr/m/n/10 coerce,atomicVector,sparseVector-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 8002--8004 []\T1/pcr/m/n/10 coerce,BunchKaufman,lMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 8008--8010 []\T1/pcr/m/n/10 coerce,CHMfactor,sparseMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 8010--8012 []\T1/pcr/m/n/10 coerce,CHMfactor,triangularMatrix-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 8014--8016 []\T1/pcr/m/n/10 coerce,CsparseMatrix,denseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 8016--8018 []\T1/pcr/m/n/10 coerce,CsparseMatrix,lMatrix-method Overfull \hbox (56.8567pt too 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too wide) in paragraph at lines 11376--11378 []\T1/pcr/m/n/10 expand,MatrixFactorization-method Overfull \hbox (10.01662pt too wide) in paragraph at lines 11376--11378 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 MatrixFactorization-class\T1/ptm/m/it/10 )\T1/ ptm/m/n/10 , [3698] Overfull \hbox (46.01662pt too wide) in paragraph at lines 11577--11579 \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 , [3699] Overfull \hbox (56.8567pt too wide) in paragraph at lines 11917--11919 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,character-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11919--11921 []\T1/pcr/m/n/10 forceSymmetric,corMatrix,missing-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 11921--11923 []\T1/pcr/m/n/10 forceSymmetric,CsparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 11923--11925 []\T1/pcr/m/n/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (56.8567pt too wide) 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(\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3705] Overfull \hbox (20.8567pt too wide) in paragraph at lines 13270--13272 []\T1/pcr/m/n/10 groupGenericFunctionWithTrace-class [3706] [3707] [3708] [3709] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14044--14046 []\T1/pcr/m/n/10 is.infinite,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14046--14048 []\T1/pcr/m/n/10 is.infinite,dsparseMatrix-method [3710] Overfull \hbox (2.8567pt too wide) in paragraph at lines 14054--14056 []\T1/pcr/m/n/10 is.infinite,nsparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14219--14221 []\T1/pcr/m/n/10 isDiagonal,diagonalMatrix-method [3711] Overfull \hbox (8.8567pt too wide) in paragraph at lines 14225--14227 []\T1/pcr/m/n/10 isDiagonal,symmetricMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 14227--14229 []\T1/pcr/m/n/10 isDiagonal,triangularMatrix-method Overfull \hbox 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wide) in paragraph at lines 14470--14472 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14472--14474 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 14474--14476 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14478--14480 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14480--14482 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 14482--14484 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 14484--14486 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14486--14488 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3713] [3714] [3715] [3716] Overfull \hbox (50.8567pt too wide) in paragraph at lines 15288--15290 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15294--15296 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 15296--15298 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15298--15300 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15300--15302 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15302--15304 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 15308--15310 []\T1/pcr/m/n/10 Logic,lMatrix,sparseVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15318--15320 []\T1/pcr/m/n/10 Logic,lsCMatrix,lsCMatrix-method 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too wide) in paragraph at lines 16962--16964 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16968--16970 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16986--16988 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16992--16994 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16994--16996 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3725] Overfull \hbox (26.8567pt too wide) in paragraph at lines 17252--17254 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 17258--17260 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method [3726] Overfull \hbox (8.8567pt too wide) in paragraph at lines 17270--17272 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 17272--17274 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 17274--17276 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17276--17278 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 17278--17280 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17298--17300 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17300--17302 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17316--17318 []\T1/pcr/m/n/10 Ops,ldiMatrix,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17336--17338 []\T1/pcr/m/n/10 Ops,lsparseMatrix,lsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17338--17340 []\T1/pcr/m/n/10 Ops,lsparseMatrix,nsparseMatrix-method [3727] Overfull \hbox (26.8567pt too wide) in paragraph at lines 17358--17360 []\T1/pcr/m/n/10 Ops,ndenseMatrix,ndenseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 17366--17368 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17370--17372 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17372--17374 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 17374--17376 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 17394--17396 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 17396--17398 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method 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\hbox (46.01662pt too wide) in paragraph at lines 18944--18946 \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 18947--18949 \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 18949--18951 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18951--18953 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18953--18955 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18955--18957 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18957--18959 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18959--18961 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18961--18963 \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 18963--18965 \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 18967--18969 \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 18969--18971 \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 18971--18973 \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 18973--18975 \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 18975--18977 \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 18977--18979 \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 , [3735] [3736] Overfull \hbox (4.01662pt too wide) in paragraph at lines 19326--19328 \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 19398--19400 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3737] [3738] [3739] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19868--19870 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19877--19879 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19879--19881 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19881--19883 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19883--19885 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19895--19897 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method [3740] Overfull \hbox (14.8567pt too wide) in paragraph at lines 19905--19907 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19920--19922 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19926--19928 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 20046--20048 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3741] Overfull \hbox (26.8567pt too wide) in paragraph at lines 20256--20258 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20258--20260 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20260--20262 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 20262--20264 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method [3742] Overfull \hbox (32.8567pt too wide) in paragraph at lines 20266--20268 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20268--20270 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[]\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20302--20304 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20304--20306 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 20306--20308 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 20308--20310 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20310--20312 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20312--20314 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 20314--20316 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20343--20345 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 20345--20347 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 20347--20349 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20349--20351 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20353--20355 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20357--20359 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20361--20363 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20365--20367 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 20369--20371 []\T1/pcr/m/n/10 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in paragraph at lines 22258--22260 []\T1/pcr/m/n/10 solve,dtrMatrix,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22270--22272 []\T1/pcr/m/n/10 solve,Matrix,diagonalMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 22282--22284 []\T1/pcr/m/n/10 solve,Matrix,sparseVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 22284--22286 []\T1/pcr/m/n/10 solve,MatrixFactorization,ANY-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22286--22288 []\T1/pcr/m/n/10 solve,MatrixFactorization,missing-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 22288--22290 []\T1/pcr/m/n/10 solve,MatrixFactorization,numeric-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 22300--22302 []\T1/pcr/m/n/10 solve,TsparseMatrix,missing-method [3754] Overfull \hbox (52.01662pt too wide) in paragraph at lines 22446--22448 \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 , [3755] [3756] Overfull \hbox (44.8567pt too wide) in paragraph at lines 22887--22889 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_depends Overfull \hbox (44.8567pt too wide) in paragraph at lines 22889--22891 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_results Overfull \hbox (44.8567pt too wide) in paragraph at lines 22891--22893 []\T1/pcr/m/n/10 summarize_check_packages_in_dir_timings [3757] [3758] [3759] [3760] [3761] Overfull \hbox (32.8567pt too wide) in paragraph at lines 23776--23778 []\T1/pcr/m/n/10 tcrossprod,ANY,symmetricMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 23778--23780 []\T1/pcr/m/n/10 tcrossprod,ANY,TsparseMatrix-method Overfull \hbox (80.8567pt too wide) in paragraph at lines 23780--23782 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 23782--23784 []\T1/pcr/m/n/10 tcrossprod,CsparseMatrix,ddenseMatrix-method Overfull \hbox (86.8567pt too 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Transcript written on fullrefman.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/doc/manual' + exit 0 Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.26433 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + /bin/chmod -Rf u+rwX -- /usr/src/tmp/R-base-buildroot + : + /bin/rm -rf -- /usr/src/tmp/R-base-buildroot + PATH=/usr/libexec/rpm-build:/usr/src/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games + cd R-4.0.5 + make 'INSTALL=/usr/libexec/rpm-build/install -p' install DESTDIR=/usr/src/tmp/R-base-buildroot install-pdf install-info make: Entering directory '/usr/src/RPM/BUILD/R-4.0.5' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib/R make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/m4' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/m4' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tools' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory 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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-4.0.5/doc/manual' make: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5' + mv /usr/src/tmp/R-base-buildroot/usr/lib/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib/libR.so ++ relative /usr/lib/libR.so /usr/lib/R/lib/libR.so + ln -s ../../libR.so /usr/src/tmp/R-base-buildroot/usr/lib/R/lib/libR.so + ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib/libR-2.11.so ++ relative /usr/share/doc/R-4.0 /usr/lib/R/doc + ln -s ../../share/doc/R-4.0 /usr/src/tmp/R-base-buildroot/usr/lib/R/doc ++ relative /usr/include/R /usr/lib/R/include + ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib/R/include + cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib/R/bin/R ++ relative /usr/lib/R/bin/R /usr/bin/R + ln -snfv ../lib/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R '/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib/R/bin/R' + cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib/R/bin/Rscript ++ relative /usr/lib/R/bin/Rscript /usr/bin/Rscript + ln -snfv ../lib/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript '/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib/R/bin/Rscript' + fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot + mkdir -p /usr/src/tmp/R-base-buildroot/etc/R + mv /usr/src/tmp/R-base-buildroot/usr/lib/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/ + rmdir /usr/src/tmp/R-base-buildroot/usr/lib/R/etc ++ relative /etc/R /usr/lib/R/etc + ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib/R/etc + mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications + cat + '[' -f /usr/src/tmp/R-base-buildroot/usr/lib/R/bin/libtool ']' ++ relative /usr/bin/libtool /usr/lib/R/bin/libtool + ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib/R/bin/libtool '/usr/src/tmp/R-base-buildroot/usr/lib/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/lib/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib/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/lib/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -pthread -L/usr/local/lib -L${rlibdir} -lR' --> '-Wl,--export-dynamic -pthread -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/lib: (from :0) libR.so -> libR.so ./usr/lib/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) verify-elf: WARNING: ./usr/lib/R/library/mgcv/libs/mgcv.so: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/lib/R/library/Matrix/libs/Matrix.so: uses non-LFS functions: fopen verify-elf: WARNING: ./usr/lib/R/library/foreign/libs/foreign.so: uses non-LFS functions: fgetpos fopen fsetpos Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.99212 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.0.5 + export TZ= + TZ= + make check make: Entering directory '/usr/src/RPM/BUILD/R-4.0.5' make[1]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/tests/Examples' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' running strict specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/tests' running sloppy specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to './eval-etc-2.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' ...383,387c383,387 < [1,] -0.4023 0.2877 -0.3638 0.5 0.6108 < [2,] -0.5338 -0.3474 -0.5742 -0.5 -0.1207 < [3,] -0.4177 -0.5380 0.6384 0.0 0.3585 < [4,] -0.4959 0.0733 0.1273 0.5 -0.6946 < [5,] -0.3644 0.7084 0.3378 -0.5 0.0369 --- > [1,] -0.4023 0.2877 0.3638 0.5 0.6108 > [2,] -0.5338 -0.3474 0.5742 -0.5 -0.1207 > [3,] -0.4177 -0.5380 -0.6384 0.0 0.3585 > [4,] -0.4959 0.0733 -0.1273 0.5 -0.6946 > [5,] -0.3644 0.7084 -0.3378 -0.5 0.0369 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 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' checking Sys.timezone ... make[4]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' running code in 'timezone.R' ...make[4]: *** [Makefile.common:108: timezone.Rout] Error 1 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' Sys.timezone() appears unknown make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' running regression tests ... make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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 '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-4.0.5/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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' ...1319,1320c1319,1320 < [7] "number" "index" "replValue" < [10] "numLike" "Mnumeric" "replValueSp" --- > [7] "index" "replValue" "numLike" > [10] "number" "Mnumeric" "replValueSp" 1326,1327c1326,1327 < [7] "number" "index" "replValue" < [10] "numLike" "Mnumeric" "NumOrMyClass" --- > [7] "index" "replValue" "numLike" > [10] "number" "Mnumeric" "NumOrMyClass" OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/tests' running tests of Internet functions make[3]: Entering directory '/usr/src/RPM/BUILD/R-4.0.5/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-4.0.5/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5/tests' make: Leaving directory '/usr/src/RPM/BUILD/R-4.0.5' + exit 0 Processing files: R-base-4.0.5-alt1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.21016 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-4.0.5 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-4.0.5 + exit 0 warning: File listed twice: /usr/lib/R/library/KernSmooth/html warning: File listed twice: /usr/lib/R/library/KernSmooth/html/00Index.html 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/usr/lib/R/library/utils/html/utils-package.html warning: File listed twice: /usr/lib/R/library/utils/html/vignette.html warning: File listed twice: /usr/lib/R/library/utils/html/warnErrList.html warning: File listed twice: /usr/lib/R/library/utils/html/winDialog.html warning: File listed twice: /usr/lib/R/library/utils/html/winMenus.html warning: File listed twice: /usr/lib/R/library/utils/html/winProgressBar.html warning: File listed twice: /usr/lib/R/library/utils/html/winextras.html warning: File listed twice: /usr/lib/R/library/utils/html/write.table.html warning: File listed twice: /usr/lib/R/library/utils/html/zip.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.IlnfCc find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib) lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib/libR.so: 1255 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2021-04-30 11:18:08.871039427 +0000 +++ filter-provides-deps 2021-04-30 11:18:08.873039354 +0000 @@ -1 +1,2 @@ libR.so = set: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 +libR-2.11.so = set: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 Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.8nrbDf find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/MASS/libs/MASS.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/foreign/libs/foreign.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/graphics/libs/graphics.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/grid/libs/grid.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/lattice/libs/lattice.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/nnet/libs/nnet.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/rpart/libs/rpart.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/spatial/libs/spatial.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/survival/libs/survival.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/library/utils/libs/utils.so: underlinked libraries: /lib/liblzma.so.5 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/modules/internet.so: underlinked libraries: /lib/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib/R/modules/lapack.so: underlinked libraries: /lib/libdl.so.2 shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib/R/share/sh/echo.sh is not executable find-requires: FINDPACKAGE-COMMANDS: cat grep sh Provides: libR.so = set: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, libR-2.11.so = set: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 Requires: /bin/sh, /lib/ld-linux.so.2, coreutils, grep, ld-linux.so.2 >= set:ihbW3, ld-linux.so.2(GLIBC_2.1), libX11.so.6 >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6 >= set:ljat5WdZ0, libXt.so.6 >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1 >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.0), libc.so.6(GLIBC_2.1), libc.so.6(GLIBC_2.1.3), libc.so.6(GLIBC_2.11), libc.so.6(GLIBC_2.15), libc.so.6(GLIBC_2.16), libc.so.6(GLIBC_2.17), libc.so.6(GLIBC_2.2), libc.so.6(GLIBC_2.27), libc.so.6(GLIBC_2.28), libc.so.6(GLIBC_2.3), libc.so.6(GLIBC_2.3.4), libc.so.6(GLIBC_2.4), libc.so.6(GLIBC_2.6), libc.so.6(GLIBC_2.7), libc.so.6(GLIBC_2.8), libcairo.so.2 >= set:mgBeCp25NOIyrlQHFsTG1phW01upHNOW8SpbeVohC5Pwchq6KplkgZIPAQh02Zr5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libcurl.so.4 >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libdl.so.2(GLIBC_2.0), libdl.so.2(GLIBC_2.1), libgobject-2.0.so.0 >= set:ml6W90, libicui18n.so.67 >= set:ro8QoNSM7N8mnCGZIS8D3qcHd0, libicuuc.so.67 >= set:pm6zZ0Uf099eu65yc, libjpeg.so.62 >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4 >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITkXeYooZo0Vt8WFt6QYIOIZmWow6fzRMDwp9MGO0mKS7RhQ3GVqZb9tmpDVzoHaQByPHyhixGdIIpkSTvJQ1ifnZkTXQSQh1gp2EYbdIC9EweDuafV2FMlA13g1MukRM6QdwV1AkslhaI00W830w1g7el, liblzma.so.5 >= set:kgIy0DJdgZuHF5yXYppdmYIDYAa1, liblzma.so.5(XZ_5.0), libm.so.6(GLIBC_2.0), libm.so.6(GLIBC_2.1), libm.so.6(GLIBC_2.23), libm.so.6(GLIBC_2.29), libopenblas.so.0 >= set:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, libpango-1.0.so.0 >= set:miPmiaRgNQCfq9fPhNQgw41BExdcI9mdt, libpangocairo-1.0.so.0 >= set:jhWzZgd5, libpcre2-8.so.0 >= set:kfq9tJAJZakapZcr8gHlRiHX2PuBva483hqVseVZw6HMZF1, libpng16.so.16 >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0), libpthread.so.0(GLIBC_2.0), libpthread.so.0(GLIBC_2.2), libreadline.so.7 >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPRdDv8sK6EUfgoB1, libtiff.so.5 >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1 >= 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.sudEhc Creating R-base-debuginfo package Processing files: R-full-4.0.5-alt1 Requires: R-devel = 4.0.5-alt1, R-tcltk = 4.0.5-alt1, R-doc-html = 4.0.5-alt1, gcc-c++, gcc-fortran, liblapack-devel, make Processing files: R-devel-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.gW6Qtf find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib/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,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.AIXdlc find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,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) = 4.0.5 Requires: /bin/sh, /usr/bin/libtool, /usr/lib/R/lib/libR.so, /usr/lib/pkgconfig, coreutils Requires(pre): R-base = 4.0.5-alt1 Requires(postun): R-base = 4.0.5-alt1 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.QMMZTc Processing files: R-tcltk-4.0.5-alt1 warning: File listed twice: /usr/lib/R/library/tcltk/html warning: File listed twice: /usr/lib/R/library/tcltk/html/00Index.html warning: File listed twice: /usr/lib/R/library/tcltk/html/R.css warning: File listed twice: /usr/lib/R/library/tcltk/html/TclInterface.html warning: File listed twice: /usr/lib/R/library/tcltk/html/TkCommands.html warning: File listed twice: /usr/lib/R/library/tcltk/html/TkWidgetcmds.html warning: File listed twice: /usr/lib/R/library/tcltk/html/TkWidgets.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tclServiceMode.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tcltk-defunct.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tcltk-package.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tkProgressBar.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tkStartGUI.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tk_choose.dir.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tk_choose.files.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tk_messageBox.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tk_select.list.html warning: File listed twice: /usr/lib/R/library/tcltk/html/tkpager.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.DZX2Vc find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,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.0Iqhif find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,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 = 4.0.5-alt1, libR.so >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE1atzKMNmL5wj1XTzOOW0cQ6tL1K6wORZKdU6tciyJjuVTkIHiOQO1D71LZCEMTQx9TL6bQBvkaBdv04KsFO982AnbOG1iel0emzQxmCwIskwuypnxI3MGYYBtx1X1, libc.so.6(GLIBC_2.0), libc.so.6(GLIBC_2.1.3), libc.so.6(GLIBC_2.3.4), libc.so.6(GLIBC_2.4), libc.so.6(GLIBC_2.7), libtcl8.6.so >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so >= 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.FHkjvf Creating R-tcltk-debuginfo package Processing files: R-doc-html-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.mZseHd find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.NgmHXf find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: R-base = 4.0.5-alt1 Processing files: R-doc-pdf-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.RCLUug find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.SEQyxe find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 4.0.5, R-base < 4.0.5 Processing files: R-doc-info-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.bRbOLf find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.LsVMig find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 4.0.5, R-base < 4.0.5 Processing files: R-base-debuginfo-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.uTaeDd 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.qkAvud find-requires: running scripts (debuginfo) Provides: debug(libR.so) Requires: R-base = 4.0.5-alt1, /usr/lib/debug/lib/ld-linux.so.2.debug, debug(ld-linux.so.2), debug(libX11.so.6), debug(libXmu.so.6), debug(libXt.so.6), debug(libbz2.so.1), debug(libc.so.6), debug(libcairo.so.2), debug(libcurl.so.4), debug(libdl.so.2), debug(libgobject-2.0.so.0), debug(libicui18n.so.67), debug(libicuuc.so.67), debug(libjpeg.so.62), debug(liblapack.so.4), debug(liblzma.so.5), debug(libm.so.6), debug(libopenblas.so.0), debug(libpango-1.0.so.0), debug(libpangocairo-1.0.so.0), debug(libpcre2-8.so.0), debug(libpng16.so.16), debug(libpthread.so.0), debug(libreadline.so.7), debug(libtiff.so.5), debug(libz.so.1) Processing files: R-tcltk-debuginfo-4.0.5-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.cxjPag find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.fWCu1f find-requires: running scripts (debuginfo) Requires: R-tcltk = 4.0.5-alt1, debug(libR.so), debug(libc.so.6), debug(libtcl8.6.so), debug(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-4.0.5/include/R_ext also prunning dir /usr/src/debug/R-4.0.5/src/include also prunning dir /usr/src/debug/R-4.0.5/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 7 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/lib/R/COPYING /usr/lib/R/SVN-REVISION Wrote: /usr/src/RPM/RPMS/i586/R-base-4.0.5-alt1.i586.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-full-4.0.5-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/i586/R-devel-4.0.5-alt1.i586.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/i586/R-tcltk-4.0.5-alt1.i586.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-4.0.5-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-4.0.5-alt1.noarch.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-4.0.5-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/i586/R-base-debuginfo-4.0.5-alt1.i586.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/i586/R-tcltk-debuginfo-4.0.5-alt1.i586.rpm (w2.lzdio) 2274.92user 172.30system 23:48.17elapsed 171%CPU (0avgtext+0avgdata 677016maxresident)k 0inputs+0outputs (0major+19516932minor)pagefaults 0swaps 2505.35user 202.43system 28:08.28elapsed 160%CPU (0avgtext+0avgdata 677016maxresident)k 2068728inputs+0outputs (0major+20914022minor)pagefaults 0swaps --- R-base-debuginfo-4.0.5-alt1.i586.rpm.repo 2021-04-04 10:34:12.000000000 +0000 +++ R-base-debuginfo-4.0.5-alt1.i586.rpm.hasher 2021-04-30 11:19:40.948697113 +0000 @@ -663,3 +663,3 @@ Requires: R-base = 4.0.5-alt1:sisyphus+268929.100.1.1 -Requires: rpmlib(PayloadIsLzma) +Requires: rpmlib(PayloadIsXz) Provides: debug(libR.so) --- R-doc-pdf-4.0.5-alt1.noarch.rpm.repo 2021-04-04 10:26:42.000000000 +0000 +++ R-doc-pdf-4.0.5-alt1.noarch.rpm.hasher 2021-04-30 11:19:41.062692975 +0000 @@ -10,3 +10,3 @@ /usr/share/doc/R-4.0/manual/fullrefman.pdf 100644 -Requires: rpmlib(PayloadIsLzma) +Requires: rpmlib(PayloadIsXz) Provides: R-doc-pdf = 4.0.5-alt1:sisyphus+268929.100.1.1