<86>Jan 31 04:18:51 userdel[906146]: delete user 'rooter'
<86>Jan 31 04:18:51 userdel[906146]: removed shadow group 'rooter' owned by 'rooter'
<86>Jan 31 04:18:51 groupadd[906246]: group added to /etc/group: name=rooter, GID=972
<86>Jan 31 04:18:51 groupadd[906246]: group added to /etc/gshadow: name=rooter
<86>Jan 31 04:18:51 groupadd[906246]: new group: name=rooter, GID=972
<86>Jan 31 04:18:51 useradd[906357]: new user: name=rooter, UID=972, GID=972, home=/root, shell=/bin/bash
<86>Jan 31 04:18:51 userdel[906411]: delete user 'builder'
<86>Jan 31 04:18:51 userdel[906411]: removed group 'builder' owned by 'builder'
<86>Jan 31 04:18:51 userdel[906411]: removed shadow group 'builder' owned by 'builder'
<86>Jan 31 04:18:51 groupadd[906482]: group added to /etc/group: name=builder, GID=973
<86>Jan 31 04:18:51 groupadd[906482]: group added to /etc/gshadow: name=builder
<86>Jan 31 04:18:52 groupadd[906482]: new group: name=builder, GID=973
<86>Jan 31 04:18:52 useradd[906649]: new user: name=builder, UID=973, GID=973, home=/usr/src, shell=/bin/bash
warning: Macro %add_tcl_lib_path not found
<13>Jan 31 04:19:05 rpmi: libpng16-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed
<13>Jan 31 04:19:06 rpmi: xorg-proto-devel-2021.4-alt1 p9+272150.100.1.1 1621427342 installed
<13>Jan 31 04:19:06 rpmi: libjpeg-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Jan 31 04:19:06 rpmi: libexpat-2.2.10-alt1 p9+261554.100.1.1 1605103332 installed
<13>Jan 31 04:19:06 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed
<13>Jan 31 04:19:06 rpmi: perl-libnet-1:3.11-alt1 1511423541 installed
<13>Jan 31 04:19:06 rpmi: javapackages-tools-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed
<13>Jan 31 04:19:06 rpmi: perl-Module-Runtime-0.016-alt1 1509549848 installed
<13>Jan 31 04:19:06 rpmi: perl-HTTP-Date-6.02-alt1 1348645274 installed
<13>Jan 31 04:19:06 rpmi: perl-Term-ANSIColor-4.06-alt1 1479407083 installed
<13>Jan 31 04:19:06 rpmi: libICE-1.0.9-alt1 1409902719 installed
<13>Jan 31 04:19:06 rpmi: libgdbm-1.8.3-alt10 1454943313 installed
<13>Jan 31 04:19:06 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Jan 31 04:19:06 rpmi: libglvnd-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:06 rpmi: tex-common-0.2-alt4 1244804096 installed
<13>Jan 31 04:19:06 rpmi: libopenblas-0.3.9-alt2 p9+274919.40.2.1 1624305203 installed
<13>Jan 31 04:19:06 rpmi: perl-Unicode-Normalize-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed
<13>Jan 31 04:19:06 rpmi: libpaper-1.1.26-alt1 sisyphus+221360.100.1.1 1549974198 installed
<13>Jan 31 04:19:06 rpmi: libidn2-2.2.0-alt1 p9+229971.100.2.1 1558696275 installed
<13>Jan 31 04:19:06 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520810 installed
<13>Jan 31 04:19:06 rpmi: perl-Dist-CheckConflicts-0.11-alt1 1397076608 installed
<13>Jan 31 04:19:06 rpmi: perl-Module-Implementation-0.09-alt1 1418836057 installed
<13>Jan 31 04:19:06 rpmi: libjasper-2.0.22-alt1 p9+259398.100.5.1 1602695042 installed
<13>Jan 31 04:19:06 rpmi: rpm-macros-info-install-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Jan 31 04:19:06 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550600768 installed
<13>Jan 31 04:19:06 rpmi: liblksctp-1.0.17-alt2 1523113258 installed
<13>Jan 31 04:19:06 rpmi: libnspr-1:4.28-alt1 p9+254920.20.18.1 1601209852 installed
<13>Jan 31 04:19:06 rpmi: libpixman-3:0.38.4-alt1 sisyphus+228006.100.1.1 1556013486 installed
<13>Jan 31 04:19:06 rpmi: libwayland-server-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed
<13>Jan 31 04:19:06 rpmi: libtcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Jan 31 04:19:06 rpmi: tcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Jan 31 04:19:06 rpmi: libsqlite3-3.33.0-alt1 p9+258834.40.2.1 1601364885 installed
<13>Jan 31 04:19:06 rpmi: python-module-sphinxcontrib-2.1.1-alt2.1.2 sisyphus+227529.1100.1.2 1555924423 installed
<13>Jan 31 04:19:06 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed
<13>Jan 31 04:19:06 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed
<13>Jan 31 04:19:06 rpmi: perl-Devel-StackTrace-1:2.03-alt1 1511420922 installed
<13>Jan 31 04:19:06 rpmi: perl-Sub-Exporter-Progressive-0.001013-alt1 1479395404 installed
<13>Jan 31 04:19:06 rpmi: perl-File-Which-1.23-alt1 sisyphus.218871.100 1546337313 installed
<13>Jan 31 04:19:06 rpmi: perl-Tie-RefHash-1.39-alt1 1316492563 installed
<13>Jan 31 04:19:06 rpmi: perl-TimeDate-2.32-alt1 p9+252601.500.11.1 1592659283 installed
<13>Jan 31 04:19:06 rpmi: perl-IO-Socket-IP-0.39-alt1 1494508514 installed
<13>Jan 31 04:19:06 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed
<13>Jan 31 04:19:06 rpmi: perl-Compress-Raw-Zlib-2.086-alt1 sisyphus+226395.100.1.2 1554269783 installed
<13>Jan 31 04:19:06 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed
<13>Jan 31 04:19:06 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Jan 31 04:19:06 rpmi: libwebp7-1.0.3-alt1 p9+234901.200.1.1 1563552213 installed
<13>Jan 31 04:19:06 rpmi: libjbig-2.1-alt1 1401380921 installed
<13>Jan 31 04:19:06 rpmi: libtiff5-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed
<13>Jan 31 04:19:06 rpmi: libopenjpeg2.0-2.3.1-alt1 sisyphus+226454.100.1.1 1554284336 installed
<13>Jan 31 04:19:06 rpmi: libnettle6-3.4.1-alt1 sisyphus+226533.100.2.1 1554512181 installed
<13>Jan 31 04:19:06 rpmi: libquadmath0-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:06 rpmi: libgfortran5-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:07 rpmi: libicu65-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed
<13>Jan 31 04:19:07 rpmi: libgraphite2-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed
<13>Jan 31 04:19:07 rpmi: libharfbuzz-2.6.2-alt1 p9+277458.500.1.1 1625577087 installed
<13>Jan 31 04:19:07 rpmi: libfreetype-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed
<13>Jan 31 04:19:07 rpmi: fontconfig-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed
Updating fonts cache: <29>Jan 31 04:19:08 fontconfig: Updating fonts cache: succeeded
[ DONE ]
<13>Jan 31 04:19:08 rpmi: libp11-kit-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed
<13>Jan 31 04:19:08 rpmi: libtasn1-4.14-alt1 p9+235792.100.2.1 1565425233 installed
<13>Jan 31 04:19:08 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed
<13>Jan 31 04:19:08 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed
<13>Jan 31 04:19:08 rpmi: libharfbuzz-icu-2.6.2-alt1 p9+277458.500.1.1 1625577087 installed
<13>Jan 31 04:19:08 rpmi: libgraphite2-devel-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed
<13>Jan 31 04:19:08 rpmi: icu-utils-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed
<13>Jan 31 04:19:09 rpmi: libicu-devel-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed
<13>Jan 31 04:19:09 rpmi: libquadmath8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:09 rpmi: libhogweed4-3.4.1-alt1 sisyphus+226533.100.2.1 1554512181 installed
<13>Jan 31 04:19:09 rpmi: libgnutls30-3.6.16-alt1 p9+273087.100.1.1 1622486710 installed
<13>Jan 31 04:19:09 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed
<13>Jan 31 04:19:09 rpmi: perl-autodie-2.29-alt1 1445013559 installed
<13>Jan 31 04:19:09 rpmi: perl-File-HomeDir-1.004-alt1 1525450444 installed
<13>Jan 31 04:19:09 rpmi: perl-Devel-GlobalDestruction-1:0.14-alt1 1479389769 installed
<13>Jan 31 04:19:09 rpmi: perl-OLE-Storage_Lite-0.20-alt1 p9+252601.400.11.1 1592659257 installed
<13>Jan 31 04:19:09 rpmi: lksctp-tools-1.0.17-alt2 1523113258 installed
<13>Jan 31 04:19:09 rpmi: libpng-devel-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed
<13>Jan 31 04:19:09 rpmi: perl-unicore-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed
<13>Jan 31 04:19:09 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+221481.100.1.1 1550127189 installed
<13>Jan 31 04:19:09 rpmi: libopenblas-devel-0.3.9-alt2 p9+274919.40.2.1 1624305203 installed
<13>Jan 31 04:19:09 rpmi: libOpenGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:09 rpmi: libgdbm-devel-1.8.3-alt10 1454943313 installed
<13>Jan 31 04:19:09 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed
<13>Jan 31 04:19:09 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed
<13>Jan 31 04:19:09 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed
<13>Jan 31 04:19:09 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed
<13>Jan 31 04:19:09 rpmi: java-common-1.6.0-alt1 p9+234085.100.1.1 1562573623 installed
<13>Jan 31 04:19:09 rpmi: rpm-build-tcl-0.5.1-alt1 1519671307 installed
<13>Jan 31 04:19:09 rpmi: tcl-devel-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed
<13>Jan 31 04:19:09 rpmi: rpm-macros-java-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed
<13>Jan 31 04:19:09 rpmi: perl-Algorithm-Diff-1.1903-alt1 1418755800 installed
<13>Jan 31 04:19:09 rpmi: perl-Unicode-EastAsianWidth-1.40-alt1 sisyphus.217785.100 1544703272 installed
<13>Jan 31 04:19:09 rpmi: libtre5-0.8.0-alt2.1 1334590818 installed
<13>Jan 31 04:19:09 rpmi: libpcre16-8.44-alt1 p9+249555.100.1.1 1586300287 installed
<13>Jan 31 04:19:09 rpmi: pcretest-8.44-alt1 p9+249555.100.1.1 1586300287 installed
<13>Jan 31 04:19:09 rpmi: libgomp1-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:09 rpmi: libpcsclite-1.9.0-alt1 p9+260393.100.3.1 1604003766 installed
<13>Jan 31 04:19:09 rpmi: javazi-2021a-alt1 p9+265336.400.3.1 1612252875 installed
<13>Jan 31 04:19:09 rpmi: libgif-4.1.6-alt3 1299634266 installed
<13>Jan 31 04:19:09 rpmi: libgtk+2-locales-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Jan 31 04:19:09 rpmi: libfribidi-1.0.7-alt1 p9+238309.200.1.1 1569787041 installed
<13>Jan 31 04:19:09 rpmi: libatk-locales-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed
<13>Jan 31 04:19:09 rpmi: libatk-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed
<13>Jan 31 04:19:09 rpmi: icon-theme-hicolor-0.17-alt2 p9+248347.100.1.1 1584981172 installed
<13>Jan 31 04:19:09 rpmi: shared-mime-info-1.13.1-alt1 p9+238204.100.1.1 1569496447 installed
<13>Jan 31 04:19:09 rpmi: libgdk-pixbuf-locales-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed
<13>Jan 31 04:19:10 rpmi: gsettings-desktop-schemas-data-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed
<13>Jan 31 04:19:10 rpmi: libgio-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed
<13>Jan 31 04:19:10 rpmi: gsettings-desktop-schemas-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed
<13>Jan 31 04:19:10 rpmi: libgdk-pixbuf-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed
<13>Jan 31 04:19:10 rpmi: gtk-update-icon-cache-3.24.29-alt0.M90P.1 p9+277455.200.2.1 1625582389 installed
<13>Jan 31 04:19:10 rpmi: libkpathsea6-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Jan 31 04:19:10 rpmi: libptexenc1-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Jan 31 04:19:10 rpmi: libsynctex2-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Jan 31 04:19:10 rpmi: libtexlua5-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Jan 31 04:19:10 rpmi: zziplib-0.13.69-alt3 p9+240930.100.1.1 1574080033 installed
<13>Jan 31 04:19:10 rpmi: liblcms2-2.9-alt1 1516411888 installed
<13>Jan 31 04:19:10 rpmi: publicsuffix-list-dafsa-20211230-alt1 p9+293277.100.2.1 1643036039 installed
<13>Jan 31 04:19:10 rpmi: libpsl-0.21.1-alt1 p9+255207.100.1.1 1595355041 installed
<13>Jan 31 04:19:10 rpmi: libnghttp2-1.41.0-alt1 p9+256449.100.1.1 1597829543 installed
<13>Jan 31 04:19:10 rpmi: openldap-common-2.4.59-alt0.p9.1 p9+281540.300.5.1 1629898589 installed
<13>Jan 31 04:19:10 rpmi: libbrotlicommon-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Jan 31 04:19:10 rpmi: libbrotlidec-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed
<13>Jan 31 04:19:10 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed
<13>Jan 31 04:19:10 rpmi: libicu64-1:6.4.2-alt3 p9+270873.100.1.1 1619612690 installed
<13>Jan 31 04:19:10 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268594 installed
<13>Jan 31 04:19:10 rpmi: libwayland-client-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed
<13>Jan 31 04:19:10 rpmi: libpciaccess-1:0.14-alt1 1528969624 installed
<13>Jan 31 04:19:10 rpmi: libdrm-1:2.4.105-alt2 p9+271012.100.1.1 1619786664 installed
<13>Jan 31 04:19:10 rpmi: libgbm-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed
<13>Jan 31 04:19:10 rpmi: t1utils-1.41-alt1 1502978415 installed
<13>Jan 31 04:19:10 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267504 installed
<13>Jan 31 04:19:10 rpmi: libqqwing-1.3.4-alt2 1436192940 installed
<13>Jan 31 04:19:10 rpmi: qqwing-1.3.4-alt2 1436192940 installed
<13>Jan 31 04:19:10 rpmi: python-module-iniconfig-1.0.0-alt1 sisyphus+227494.1100.1.3 1555839106 installed
<13>Jan 31 04:19:10 rpmi: python-module-apipkg-1.5-alt1 1531926894 installed
<13>Jan 31 04:19:10 rpmi: python-module-imagesize-1.1.0-alt1 sisyphus+229015.100.2.1 1557233756 installed
<13>Jan 31 04:19:10 rpmi: python-sphinx-objects.inv-1:2.3.8.20190514-alt1 p9+229421.100.1.1 1557927689 installed
<13>Jan 31 04:19:11 rpmi: libxapian-1.4.15-alt1 p9+258827.100.1.1 1601305414 installed
<13>Jan 31 04:19:11 rpmi: python-module-google-0.4.2-alt2.1 sisyphus+228356.1500.3.1 1556633038 installed
<13>Jan 31 04:19:11 rpmi: python-module-markupsafe-1.1.1-alt1 p9+254838.60.14.1 1602882123 installed
<13>Jan 31 04:19:11 rpmi: python-module-enum34-1.1.6-alt3 1527251693 installed
<13>Jan 31 04:19:11 rpmi: libnumpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed
<13>Jan 31 04:19:11 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388758 installed
<13>Jan 31 04:19:11 rpmi: liblapack-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Jan 31 04:19:11 rpmi: python-modules-curses-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:11 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed
<13>Jan 31 04:19:11 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed
<13>Jan 31 04:19:11 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed
<13>Jan 31 04:19:11 rpmi: libdatrie-0.2.9-alt1_6 1511686677 installed
<13>Jan 31 04:19:11 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed
<13>Jan 31 04:19:11 rpmi: libsombok-2.4.0-alt1_8 sisyphus+226104.100.1.1 1554121176 installed
<13>Jan 31 04:19:11 rpmi: perl-Unicode-Map-0.112-alt7.1 sisyphus+219907.5000.1.1 1548349925 installed
<13>Jan 31 04:19:11 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed
<13>Jan 31 04:19:11 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed
<13>Jan 31 04:19:11 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed
<13>Jan 31 04:19:11 rpmi: perl-XML-RegExp-0.04-alt1 1348526543 installed
<13>Jan 31 04:19:11 rpmi: perl-DBI-1.642-alt1.1 sisyphus+219907.3200.1.1 1548345175 installed
<13>Jan 31 04:19:11 rpmi: perl-Package-Stash-XS-0.29-alt1.1 sisyphus+219907.3400.1.1 1548345296 installed
<13>Jan 31 04:19:11 rpmi: perl-Package-Stash-0.38-alt1 sisyphus.218845.100 1546250118 installed
<13>Jan 31 04:19:11 rpmi: perl-Sub-Identify-0.14-alt1.2 sisyphus+219907.3700.1.1 1548345423 installed
<13>Jan 31 04:19:11 rpmi: perl-Variable-Magic-0.62-alt1.2 sisyphus+219907.3600.1.1 1548345381 installed
<13>Jan 31 04:19:11 rpmi: perl-B-Hooks-EndOfScope-0.24-alt1 1524680298 installed
<13>Jan 31 04:19:11 rpmi: perl-namespace-clean-0.27-alt1 1464272543 installed
<13>Jan 31 04:19:11 rpmi: perl-namespace-autoclean-0.28-alt1 1444994071 installed
<13>Jan 31 04:19:11 rpmi: perl-Sub-Quote-2.006003-alt1 sisyphus+224895.100.1.1 1552434926 installed
<13>Jan 31 04:19:11 rpmi: perl-Role-Tiny-2.000006-alt1 1513709006 installed
<13>Jan 31 04:19:11 rpmi: perl-MRO-Compat-0.13-alt2 p9+261964.200.3.1 1606316246 installed
<13>Jan 31 04:19:11 rpmi: perl-Class-Data-Inheritable-0.08-alt2 1316996762 installed
<13>Jan 31 04:19:11 rpmi: perl-Exception-Class-1.44-alt1 1513614520 installed
<13>Jan 31 04:19:11 rpmi: perl-PadWalker-2.3-alt1.2 sisyphus+219907.3500.1.1 1548345336 installed
<13>Jan 31 04:19:11 rpmi: perl-Devel-Caller-2.06-alt2.2 sisyphus+219907.4000.1.1 1548345464 installed
<13>Jan 31 04:19:11 rpmi: perl-Devel-LexAlias-0.05-alt3_17 sisyphus+219907.4100.1.1 1548345510 installed
<13>Jan 31 04:19:11 rpmi: perl-Eval-Closure-0.14-alt1 1465147597 installed
<13>Jan 31 04:19:11 rpmi: perl-Params-ValidationCompiler-0.30-alt1 1533170707 installed
<13>Jan 31 04:19:11 rpmi: perl-Mail-Sendmail-0.80-alt1 1504118031 installed
<13>Jan 31 04:19:11 rpmi: perl-Mail-Sender-1:0.903-alt1 1479576662 installed
<13>Jan 31 04:19:11 rpmi: perl-Email-Date-Format-1.005-alt1 1413796337 installed
<13>Jan 31 04:19:11 rpmi: ppp-common-0.5.1-alt1 1244040597 installed
<13>Jan 31 04:19:11 rpmi: sendmail-common-1.7-alt3 1353029717 installed
<13>Jan 31 04:19:11 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed
<13>Jan 31 04:19:11 rpmi: perl-IPC-System-Simple-1.25-alt2_1 1388863478 installed
<13>Jan 31 04:19:11 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed
<13>Jan 31 04:19:11 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed
<13>Jan 31 04:19:11 rpmi: perl-File-Copy-Recursive-0.44-alt1 1525447381 installed
<13>Jan 31 04:19:11 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+219907.4500.1.1 1548349730 installed
<13>Jan 31 04:19:11 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed
<13>Jan 31 04:19:11 rpmi: perl-Compress-Raw-Bzip2-2.086-alt1 sisyphus+226394.100.1.2 1554269409 installed
<13>Jan 31 04:19:11 rpmi: libdb4.7-devel-4.7.25-alt9 1490438456 installed
<13>Jan 31 04:19:11 rpmi: perl-devel-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed
<13>Jan 31 04:19:11 rpmi: perl-Test-Fatal-0.014-alt1 1418768336 installed
<13>Jan 31 04:19:11 rpmi: perl-Specio-0.43-alt1 sisyphus.215861.100 1540964587 installed
<13>Jan 31 04:19:11 rpmi: hd2u-1.0.3-alt2 1400842666 installed
<13>Jan 31 04:19:11 rpmi: perl-Filter-1.59-alt1.1 sisyphus+219907.400.1.1 1548343225 installed
<13>Jan 31 04:19:11 rpmi: perl-Encode-3.01-alt1 sisyphus+224923.100.1.1 1552474113 installed
<13>Jan 31 04:19:11 rpmi: perl-URI-1.76-alt1 sisyphus+220243.100.1.1 1548863244 installed
<13>Jan 31 04:19:11 rpmi: perl-HTML-Parser-3.72-alt1.2 sisyphus+219907.600.1.1 1548343407 installed
<13>Jan 31 04:19:11 rpmi: perl-IO-Compress-2.086-alt1 sisyphus+226399.100.2.1 1554270186 installed
<13>Jan 31 04:19:11 rpmi: perl-Net-HTTP-6.18-alt1 1526560501 installed
<13>Jan 31 04:19:11 rpmi: perl-Pod-Simple-3.35-alt1 1482098090 installed
<13>Jan 31 04:19:11 rpmi: perl-Pod-Usage-1.69-alt1 1464274721 installed
<13>Jan 31 04:19:11 rpmi: perl-podlators-4.11-alt1 1525935408 installed
<13>Jan 31 04:19:11 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed
<13>Jan 31 04:19:11 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed
<13>Jan 31 04:19:11 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed
<13>Jan 31 04:19:11 rpmi: perl-HTTP-Message-6.18-alt1 1528288416 installed
<13>Jan 31 04:19:11 rpmi: perl-HTTP-Cookies-6.04-alt1 1504116575 installed
<13>Jan 31 04:19:11 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed
<13>Jan 31 04:19:11 rpmi: perl-libwww-6.39-alt1 sisyphus+229237.100.1.1 1557650051 installed
<13>Jan 31 04:19:11 rpmi: perl-XML-Parser-2.44-alt2.2 sisyphus+219907.1300.1.1 1548343654 installed
<13>Jan 31 04:19:11 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed
<13>Jan 31 04:19:11 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed
<13>Jan 31 04:19:11 rpmi: perl-XML-DOM-1.46-alt1 1474815568 installed
<13>Jan 31 04:19:11 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed
<13>Jan 31 04:19:11 rpmi: perl-HTML-Form-6.04-alt1 sisyphus+225750.100.1.1 1553678430 installed
<13>Jan 31 04:19:11 rpmi: perl-WWW-Mechanize-1.91-alt1 sisyphus+219761.100.1.2 1548132822 installed
<13>Jan 31 04:19:11 rpmi: perl-XML-Writer-0.625-alt1 1402417374 installed
<13>Jan 31 04:19:11 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+223919.100.1.1 1551893088 installed
<13>Jan 31 04:19:11 rpmi: perl-MIME-Types-2.17-alt1 1517533413 installed
<13>Jan 31 04:19:11 rpmi: perl-Text-CSV_XS-1.39-alt1 sisyphus+225184.100.1.2 1552965519 installed
<13>Jan 31 04:19:11 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed
<13>Jan 31 04:19:11 rpmi: perl-MIME-Charset-1.012.2-alt1 1494353584 installed
<13>Jan 31 04:19:11 rpmi: perl-Unicode-LineBreak-2019.001-alt1.1 sisyphus+219907.4700.1.1 1548349872 installed
<13>Jan 31 04:19:11 rpmi: perl-YAML-Tiny-1.73-alt1 1520430664 installed
<13>Jan 31 04:19:11 rpmi: perl-libintl-1.31-alt1.1 sisyphus+219907.6300.1.1 1548352427 installed
<13>Jan 31 04:19:11 rpmi: libteckit-2.5.1-alt2.1 1319227424 installed
<13>Jan 31 04:19:11 rpmi: libteckit-utils-2.5.1-alt2.1 1319227424 installed
<13>Jan 31 04:19:11 rpmi: rgb-1.0.6-alt3 p9+229442.100.1.1 1557941137 installed
<13>Jan 31 04:19:11 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Jan 31 04:19:11 rpmi: mailx-8.1.2-alt7 1366314831 installed
<13>Jan 31 04:19:11 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed
<13>Jan 31 04:19:11 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed
<13>Jan 31 04:19:11 rpmi: libX11-locales-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed
<13>Jan 31 04:19:11 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949347 installed
<13>Jan 31 04:19:12 rpmi: libxcb-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed
<13>Jan 31 04:19:12 rpmi: libX11-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed
<13>Jan 31 04:19:12 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Jan 31 04:19:12 rpmi: libXrender-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed
<13>Jan 31 04:19:12 rpmi: libXt-1.1.4-alt1 1369984716 installed
<13>Jan 31 04:19:12 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Jan 31 04:19:12 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Jan 31 04:19:12 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614842 installed
<13>Jan 31 04:19:12 rpmi: libXpm-3.5.12-alt1 sisyphus+223149.400.2.1 1551268300 installed
<13>Jan 31 04:19:12 rpmi: libXi-1.7.9-alt2 sisyphus+226377.100.1.2 1554260258 installed
<13>Jan 31 04:19:12 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949136 installed
<13>Jan 31 04:19:13 rpmi: libxcb-devel-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed
<13>Jan 31 04:19:13 rpmi: libX11-devel-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed
<13>Jan 31 04:19:13 rpmi: libXrender-devel-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed
<13>Jan 31 04:19:13 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed
<13>Jan 31 04:19:13 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed
<13>Jan 31 04:19:13 rpmi: libXaw-1.0.12-alt1 1391072621 installed
<13>Jan 31 04:19:13 rpmi: libgd3-2.2.5-alt3 sisyphus+226800.200.2.1 1554649314 installed
<13>Jan 31 04:19:13 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949214 installed
<13>Jan 31 04:19:13 rpmi: perl-Tk-804.034-alt1.2 sisyphus+219907.4300.1.1 1548345831 installed
<13>Jan 31 04:19:13 rpmi: libtk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Jan 31 04:19:13 rpmi: tk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Jan 31 04:19:13 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438593 installed
<13>Jan 31 04:19:13 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949698 installed
<13>Jan 31 04:19:13 rpmi: libXxf86vm-1.1.4-alt2 1527672159 installed
<13>Jan 31 04:19:13 rpmi: libGLX-mesa-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed
<13>Jan 31 04:19:13 rpmi: libEGL-mesa-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed
<13>Jan 31 04:19:13 rpmi: libEGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:13 rpmi: libGLX-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:13 rpmi: libGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:14 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Jan 31 04:19:14 rpmi: libpango-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed
<13>Jan 31 04:19:14 rpmi: libglvnd-devel-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed
<13>Jan 31 04:19:14 rpmi: libEGL-devel-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed
<13>Jan 31 04:19:14 rpmi: libGL-devel-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed
<13>Jan 31 04:19:14 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268223 installed
<13>Jan 31 04:19:14 rpmi: libXtst-1.2.3-alt1 p9+261891.100.2.1 1606149065 installed
<13>Jan 31 04:19:14 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed
<13>Jan 31 04:19:14 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949282 installed
<13>Jan 31 04:19:14 rpmi: xprop-1.2.4-alt1 sisyphus+225764.100.1.1 1553680701 installed
<13>Jan 31 04:19:14 rpmi: xdg-utils-1.1.3-alt7 p9+259359.100.1.1 1602061025 installed
<13>Jan 31 04:19:14 rpmi: liblz4-1:1.9.2-alt1 p9+238696.500.1.1 1570228072 installed
<13>Jan 31 04:19:14 rpmi: libgpg-error-1.36-alt1 p9+261942.140.4.1 1606237682 installed
<13>Jan 31 04:19:14 rpmi: libgcrypt20-1.8.5-alt3 p9+261942.200.4.1 1606237844 installed
<13>Jan 31 04:19:14 rpmi: libxslt-1.1.34-alt1.p9.1 p9+261811.300.3.1 1605513910 installed
<13>Jan 31 04:19:14 rpmi: libsystemd-1:246.16-alt2 p9+287049.100.2.1 1634920961 installed
<13>Jan 31 04:19:14 rpmi: libdbus-1.12.16-alt2 p9+240607.100.1.1 1573553670 installed
<13>Jan 31 04:19:14 rpmi: libavahi-0.8-alt2 p9+270905.100.1.1 1619639855 installed
<13>Jan 31 04:19:14 rpmi: libcups-2.3.3-alt7.op2 p9+289603.100.2.1 1637911367 installed
<13>Jan 31 04:19:14 rpmi: libgtk+2-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Jan 31 04:19:14 rpmi: libgail-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed
<13>Jan 31 04:19:15 rpmi: libgs-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed
<13>Jan 31 04:19:15 rpmi: ghostscript-common-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed
<13>Jan 31 04:19:15 rpmi: ghostscript-classic-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed
<13>Jan 31 04:19:15 rpmi: ghostscript-module-X-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed
<13>Jan 31 04:19:15 rpmi: gcc-fortran-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed
<13>Jan 31 04:19:15 rpmi: libgfortran8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:16 rpmi: gcc8-fortran-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:16 rpmi: gcc-c++-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed
<13>Jan 31 04:19:16 rpmi: libstdc++8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:17 rpmi: gcc8-c++-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:19:17 rpmi: xml-utils-1:2.9.10-alt6 p9+266566.100.3.1 1614357016 installed
<13>Jan 31 04:19:17 rpmi: rpm-build-gir-0.7.3-alt2 p9+234356.40.2.1 1562933848 installed
<13>Jan 31 04:19:17 rpmi: ed-1:0.2-alt10 1449768441 installed
<13>Jan 31 04:19:17 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed
<13>Jan 31 04:19:17 rpmi: dialog-1.3.20171209-alt1 1529583087 installed
<13>Jan 31 04:19:17 rpmi: libruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:17 rpmi: libyaml2-0.2.2-alt1 sisyphus+229134.100.1.1 1557342720 installed
<13>Jan 31 04:19:17 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587848 installed
<13>Jan 31 04:19:17 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Jan 31 04:19:17 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Jan 31 04:19:17 rpmi: libnss-3.56.0-alt1 p9+254920.30.20.1 1601657858 installed
<13>Jan 31 04:19:17 rpmi: ca-certificates-2021.10.06-alt1 p9+289862.100.1.1 1637033643 installed
<13>Jan 31 04:19:17 rpmi: ca-trust-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed
<13>Jan 31 04:19:17 rpmi: p11-kit-trust-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed
<13>Jan 31 04:19:17 rpmi: libcrypto1.1-1.1.1l-alt1 p9+283690.100.2.1 1630572181 installed
<13>Jan 31 04:19:17 rpmi: libssl1.1-1.1.1l-alt1 p9+283690.100.2.1 1630572181 installed
<13>Jan 31 04:19:18 rpmi: libpython3-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<13>Jan 31 04:19:18 rpmi: python3-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<13>Jan 31 04:19:18 rpmi: python3-base-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<86>Jan 31 04:19:18 groupadd[1084885]: group added to /etc/group: name=_keytab, GID=499
<86>Jan 31 04:19:18 groupadd[1084885]: group added to /etc/gshadow: name=_keytab
<86>Jan 31 04:19:18 groupadd[1084885]: new group: name=_keytab, GID=499
<13>Jan 31 04:19:18 rpmi: libkrb5-1.17.2-alt2 p9+280683.100.2.1 1627489159 installed
<13>Jan 31 04:19:18 rpmi: glib2-devel-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed
<13>Jan 31 04:19:18 rpmi: libharfbuzz-devel-2.6.2-alt1 p9+277458.500.1.1 1625577087 installed
<13>Jan 31 04:19:19 rpmi: libfreetype-devel-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed
<13>Jan 31 04:19:19 rpmi: fontconfig-devel-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed
<13>Jan 31 04:19:19 rpmi: python3-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed
<13>Jan 31 04:19:19 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed
<13>Jan 31 04:19:19 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed
<13>Jan 31 04:19:19 rpmi: libtirpc-1.0.3-alt1 1532008015 installed
<13>Jan 31 04:19:19 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed
<13>Jan 31 04:19:19 rpmi: python-modules-encodings-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-compiler-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-email-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-unittest-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-nis-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-xml-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-ctypes-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed
<13>Jan 31 04:19:19 rpmi: python-module-pkg_resources-1:40.8.0-alt2 sisyphus+229158.200.2.1 1557735221 installed
<13>Jan 31 04:19:19 rpmi: python-modules-multiprocessing-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-logging-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-modules-json-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-module-jinja2-2.11.2-alt1 p9+254838.40.14.1 1602882082 installed
<13>Jan 31 04:19:19 rpmi: python-modules-hotshot-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-module-webencodings-0.5.1-alt1.1 1517943573 installed
<13>Jan 31 04:19:19 rpmi: python-module-chardet-3.0.4-alt1 sisyphus+227476.1700.1.2 1555756717 installed
<13>Jan 31 04:19:19 rpmi: python-tools-2to3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-module-future-0.16.0-alt2 sisyphus+228356.200.3.3 1556645013 installed
<13>Jan 31 04:19:19 rpmi: python-module-pyglet-1.3.0-alt4.a1.hg20150730.1.1.1 1460413686 installed
<13>Jan 31 04:19:19 rpmi: python-module-whoosh-2.7.4-alt1 1527697941 installed
<13>Jan 31 04:19:19 rpmi: python-modules-bsddb-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:19 rpmi: python-strict-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:20 rpmi: python-modules-distutils-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:20 rpmi: python-module-numpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed
<13>Jan 31 04:19:20 rpmi: python-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed
<13>Jan 31 04:19:20 rpmi: python-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed
<13>Jan 31 04:19:20 rpmi: python-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed
<13>Jan 31 04:19:20 rpmi: python-module-docutils-0.14-alt2 1535729778 installed
<13>Jan 31 04:19:20 rpmi: python-module-idna-2.8-alt1 sisyphus+227494.400.1.3 1555838720 installed
<13>Jan 31 04:19:20 rpmi: python-module-pycparser-2.19-alt1 sisyphus+228366.1000.2.3 1556706938 installed
<13>Jan 31 04:19:20 rpmi: python-module-cffi-1.12.3-alt1 sisyphus+229040.200.3.1 1557316502 installed
<13>Jan 31 04:19:20 rpmi: python-module-asn1crypto-0.24.0-alt1 sisyphus+227473.1300.1.2 1555756512 installed
<13>Jan 31 04:19:20 rpmi: python-module-ntlm-1.1.0-alt1.2 sisyphus+228512.100.1.1 1556654575 installed
<13>Jan 31 04:19:20 rpmi: python-module-pytz-1:2016.10-alt1 1484291011 installed
<13>Jan 31 04:19:21 rpmi: python-module-babel-1:2.6.0-alt1 sisyphus+228351.2400.6.2 1556652168 installed
<13>Jan 31 04:19:21 rpmi: python-module-PyStemmer-1.0.1-alt1.2.1 1321387369 installed
<13>Jan 31 04:19:21 rpmi: python-module-snowballstemmer-1.2.0-alt2.1 1457859319 installed
<13>Jan 31 04:19:21 rpmi: python-module-simplejson-3.15.0-alt1.qa1 sisyphus+225625.16100.91.1 1555293606 installed
<13>Jan 31 04:19:21 rpmi: python-module-ipaddress-1.0.18-alt1.1 sisyphus+227494.1700.1.3 1555839523 installed
<13>Jan 31 04:19:21 rpmi: python-module-cryptography-2.6.1-alt1 sisyphus+225625.24400.91.1 1555299604 installed
<13>Jan 31 04:19:21 rpmi: python-module-OpenSSL-18.0.0-alt1 1532996168 installed
<13>Jan 31 04:19:21 rpmi: python-module-ndg-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Jan 31 04:19:21 rpmi: python-module-ndg-httpsclient-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed
<13>Jan 31 04:19:21 rpmi: python-module-backports-3.5.0.1-alt1.1.1 1517645428 installed
<13>Jan 31 04:19:21 rpmi: python-module-backports.ssl_match_hostname-3.5.0.1-alt1.1.1 1517645428 installed
<13>Jan 31 04:19:21 rpmi: python-module-urllib3-2:1.25.6-alt1 p9+250567.200.5.1 1590420860 installed
<13>Jan 31 04:19:21 rpmi: python-module-requests-2.23.0-alt1 p9+250567.400.5.1 1590420890 installed
<13>Jan 31 04:19:21 rpmi: python-module-typing-3.6.6-alt2 sisyphus+220108.100.1.1 1548749697 installed
<13>Jan 31 04:19:21 rpmi: python-modules-sqlite3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Jan 31 04:19:21 rpmi: python-module-SQLAlchemy-1.2.15-alt1 sisyphus+225625.4500.91.1 1555285684 installed
<13>Jan 31 04:19:21 rpmi: python-module-py-1.8.0-alt2 sisyphus+228349.1400.4.1 1556631070 installed
<13>Jan 31 04:19:21 rpmi: python-module-mpmath-0.19-alt1.git20150621.1.1.1.1 sisyphus+227503.2100.1.3 1555860908 installed
<13>Jan 31 04:19:21 rpmi: python-module-sympy-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Jan 31 04:19:22 rpmi: python-module-sympy-tests-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed
<13>Jan 31 04:19:22 rpmi: python-module-xapian-1.4.15-alt1 p9+258827.200.2.1 1601308059 installed
<13>Jan 31 04:19:22 rpmi: python-module-sphinxcontrib-websupport-1.0.1-alt5 p9+247680.340.15.1 1585331199 installed
<13>Jan 31 04:19:22 rpmi: python-module-alabaster-0.7.6-alt3 sisyphus+228351.700.4.1 1556637370 installed
<13>Jan 31 04:19:22 rpmi: python-module-Pygments-2.4.2-alt3 p9+263160.400.4.1 1607939146 installed
<13>Jan 31 04:19:22 rpmi: python-module-sphinx-1:1.6.5-alt8 p9+250806.100.2.1 1588178467 installed
<86>Jan 31 04:19:22 groupadd[1107469]: group added to /etc/group: name=sasl, GID=498
<86>Jan 31 04:19:22 groupadd[1107469]: group added to /etc/gshadow: name=sasl
<86>Jan 31 04:19:22 groupadd[1107469]: new group: name=sasl, GID=498
<13>Jan 31 04:19:22 rpmi: libsasl2-3-2.1.27-alt2.1 p9+256192.100.1.1 1597226707 installed
<13>Jan 31 04:19:22 rpmi: libldap-2.4.59-alt0.p9.1 p9+281540.300.5.1 1629898589 installed
<13>Jan 31 04:19:22 rpmi: libcurl-7.79.0-alt2 p9+285689.100.2.1 1632758193 installed
<13>Jan 31 04:19:22 rpmi: libpoppler90-0.80.0-alt1 p9+237607.100.1.1 1568643072 installed
<13>Jan 31 04:19:22 rpmi: python3-module-genshi-0.7-alt2 sisyphus+229363.100.1.1 1557847321 installed
<13>Jan 31 04:19:22 rpmi: python3-module-webencodings-0.5.1-alt1.1 1517943573 installed
<13>Jan 31 04:19:22 rpmi: python3-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed
<13>Jan 31 04:19:22 rpmi: python3-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed
<13>Jan 31 04:19:22 rpmi: python3-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed
<13>Jan 31 04:19:22 rpmi: python3-module-javapackages-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed
<13>Jan 31 04:19:22 rpmi: rpm-build-java-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed
<13>Jan 31 04:19:22 rpmi: openssl-1.1.1l-alt1 p9+283690.100.2.1 1630572181 installed
<13>Jan 31 04:19:23 rpmi: ruby-rubygems-update-3.0.4-alt1 p9+247371.35300.135.1 1590436206 installed
<13>Jan 31 04:19:23 rpmi: gem-did-you-mean-1.3.0-alt2.1 p9+247371.40400.161.1 1591376055 installed
<13>Jan 31 04:19:23 rpmi: gem-minitest-5.14.0-alt1.1 p9+247371.67710.170.1 1592235999 installed
<13>Jan 31 04:19:23 rpmi: ruby-net-telnet-0.2.0-alt1 sisyphus+219345.2700.8.1 1547631566 installed
<13>Jan 31 04:19:23 rpmi: gem-rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed
<13>Jan 31 04:19:23 rpmi: ruby-xmlrpc-0.3.0-alt1 sisyphus+219345.3300.8.1 1547631818 installed
<13>Jan 31 04:19:23 rpmi: gem-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:23 rpmi: ri-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Jan 31 04:19:23 rpmi: rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Jan 31 04:19:23 rpmi: ruby-rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed
<13>Jan 31 04:19:23 rpmi: rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed
<13>Jan 31 04:19:23 rpmi: erb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:23 rpmi: irb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:24 rpmi: gem-bundler-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed
<13>Jan 31 04:19:24 rpmi: gem-test-unit-3.3.5-alt0.1 p9+247371.60440.162.1 1591424158 installed
<13>Jan 31 04:19:24 rpmi: gem-power-assert-1.1.7-alt1 p9+247371.60200.162.1 1591424056 installed
<13>Jan 31 04:19:24 rpmi: ruby-stdlibs-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:24 rpmi: bundle-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed
<13>Jan 31 04:19:24 rpmi: ruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed
<13>Jan 31 04:19:24 rpmi: perl-Net-SSLeay-1.86_09-alt2 sisyphus+227568.100.1.1 1555676534 installed
<13>Jan 31 04:19:24 rpmi: perl-IO-Socket-SSL-2.066-alt1 sisyphus+223890.100.1.1 1551873760 installed
<13>Jan 31 04:19:24 rpmi: perl-Net-HTTPS-6.18-alt1 1526560501 installed
<13>Jan 31 04:19:24 rpmi: perl-LWP-Protocol-https-6.07-alt1 1494527383 installed
<13>Jan 31 04:19:24 rpmi: perl-Net-SMTP-SSL-1.04-alt1 1479470835 installed
<13>Jan 31 04:19:24 rpmi: perl-MailTools-2.20-alt1 1517533205 installed
<13>Jan 31 04:19:24 rpmi: perl-MIME-Lite-3.030-alt1 1383865152 installed
<13>Jan 31 04:19:24 rpmi: perl-Log-Dispatch-2.68-alt2 sisyphus.218872.100 1546338428 installed
<13>Jan 31 04:19:24 rpmi: perl-Log-Log4perl-1.49-alt1 1489613295 installed
<13>Jan 31 04:19:24 rpmi: ca-trust-java-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed
<13>Jan 31 04:19:26 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Jan 31 04:19:29 rpmi: gambit-4.9.3-alt1 sisyphus+220998.100.1.4 1549742897 installed
<13>Jan 31 04:19:29 rpmi: foomatic-db-engine-4.0.12-alt1 1449527980 installed
<13>Jan 31 04:19:29 rpmi: ghostscript-utils-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed
<13>Jan 31 04:19:29 rpmi: texlive-2019-alt1_2 p9+238369.100.3.1 1569961493 installed
<13>Jan 31 04:19:39 rpmi: texlive-collection-basic-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Jan 31 04:19:39 rpmi: texlive-texmf-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Jan 31 04:20:28 rpmi: texlive-dist-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed
<13>Jan 31 04:20:28 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed
<13>Jan 31 04:20:28 rpmi: alsa-ucm-conf-1.2.4-alt1 p9+250722.2300.14.1 1614269485 installed
<13>Jan 31 04:20:28 rpmi: alsa-topology-conf-1.2.4-alt1 p9+250722.2200.14.1 1614269467 installed
<13>Jan 31 04:20:28 rpmi: libalsa-1:1.2.4-alt1 p9+250722.2400.14.1 1614269549 installed
<13>Jan 31 04:20:28 rpmi: java-1.8.0-openjdk-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Jan 31 04:20:29 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed
<13>Jan 31 04:20:29 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed
<13>Jan 31 04:20:29 rpmi: libcurl-devel-7.79.0-alt2 p9+285689.100.2.1 1632758193 installed
<13>Jan 31 04:20:29 rpmi: libpango-devel-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed
<13>Jan 31 04:20:29 rpmi: gcc-c++-8-alt2 p9+246536.100.3.1 1582643803 installed
<13>Jan 31 04:20:29 rpmi: gcc-fortran-8-alt2 p9+246536.100.3.1 1582643803 installed
<13>Jan 31 04:20:29 rpmi: tk-devel-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed
<13>Jan 31 04:20:29 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed
<13>Jan 31 04:20:29 rpmi: makeinfo-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Jan 31 04:20:29 rpmi: liblapack-devel-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed
<13>Jan 31 04:20:29 rpmi: libgomp8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed
<13>Jan 31 04:20:29 rpmi: libpcre-devel-8.44-alt1 p9+249555.100.1.1 1586300287 installed
<13>Jan 31 04:20:29 rpmi: libtre-devel-0.8.0-alt2.1 1334590818 installed
<13>Jan 31 04:20:29 rpmi: libtiff-devel-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed
<13>Jan 31 04:20:29 rpmi: texi2dvi-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed
<13>Jan 31 04:20:29 rpmi: libjpeg-devel-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed
<13>Jan 31 04:20:29 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686325 installed
<13>Jan 31 04:20:29 rpmi: liblzma-devel-5.2.5-alt1 p9+268339.40.3.1 1616664413 installed
<13>Jan 31 04:20:29 rpmi: bzlib-devel-1:1.0.8-alt1 p9+261810.100.1.1 1605510817 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/nosrpm/R-base-3.6.1-alt1.nosrc.rpm (w1.gzdio)
Installing R-base-3.6.1-alt1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.8645
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ rm -rf R-3.6.1
+ echo 'Source #0 (R-3.6.1.tar):'
Source #0 (R-3.6.1.tar):
+ /bin/tar -xf /usr/src/RPM/SOURCES/R-3.6.1.tar
+ cd R-3.6.1
+ /bin/chmod -c -Rf u+rwX,go-w .
+ echo 'Patch #0 (R-3.6.1-alt1.patch):'
Patch #0 (R-3.6.1-alt1.patch):
+ /usr/bin/patch -p1
patching file .gear/rules
patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0
patching file .gear/tags/1af743c7e25d963067c0a7736c2f362bc1a54087
patching file .gear/tags/2c68f436cffd98cb9581510d928bea5942555c48
patching file .gear/tags/70ae5201e8ecc68e51ed59c0bedcfa01dbb4b579
patching file .gear/tags/890191223501f9206c89761358c534357f6c76b8
patching file .gear/tags/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0
patching file .gear/tags/a267957eb382565da32225335ac89fb8c75df0da
patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5
patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e
patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020
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.8645
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.6.1
+ 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 -fno-strict-aliasing'
+ export CFLAGS
+ CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export CXXFLAGS
+ FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export FFLAGS
+ FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
+ export FCFLAGS
+ '[' -n '' ']'
++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing'
++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g'
+ ASFLAGS=
+ export ASFLAGS
+ export lt_cv_deplibs_check_method=pass_all
+ lt_cv_deplibs_check_method=pass_all
+ readlink -e -- ./configure
+ xargs -ri dirname -- '{}'
+ xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n'
+ sort -u
+ xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess
+ ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --disable-silent-rules --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --disable-rpath --with-system-tre --with-gnu-ld --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.6'
configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules
checking build system type... x86_64-alt-linux-gnu
checking host system type... x86_64-alt-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... (cached) less -isR
checking for gtar... /usr/bin/gtar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... /usr/bin/texi2any
checking whether texi2any version is at least 5.1... yes
checking for ginstall-info... no
checking for install-info... no
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
checking for unzip... (cached) unzip
checking for zip... (cached) zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... (cached) 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 x86_64-alt-linux-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-alt-linux-gcc accepts -g... yes
checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-alt-linux-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether x86_64-alt-linux-gcc needs -traditional... no
checking for 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... x86_64-alt-linux-gcc -E
looking for a modern Fortran compiler
checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether x86_64-alt-linux-gfortran accepts -g... yes
checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-alt-linux-g++ accepts -g... yes
checking whether x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing can compile C++ code... yes
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes
checking whether x86_64-alt-linux-g++ accepts -fvisibility... yes
checking whether x86_64-alt-linux-gfortran accepts -fvisibility... yes
checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc
checking whether we are using the GNU Objective C compiler... no
checking whether x86_64-alt-linux-gcc accepts -g... no
checking whether x86_64-alt-linux-g++ can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-alt-linux-gnu file names to x86_64-alt-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-alt-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-alt-linux-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... (cached) pass_all
checking for x86_64-alt-linux-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-alt-linux-ar... (cached) ar
checking for archiver @FILE support... @
checking for x86_64-alt-linux-strip... no
checking for strip... strip
checking for x86_64-alt-linux-ranlib... no
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for x86_64-alt-linux-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-gcc static flag -static works... no
checking if x86_64-alt-linux-gcc supports -c -o file.o... yes
checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E
checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-alt-linux-g++ static flag -static works... no
checking if x86_64-alt-linux-g++ supports -c -o file.o... yes
checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC
checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes
checking if x86_64-alt-linux-gfortran static flag -static works... no
checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes
checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes
checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking 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_callback_sigcleanup exists and is declared... 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 x86_64-alt-linux-gcc option to accept ISO C99... none needed
checking for x86_64-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... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes
checking for x86_64-alt-linux-gcc option to support OpenMP... -fopenmp
checking how to get verbose linking output from x86_64-alt-linux-gfortran... -v
checking for Fortran libraries of x86_64-alt-linux-gfortran...  -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from x86_64-alt-linux-gcc... -v
checking for C libraries of x86_64-alt-linux-gcc...  -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether x86_64-alt-linux-gfortran appends underscores to external names... yes
checking whether x86_64-alt-linux-gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on int and double... yes
checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on double complex... yes
checking for x86_64-alt-linux-gfortran option to support OpenMP... -fopenmp
checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes
checking whether we can compute ObjC Make dependencies... no
checking for ObjC runtime library... 
checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no
checking if need -fno-optimize-sibling-calls for gfortran... yes
checking for xmkmf... no
checking whether x86_64-alt-linux-g++  supports C++98 features with -std=gnu++98... yes
checking whether x86_64-alt-linux-g++  supports C++11 features with -std=gnu++11... yes
checking whether x86_64-alt-linux-g++  supports C++14 features with -std=gnu++14... yes
checking whether x86_64-alt-linux-g++  supports C++17 features with -std=gnu++17... yes
checking for x86_64-alt-linux-g++ -std=gnu++11 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking 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... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... yes
checking whether mktime works correctly outside 1902-2037... yes
checking 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/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh
checking for /usr/lib64/tkConfig.sh... /usr/lib64/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... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
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 mmap support for zlib... 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 for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... no
checking pcre.h presence... no
checking for pcre.h... no
checking pcre/pcre.h usability... yes
checking pcre/pcre.h presence... yes
checking for pcre/pcre.h... yes
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for pcre2-config... no
checking for tre_regncompb in -ltre... no
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.79.0
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 >= 7.22.0... yes
checking if libcurl supports https... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... 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... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... (cached) lpr
checking for paperconf... /usr/bin/paperconf
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for x86_64-alt-linux-gfortran option to support OpenMP... (cached) -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for x86_64-alt-linux-ranlib... ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... 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 x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking 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... 3.0.5, 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... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
config.status: creating etc/Makeconf
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configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules

R is now configured for x86_64-alt-linux-gnu

  Source directory:            .
  Installation directory:      /usr

  C compiler:                  x86_64-alt-linux-gcc  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  Fortran fixed-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing

  Default C++ compiler:        x86_64-alt-linux-g++ -std=gnu++11  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  C++98 compiler:              x86_64-alt-linux-g++ -std=gnu++98  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  C++11 compiler:              x86_64-alt-linux-g++ -std=gnu++11  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  C++14 compiler:              x86_64-alt-linux-g++ -std=gnu++14  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  C++17 compiler:              x86_64-alt-linux-g++ -std=gnu++17  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  Fortran free-form compiler:  x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing
  Obj-C compiler:	       x86_64-alt-linux-gcc 

  Interfaces supported:        X11, tcltk
  External libraries:          readline, BLAS(OpenBLAS), LAPACK(generic), curl
  Additional capabilities:     PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:             shared R library, R profiling, static HTML

  Capabilities skipped:        
  Options not enabled:         shared BLAS, memory profiling

  Recommended packages:        yes

configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
+ make -j16
make[1]: Nothing to be done for 'R'.
make[1]: Nothing to be done for 'R'.
make[2]: Nothing to be done for 'R'.
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts'
creating src/scripts/R.fe
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mkdir -p -- ../../bin
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mkdir -p -- ../../include
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making regcomp.d from regcomp.c
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making regerror.d from regerror.c
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making regexec.d from regexec.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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making tre-ast.d from tre-ast.c
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making tre-compile.d from tre-compile.c
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making tre-match-approx.d from tre-match-approx.c
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making tre-match-backtrack.d from tre-match-backtrack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making tre-match-parallel.d from tre-match-parallel.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making tre-mem.d from tre-mem.c
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make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making tre-stack.d from tre-stack.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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making tre-parse.d from tre-parse.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
making xmalloc.d from xmalloc.c
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-ast.c -o tre-ast.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regerror.c -o regerror.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regcomp.c -o regcomp.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-mem.c -o tre-mem.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c regexec.c -o regexec.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-stack.c -o tre-stack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c xmalloc.c -o xmalloc.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-parse.c -o tre-parse.o
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
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x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -fvisibility=hidden -c tre-compile.c -o tre-compile.o
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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
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making integrate.d from integrate.c
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making interv.d from interv.c
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making maxcol.d from maxcol.c
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making pretty.d from pretty.c
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making uncmin.d from uncmin.c
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dposl.f -o dposl.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dpbfa.f -o dpbfa.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c maxcol.c -o maxcol.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dpbsl.f -o dpbsl.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dpodi.f -o dpodi.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c interv.c -o interv.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dqrdc2.f -o dqrdc2.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dqrsl.f -o dqrsl.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dsvdc.f -o dsvdc.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c integrate.c -o integrate.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c uncmin.c -o uncmin.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c optim.c -o optim.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making mlutils.d from mlutils.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making d1mach.d from d1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making i1mach.d from i1mach.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making fmax2.d from fmax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making fmin2.d from fmin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making fprec.d from fprec.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making fround.d from fround.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making ftrunc.d from ftrunc.c
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making sign.d from sign.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making fsign.d from fsign.c
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making imax2.d from imax2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making imin2.d from imin2.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making chebyshev.d from chebyshev.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making log1p.d from log1p.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making gammalims.d from gammalims.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making lgammacor.d from lgammacor.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making stirlerr.d from stirlerr.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making bd0.d from bd0.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making gamma.d from gamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making lgamma.d from lgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making gamma_cody.d from gamma_cody.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making beta.d from beta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making lbeta.d from lbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making polygamma.d from polygamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making cospi.d from cospi.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making bessel_i.d from bessel_i.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making bessel_j.d from bessel_j.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making bessel_k.d from bessel_k.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making bessel_y.d from bessel_y.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making choose.d from choose.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making snorm.d from snorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making sexp.d from sexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making dgamma.d from dgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making pgamma.d from pgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making qgamma.d from qgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rgamma.d from rgamma.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making dbeta.d from dbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making pbeta.d from pbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making qbeta.d from qbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rbeta.d from rbeta.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making dunif.d from dunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making punif.d from punif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making qunif.d from qunif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making runif.d from runif.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dnorm.d from dnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making pnorm.d from pnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making qnorm.d from qnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rnorm.d from rnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dlnorm.d from dlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making plnorm.d from plnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qlnorm.d from qlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rlnorm.d from rlnorm.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making df.d from df.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pf.d from pf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qf.d from qf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rf.d from rf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dnf.d from dnf.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dt.d from dt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pt.d from pt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qt.d from qt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rt.d from rt.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dnt.d from dnt.c
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making dchisq.d from dchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pchisq.d from pchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qchisq.d from qchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rchisq.d from rchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rnchisq.d from rnchisq.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making dbinom.d from dbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pbinom.d from pbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making qbinom.d from qbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
making rbinom.d from rbinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rmultinom.d from rmultinom.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dcauchy.d from dcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pcauchy.d from pcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qcauchy.d from qcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dexp.d from dexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rcauchy.d from rcauchy.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making pexp.d from pexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making qexp.d from qexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rexp.d from rexp.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making dgeom.d from dgeom.c
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making pgeom.d from pgeom.c
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making qgeom.d from qgeom.c
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making rgeom.d from rgeom.c
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making dhyper.d from dhyper.c
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making phyper.d from phyper.c
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making qhyper.d from qhyper.c
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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making rhyper.d from rhyper.c
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making dnbinom.d from dnbinom.c
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making pnbinom.d from pnbinom.c
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making qnbinom.d from qnbinom.c
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making rnbinom.d from rnbinom.c
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making dpois.d from dpois.c
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making ppois.d from ppois.c
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making qpois.d from qpois.c
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making pweibull.d from pweibull.c
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making dweibull.d from dweibull.c
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making qweibull.d from qweibull.c
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making rweibull.d from rweibull.c
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making dlogis.d from dlogis.c
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making dnchisq.d from dnchisq.c
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making qnchisq.d from qnchisq.c
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making dnbeta.d from dnbeta.c
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making pnbeta.d from pnbeta.c
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making qnbeta.d from qnbeta.c
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making pnf.d from pnf.c
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making wilcox.d from wilcox.c
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c i1mach.c -o i1mach.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fprec.c -o fprec.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c d1mach.c -o d1mach.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fmin2.c -o fmin2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mlutils.c -o mlutils.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ftrunc.c -o ftrunc.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fround.c -o fround.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sign.c -o sign.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fmax2.c -o fmax2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c imax2.c -o imax2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fsign.c -o fsign.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c imin2.c -o imin2.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c log1p.c -o log1p.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lgammacor.c -o lgammacor.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gammalims.c -o gammalims.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chebyshev.c -o chebyshev.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stirlerr.c -o stirlerr.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bd0.c -o bd0.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gamma.c -o gamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lgamma.c -o lgamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c beta.c -o beta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gamma_cody.c -o gamma_cody.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lbeta.c -o lbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sexp.c -o sexp.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cospi.c -o cospi.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgamma.c -o dgamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dbeta.c -o dbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bessel_i.c -o bessel_i.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c choose.c -o choose.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qgamma.c -o qgamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bessel_k.c -o bessel_k.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rgamma.c -o rgamma.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dunif.c -o dunif.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pbeta.c -o pbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qunif.c -o qunif.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rbeta.c -o rbeta.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c runif.c -o runif.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c punif.c -o punif.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plnorm.c -o plnorm.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dnorm.c -o dnorm.o
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plogis.c -o plogis.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rweibull.c -o rweibull.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dlogis.c -o dlogis.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rhyper.c -o rhyper.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rlogis.c -o rlogis.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pweibull.c -o pweibull.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qbeta.c -o qbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qweibull.c -o qweibull.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qnbinom.c -o qnbinom.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dnbeta.c -o dnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qnbeta.c -o qnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpois.c -o rpois.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dnchisq.c -o dnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qpois.c -o qpois.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qlogis.c -o qlogis.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qnchisq.c -o qnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qtukey.c -o qtukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qnf.c -o qnf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pnf.c -o pnf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ptukey.c -o ptukey.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qnt.c -o qnt.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c signrank.c -o signrank.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pnbeta.c -o pnbeta.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pnt.c -o pnt.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pnchisq.c -o pnchisq.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c wilcox.c -o wilcox.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c toms708.c -o toms708.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
config.status: creating src/unix/Makefile
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making Rembedded.d from Rembedded.c
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making dynload.d from dynload.c
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making system.d from system.c
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making sys-unix.d from sys-unix.c
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making sys-std.d from sys-std.c
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making X11.d from X11.c
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rembedded.c -o Rembedded.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c X11.c -o X11.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dynload.c -o dynload.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c system.c -o system.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sys-unix.c -o sys-unix.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sys-std.c -o sys-std.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
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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-3.6.1/src/unix'
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x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.6.1"' \
  -o Rscript ./Rscript.c
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
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config.status: creating src/main/Makefile
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making Rdynload.d from Rdynload.c
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making Renviron.d from Renviron.c
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making agrep.d from agrep.c
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making altrep.d from altrep.c
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making arithmetic.d from arithmetic.c
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making apply.d from apply.c
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making array.d from array.c
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making bind.d from bind.c
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making builtin.d from builtin.c
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making character.d from character.c
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making coerce.d from coerce.c
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making complex.d from complex.c
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making colors.d from colors.c
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making connections.d from connections.c
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making context.d from context.c
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making cum.d from cum.c
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making debug.d from debug.c
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making datetime.d from datetime.c
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making deparse.d from deparse.c
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making devices.d from devices.c
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making dotcode.d from dotcode.c
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making dounzip.d from dounzip.c
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making dstruct.d from dstruct.c
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making duplicate.d from duplicate.c
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making edit.d from edit.c
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making engine.d from engine.c
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making errors.d from errors.c
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making envir.d from envir.c
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making eval.d from eval.c
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making format.d from format.c
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making gevents.d from gevents.c
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making gram-ex.d from gram-ex.c
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making grep.d from grep.c
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making identical.d from identical.c
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making gram.d from gram.c
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making graphics.d from graphics.c
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making inspect.d from inspect.c
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making inlined.d from inlined.c
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making iosupport.d from iosupport.c
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making internet.d from internet.c
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making localecharset.d from localecharset.c
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making lapack.d from lapack.c
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making list.d from list.c
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making mapply.d from mapply.c
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making logic.d from logic.c
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making main.d from main.c
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making match.d from match.c
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making names.d from names.c
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making memory.d from memory.c
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making options.d from options.c
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making objects.d from objects.c
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making paste.d from paste.c
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making plot3d.d from plot3d.c
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making plot.d from plot.c
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making platform.d from platform.c
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making print.d from print.c
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making plotmath.d from plotmath.c
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making printarray.d from printarray.c
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making printvector.d from printvector.c
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making qsort.d from qsort.c
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making raw.d from raw.c
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making printutils.d from printutils.c
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making radixsort.d from radixsort.c
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making random.d from random.c
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making registration.d from registration.c
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making rlocale.d from rlocale.c
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making relop.d from relop.c
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making seq.d from seq.c
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making saveload.d from saveload.c
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making scan.d from scan.c
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making sort.d from sort.c
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making serialize.d from serialize.c
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making source.d from source.c
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making split.d from split.c
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making sprintf.d from sprintf.c
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making startup.d from startup.c
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making subassign.d from subassign.c
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making summary.d from summary.c
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making subscript.d from subscript.c
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making subset.d from subset.c
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making sysutils.d from sysutils.c
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making times.d from times.c
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making unique.d from unique.c
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making version.d from version.c
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making g_alab_her.d from g_alab_her.c
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making g_cntrlify.d from g_cntrlify.c
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making util.d from util.c
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making g_fontdb.d from g_fontdb.c
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making Rmain.d from Rmain.c
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making g_her_glyph.d from g_her_glyph.c
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making alloca.d from alloca.c
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making strdup.d from strdup.c
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making strncasecmp.d from strncasecmp.c
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making mkdtemp.d from mkdtemp.c
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c colors.c -o colors.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Renviron.c -o Renviron.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c CommandLineArgs.c -o CommandLineArgs.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c context.c -o context.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c apply.c -o apply.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rdynload.c -o Rdynload.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c altrep.c -o altrep.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c RNG.c -o RNG.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cum.c -o cum.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c debug.c -o debug.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c complex.c -o complex.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dcf.c -o dcf.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c altclasses.c -o altclasses.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agrep.c -o agrep.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devices.c -o devices.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dstruct.c -o dstruct.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c builtin.c -o builtin.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c edit.c -o edit.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dounzip.c -o dounzip.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c character.c -o character.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c format.c -o format.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c array.c -o array.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gram-ex.c -o gram-ex.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c attrib.c -o attrib.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c duplicate.c -o duplicate.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gevents.c -o gevents.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c graphics.c -o graphics.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c deparse.c -o deparse.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c internet.c -o internet.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c inspect.c -o inspect.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c identical.c -o identical.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c inlined.c -o inlined.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c iosupport.c -o iosupport.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c localecharset.c -o localecharset.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lapack.c -o lapack.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c list.c -o list.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mapply.c -o mapply.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c main.c -o main.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dotcode.c -o dotcode.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coerce.c -o coerce.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bind.c -o bind.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c datetime.c -o datetime.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gram.c -o gram.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c errors.c -o errors.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c engine.c -o engine.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c match.c -o match.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plot3d.c -o plot3d.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plot.c -o plot.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c names.c -o names.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c envir.c -o envir.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c printvector.c -o printvector.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c logic.c -o logic.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c print.c -o print.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qsort.c -o qsort.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c registration.c -o registration.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c options.c -o options.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c arithmetic.c -o arithmetic.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c platform.c -o platform.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c paste.c -o paste.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c printutils.c -o printutils.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c printarray.c -o printarray.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rlocale.c -o rlocale.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c raw.c -o raw.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c objects.c -o objects.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c random.c -o random.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c relop.c -o relop.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c startup.c -o startup.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c grep.c -o grep.o
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c scan.c -o scan.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c source.c -o source.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c split.c -o split.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plotmath.c -o plotmath.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c times.c -o times.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c connections.c -o connections.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sysutils.c -o sysutils.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c radixsort.c -o radixsort.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c version.c -o version.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c g_fontdb.c -o g_fontdb.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c g_alab_her.c -o g_alab_her.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sprintf.c -o sprintf.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c g_her_glyph.c -o g_her_glyph.o
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c xxxpr.f -o xxxpr.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c g_cntrlify.c -o g_cntrlify.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c subscript.c -o subscript.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c summary.c -o summary.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c saveload.c -o saveload.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c seq.c -o seq.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c serialize.c -o serialize.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sort.c -o sort.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c subset.c -o subset.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c unique.c -o unique.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c memory.c -o memory.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c util.c -o util.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c subassign.c -o subassign.o
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c eval.c -o eval.o
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x86_64-alt-linux-gcc -shared -fopenmp -L/usr/local/lib64  -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o 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    -lopenblas -lgfortran -lm -lquadmath   -lreadline  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n  
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mkdir -p -- /usr/src/RPM/BUILD/R-3.6.1/bin/exec
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mkdir -p -- /usr/src/RPM/BUILD/R-3.6.1/lib
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x86_64-alt-linux-gcc -I../../src/extra  -I. -I../../src/include -I../../src/include  -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rmain.c -o Rmain.o
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x86_64-alt-linux-gcc -Wl,--export-dynamic -fopenmp  -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o  -lR 
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making Rsock.d from Rsock.c
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making Lapack.d from Lapack.c
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making rbitmap.d from rbitmap.c
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making Rhttpd.d from Rhttpd.c
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making nanoftp.d from nanoftp.c
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making libcurl.d from libcurl.c
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making rotated.d from rotated.c
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making nanohttp.d from nanohttp.c
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making internet.d from internet.c
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making sock.d from sock.c
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making sockconn.d from sockconn.c
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making devX11.d from devX11.c
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c sock.c -o sock.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c sockconn.c -o sockconn.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c Rsock.c -o Rsock.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c nanohttp.c -o nanohttp.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c nanoftp.c -o nanoftp.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c internet.c -o internet.o
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x86_64-alt-linux-gcc -I/usr/include/libpng16  -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pcre -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rbitmap.c -o rbitmap.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing   -fvisibility=hidden -c libcurl.c -o libcurl.o
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x86_64-alt-linux-gcc -I/usr/include/libpng16  -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pcre -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rotated.c -o rotated.o
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x86_64-alt-linux-gcc -I/usr/include/libpng16  -I. -I../../../src/include -I../../../src/include  -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pcre -I/usr/include/libpng16 -I../../../src/library/grDevices/src/cairo -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dataentry.c -o dataentry.o
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x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Lapack.c -o Lapack.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rmd5.c -o Rmd5.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c getfmts.c -o getfmts.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c install.c -o install.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c text.c -o text.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c md5.c -o md5.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c io.c -o io.o
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src'
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mkdir -p -- ../../../../library/utils/libs
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installing 'sysdata.rda'
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byte-compiling package 'utils'
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make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices'
building package 'grDevices'
mkdir -p -- ../../../library/grDevices
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mkdir -p -- ../../../library/grDevices/R
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mkdir -p -- ../../../library/grDevices/afm
mkdir -p -- ../../../library/grDevices/enc
mkdir -p -- ../../../library/grDevices/icc
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making axis_scales.d from axis_scales.c
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making chull.d from chull.c
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making devices.d from devices.c
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making init.d from init.c
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making stubs.d from stubs.c
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making colors.d from colors.c
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making devCairo.d from devCairo.c
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making devPicTeX.d from devPicTeX.c
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making devQuartz.d from devQuartz.c
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making devPS.d from devPS.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devCairo.c -o devCairo.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c axis_scales.c -o axis_scales.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devQuartz.c -o devQuartz.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stubs.c -o stubs.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devices.c -o devices.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chull.c -o chull.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devPicTeX.c -o devPicTeX.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c colors.c -o colors.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c devPS.c -o devPS.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src'
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mkdir -p -- ../../../../library/grDevices/libs
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making cairoBM.d from cairoBM.c
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x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pcre -I/usr/include/libpng16 -I../../../../../src/modules/X11 -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cairoBM.c -o cairoBM.o
make[9]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src/cairo'
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x86_64-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm 
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byte-compiling package 'grDevices'
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building package 'graphics'
mkdir -p -- ../../../library/graphics
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mkdir -p -- ../../../library/graphics/R
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making init.d from init.c
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making base.d from base.c
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making graphics.d from graphics.c
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making par.d from par.c
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making plot3d.d from plot3d.c
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making plot.d from plot.c
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making stem.d from stem.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stem.c -o stem.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c base.c -o base.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c graphics.c -o graphics.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c par.c -o par.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plot3d.c -o plot3d.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c plot.c -o plot.o
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src'
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byte-compiling package 'graphics'
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building package 'stats'
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making init.d from init.c
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making chisqsim.d from chisqsim.c
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making d2x2xk.d from d2x2xk.c
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making smooth.d from smooth.c
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making Srunmed.d from Srunmed.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
making hclust-utils.d from hclust-utils.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
making distance.d from distance.c
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making nls.d from nls.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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making rWishart.d from rWishart.c
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making HoltWinters.d from HoltWinters.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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making PPsum.d from PPsum.c
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making arima.d from arima.c
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making burg.d from burg.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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making filter.d from filter.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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making mAR.d from mAR.c
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making pacf.d from pacf.c
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making starma.d from starma.c
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making port.d from port.c
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making family.d from family.c
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making sbart.d from sbart.c
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making approx.d from approx.c
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making loglin.d from loglin.c
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making massdist.d from massdist.c
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making lowess.d from lowess.c
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making lm.d from lm.c
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making splines.d from splines.c
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making complete_cases.d from complete_cases.c
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making cov.d from cov.c
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making deriv.d from deriv.c
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making fft.d from fft.c
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making fourier.d from fourier.c
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making optim.d from optim.c
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making optimize.d from optimize.c
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making integrate.d from integrate.c
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making model.d from model.c
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making distn.d from distn.c
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making random.d from random.c
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making zeroin.d from zeroin.c
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making rcont.d from rcont.c
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making influence.d from influence.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bandwidths.c -o bandwidths.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c d2x2xk.c -o d2x2xk.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chisqsim.c -o chisqsim.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ansari.c -o ansari.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c prho.c -o prho.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c kendall.c -o kendall.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ksmooth.c -o ksmooth.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dblcen.c -o dblcen.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c kmeans.c -o kmeans.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c line.c -o line.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c isoreg.c -o isoreg.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c monoSpl.c -o monoSpl.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ks.c -o ks.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c smooth.c -o smooth.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c swilk.c -o swilk.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c distance.c -o distance.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c HoltWinters.c -o HoltWinters.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c hclust-utils.c -o hclust-utils.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c PPsum.c -o PPsum.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rWishart.c -o rWishart.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c burg.c -o burg.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c family.c -o family.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c loessc.c -o loessc.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nls.c -o nls.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c approx.c -o approx.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c massdist.c -o massdist.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Srunmed.c -o Srunmed.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c loglin.c -o loglin.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c filter.c -o filter.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lowess.c -o lowess.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pacf.c -o pacf.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sbart.c -o sbart.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lm.c -o lm.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c port.c -o port.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c integrate.c -o integrate.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c splines.c -o splines.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fourier.c -o fourier.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rcont.c -o rcont.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c zeroin.c -o zeroin.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c starma.c -o starma.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cov.c -o cov.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c influence.c -o influence.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bvalus.f -o bvalus.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bvalue.f -o bvalue.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bsplvd.f -o bsplvd.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c complete_cases.c -o complete_cases.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qsbart.f -o qsbart.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c deriv.c -o deriv.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stxwx.f -o stxwx.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sgram.f -o sgram.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c eureka.f -o eureka.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fft.c -o fft.o
fft.c: In function 'fft_work':
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
     nfac--;/*the global one!*/
     ~~~~^~
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sinerp.f -o sinerp.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c hclust.f -o hclust.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c kmns.f -o kmns.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sslvrg.f -o sslvrg.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lminfl.f -o lminfl.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c optimize.c -o optimize.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c optim.c -o optim.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c arima.c -o arima.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stl.f -o stl.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c loessf.f -o loessf.o
loessf.f:60:14:

             j=DBLE(j)/2.D0
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1894:14:

             m=DBLE(l+u)/2.D0
              1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1399:20:

                   i=phi(pi(ii))
                    1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:928:12:

          lg=DBLE(lg)/2.D0
            1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:523:22:

       if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1205:13:

       ifloor=x
             1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:835:22:

       if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0
                      1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:1583:18:

                i1=dble((d+2)*(d+1))/2.d0
                  1
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion]
loessf.f:473:25:

       subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                         1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
loessf.f:473:39:

       subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s)
                                       1
Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument]
loessf.f:828:31:

       subroutine ehg197(deg,tau,d,f,dk,trl)
                               1
Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument]
loessf.f:1985:31:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                               1
Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument]
loessf.f:1985:47:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                                               1
Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument]
loessf.f:1985:53:

       subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi)
                                                     1
Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument]
loessf.f:1498:50:

       subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
                                                  1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1498:53:

       subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv)
                                                     1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1649:30:

       subroutine lowese(iv,liv,lv,wv,m,z,s)
                              1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1649:33:

       subroutine lowese(iv,liv,lv,wv,m,z,s)
                                 1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1668:39:

       subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
                                       1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1668:42:

       subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s)
                                          1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1700:30:

       subroutine lowesl(iv,liv,lv,wv,m,z,l)
                              1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1700:33:

       subroutine lowesl(iv,liv,lv,wv,m,z,l)
                                 1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
loessf.f:1722:33:

       subroutine lowesr(yy,iv,liv,lv,wv)
                                 1
Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument]
loessf.f:1722:36:

       subroutine lowesr(yy,iv,liv,lv,wv)
                                    1
Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c distn.c -o distn.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fexact.c -o fexact.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mAR.c -o mAR.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ppr.f -o ppr.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c random.c -o random.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fopenmp -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c model.c -o model.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gfortran -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o
portsrc.f:6658:0:

          NCOMP = NCOMP + 1
 
Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:6569:0:

       INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC,
 
Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:5516:0:

       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:5653:0:

               IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310
 
Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10407:0:

       V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA)
 
Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10324:0:

       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:10319:0:

       LK = DMAX1(LK, PHI*W(PHIPIN))
 
Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:10461:0:

       IF (KA .GE. KAMIN) GO TO 340
 
Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12238:0:

       V(NREDUC) = NRED
 
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12241:0:

       V(DST0) = DNWTST
 
Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2510:0:

       V(NREDUC) = NRED
 
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:2509:0:

  60   V(DST0) = DS0
 
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8169:0:

       V(NREDUC) = NRED
 
Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8168:0:

  90   V(DST0) = DS0
 
Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:8647:0:

  210  IV(FDH) = HES
 
Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:3582:0:

       IF (LIV .LT. MIV2) GO TO 300
 
Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized]
portsrc.f:12074:0:

  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:453:0:

  300  CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X)
 
Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
mkdir -p -- ../../../../library/stats/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats'
byte-compiling package 'stats'
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets'
building package 'datasets'
mkdir -p -- ../../../library/datasets
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets'
mkdir -p -- ../../../library/datasets/data
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
building package 'methods'
mkdir -p -- ../../../library/methods
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
mkdir -p -- ../../../library/methods/R
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
making init.d from init.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
making do_substitute_direct.d from do_substitute_direct.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
making methods_list_dispatch.d from methods_list_dispatch.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
making slot.d from slot.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
making class_support.d from class_support.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
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making tests.d from tests.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
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making utils.d from utils.c
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c slot.c -o slot.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c do_substitute_direct.c -o do_substitute_direct.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c class_support.c -o class_support.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c tests.c -o tests.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c utils.c -o utils.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H  -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c methods_list_dispatch.c -o methods_list_dispatch.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
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mkdir -p -- ../../../../library/methods/libs
make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src'
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
byte-compiling 'methods'
initializing class and method definitions ... done
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid'
building package 'grid'
mkdir -p -- ../../../library/grid
mkdir -p -- ../../../library/grid/doc
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mkdir -p -- ../../../library/grid/R
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making grid.d from grid.c
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making just.d from just.c
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making gpar.d from gpar.c
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making layout.d from layout.c
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making matrix.d from matrix.c
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making register.d from register.c
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making state.d from state.c
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making unit.d from unit.c
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making util.d from util.c
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making viewport.d from viewport.c
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make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c just.c -o just.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c register.c -o register.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c util.c -o util.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gpar.c -o gpar.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c state.c -o state.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c viewport.c -o viewport.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c layout.c -o layout.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c unit.c -o unit.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c grid.c -o grid.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src'
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mkdir -p -- ../../../../library/grid/libs
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byte-compiling package 'grid'
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building package 'splines'
mkdir -p -- ../../../library/splines
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mkdir -p -- ../../../library/splines/R
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making splines.d from splines.c
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c splines.c -o splines.o
make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src'
make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src'
x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR
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mkdir -p -- ../../../../library/splines/libs
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byte-compiling package 'splines'
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building package 'stats4'
mkdir -p -- ../../../library/stats4
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mkdir -p -- ../../../library/stats4/R
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
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x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c tcltk_unix.c -o tcltk_unix.o
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configuring Java ...
Java interpreter : /usr/lib/jvm/java/jre/bin/java
Java version     : 1.8.0_212
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JAVA_HOME        : /usr/lib/jvm/java
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Updating Java configuration in /usr/src/RPM/BUILD/R-3.6.1
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    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  
    pmatch                                  html  
    polyroot                                html  
    pos.to.env                              html  
    pretty                                  html  
    print                                   html  
Rd warning: /usr/src/RPM/BUILD/R-3.6.1/src/library/base/man/print.Rd:86: file link '.print.via.format' in package 'tools' does not exist and so has been treated as a topic
    print.dataframe                         html  
    print.default                           html  
    prmatrix                                html  
    proc.time                               html  
    prod                                    html  
    prop.table                              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  
Rd warning: /usr/src/RPM/BUILD/R-3.6.1/src/library/tools/man/check_packages_in_dir.Rd:123: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    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  
    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  
    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                                    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  
    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  
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  converting help for package 'methods'
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  converting help for package 'splines'
    asVector                                html  
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make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package MASS
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package lattice
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package codetools
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package foreign
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package rpart
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package KernSmooth
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package nnet
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package spatial
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpZbqkyw/R.INSTALL227e5b6baab6f6/nnet/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nnet.c -o nnet.o
make[3]: Leaving directory '/usr/src/tmp/RtmpZbqkyw/R.INSTALL227e5b6baab6f6/nnet/src'
make[3]: Entering directory '/usr/src/tmp/RtmpZbqkyw/R.INSTALL227e5b6baab6f6/nnet/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpZbqkyw/R.INSTALL227e5b6baab6f6/nnet/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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  
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** 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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgesl.f -o dgesl.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c linbin2D.f -o linbin2D.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgedi.f -o dgedi.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c blkest.f -o blkest.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgefa.f -o dgefa.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c linbin.f -o linbin.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c locpoly.f -o locpoly.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rlbin.f -o rlbin.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cp.f -o cp.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sdiag.f -o sdiag.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sstdiag.f -o sstdiag.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp6zdGRu/R.INSTALL227e526926611d/KernSmooth/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    dpih                                    html  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pps.c -o pps.o
make[3]: Leaving directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c krc.c -o krc.o
make[3]: Leaving directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
make[3]: Entering directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpeM7Xiu/R.INSTALL227e5e53ec2033/spatial/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rdbfwrite.c -o Rdbfwrite.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c avl.c -o avl.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Rdbfread.c -o Rdbfread.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c file-handle.c -o file-handle.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c SASxport.c -o SASxport.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c format.c -o format.o
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make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c R_systat.c -o R_systat.o
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make[3]: Entering directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c minitab.c -o minitab.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dbfopen.c -o dbfopen.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c spss.c -o spss.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c stataread.c -o stataread.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pfm-read.c -o pfm-read.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sfm-read.c -o sfm-read.o
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
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x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmp9XgKop/R.INSTALL227d9d5a9541b7/foreign/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c anovapred.c -o anovapred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c branch.c -o branch.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c bsplit.c -o bsplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c anova.c -o anova.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c free_tree.c -o free_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fix_cp.c -o fix_cp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c choose_surg.c -o choose_surg.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c make_cp_list.c -o make_cp_list.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gini.c -o gini.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c insert_split.c -o insert_split.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c make_cp_table.c -o make_cp_table.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c graycode.c -o graycode.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mysort.c -o mysort.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c partition.c -o partition.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pred_rpart.c -o pred_rpart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c print_tree.c -o print_tree.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nodesplit.c -o nodesplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c poisson.c -o poisson.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpartexp2.c -o rpartexp2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpartexp.c -o rpartexp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpcountup.c -o rpcountup.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpart_callback.c -o rpart_callback.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rundown2.c -o rundown2.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpmatrix.c -o rpmatrix.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rundown.c -o rundown.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c usersplit.c -o usersplit.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rpart.c -o rpart.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c surrogate.c -o surrogate.o
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make[3]: Entering directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c xval.c -o xval.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c xpred.c -o xpred.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpYWfvax/R.INSTALL227e8c34df021a/rpart/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    kyphosis                                html  
    labels.rpart                            html  
    meanvar.rpart                           html  
    na.rpart                                html  
    path.rpart                              html  
    plot.rpart                              html  
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    post.rpart                              html  
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    residuals.rpart                         html  
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    rpart.exp                               html  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c MASS.c -o MASS.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lqs.c -o lqs.o
make[3]: Leaving directory '/usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
make[3]: Entering directory '/usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    mvrnorm                                 html  
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    pairs.lda                               html  
Rd warning: /usr/src/tmp/Rtmpou3HAl/R.INSTALL227d4c5dae0c37/MASS/man/pairs.lda.Rd:42: missing file link 'splom'
    parcoord                                html  
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    plot.mca                                html  
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    predict.glmmPQL                         html  
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** 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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package class
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package cluster
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpoAJdtk/R.INSTALL22e0277348aca5/class/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c class.c -o class.o
make[3]: Leaving directory '/usr/src/tmp/RtmpoAJdtk/R.INSTALL22e0277348aca5/class/src'
make[3]: Entering directory '/usr/src/tmp/RtmpoAJdtk/R.INSTALL22e0277348aca5/class/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpoAJdtk/R.INSTALL22e0277348aca5/class/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    multiedit                               html  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c threeDplot.c -o threeDplot.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpaNGeVp/R.INSTALL227d643e7170c/lattice/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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'
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    Lattice                                 html  
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    trellis.par.get                         html  
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    utilities.3d                            html  
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** 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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package Matrix
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package nlme
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dysta.f -o dysta.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c daisy.f -o daisy.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c spannel.c -o spannel.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sildist.c -o sildist.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mona.c -o mona.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c fanny.c -o fanny.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c twins.c -o twins.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c clara.c -o clara.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pam.c -o pam.o
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
make[3]: Entering directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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Rd warning: /usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
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Rd warning: /usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/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/RtmpYA2Hil/R.INSTALL22e0239e18433/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  
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    lower.to.upper.tri.inds                 html  
    mona                                    html  
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    partition.object                        html  
    plantTraits                             html  
    plot.agnes                              html  
Rd warning: /usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/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  
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    print.dissimilarity                     html  
Rd warning: /usr/src/tmp/RtmpYA2Hil/R.INSTALL22e0239e18433/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  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chol.f -o chol.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nlOptimizer.c -o nlOptimizer.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gnls.c -o gnls.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pythag.c -o pythag.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nlme.c -o nlme.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pdMat.c -o pdMat.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gfortran -fno-optimize-sibling-calls  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c rs.f -o rs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c corStruct.c -o corStruct.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fvisibility=hidden -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c nlmefit.c -o nlmefit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
make[3]: Entering directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
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    BodyWeight                              html  
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    Coef                                    html  
    Covariate                               html  
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    Dim                                     html  
    Dim.corSpatial                          html  
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    Dim.pdMat                               html  
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    Fatigue                                 html  
    Gasoline                                html  
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    Glucose2                                html  
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    Initialize                              html  
    Initialize.corStruct                    html  
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    LDEsysMat                               html  
    Machines                                html  
    MathAchSchool                           html  
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    Matrix                                  html  
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    Meat                                    html  
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    Names.pdBlocked                         html  
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    anova.gls                               html  
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    as.matrix.corStruct                     html  
    as.matrix.pdMat                         html  
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    coef.modelStruct                        html  
    coef.pdMat                              html  
    coef.reStruct                           html  
    coef.varFunc                            html  
    collapse                                html  
    collapse.groupedData                    html  
    compareFits                             html  
    comparePred                             html  
    corAR1                                  html  
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    corFactor.corStruct                     html  
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    corMatrix                               html  
    corMatrix.corStruct                     html  
    corMatrix.pdMat                         html  
    corMatrix.reStruct                      html  
    corNatural                              html  
    corRatio                                html  
    corSpatial                              html  
    corSpher                                html  
    corSymm                                 html  
    ergoStool                               html  
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    fitted.glsStruct                        html  
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    fixed.effects                           html  
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    gapply                                  html  
    getCovariate                            html  
    getCovariate.corStruct                  html  
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    groupedData                             html  
    gsummary                                html  
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    intervals.gls                           html  
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    model.matrix.reStruct                   html  
    needUpdate                              html  
    needUpdate.modelStruct                  html  
    nlme                                    html  
    nlme.nlsList                            html  
    nlmeControl                             html  
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    nlmeStruct                              html  
    nlsList                                 html  
    nlsList.selfStart                       html  
    pairs.compareFits                       html  
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    phenoModel                              html  
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Rd warning: /usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    plot.lmList                             html  
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    plot.nffGroupedData                     html  
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    plot.ranef.lme                          html  
Rd warning: /usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpiafPoh/R.INSTALL22f9ce3ef5833f/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    pooledSD                                html  
    predict.gls                             html  
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    predict.lmList                          html  
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    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  
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    recalc.varFunc                          html  
    residuals.gls                           html  
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    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  
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    summary.modelStruct                     html  
    summary.nlsList                         html  
    summary.pdMat                           html  
    summary.varFunc                         html  
    update.modelStruct                      html  
    update.varFunc                          html  
    varClasses                              html  
    varComb                                 html  
    varConstPower                           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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Tsparse.c -o Tsparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgTMatrix.c -o dgTMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cs_utils.c -o cs_utils.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c CHMfactor.c -o CHMfactor.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dpoMatrix.c -o dpoMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgCMatrix.c -o dgCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dspMatrix.c -o dspMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c TMatrix_as.c -o TMatrix_as.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dtTMatrix.c -o dtTMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dppMatrix.c -o dppMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dsCMatrix.c -o dsCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dtpMatrix.c -o dtpMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dsyMatrix.c -o dsyMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c factorizations.c -o factorizations.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dtCMatrix.c -o dtCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ldense.c -o ldense.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sparseQR.c -o sparseQR.o
In file included from /usr/src/RPM/BUILD/R-3.6.1/include/R.h:91,
                 from Mutils.h:12,
                 from sparseQR.h:4,
                 from sparseQR.c:1:
sparseQR.c: In function 'sparseQR_coef':
/usr/src/RPM/BUILD/R-3.6.1/include/R_ext/RS.h:74:25: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Free(p)        (R_chk_free( (void *)(p) ), (p) = NULL)
                         ^~~~~~~~~~
sparseQR.c:172:53: note: 'x' was declared here
     double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x;
                                                     ^
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c lgCMatrix.c -o lgCMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
( cd Lib ; make clean )
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c abIndex.c -o abIndex.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dense.c -o dense.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
( cd Source ; make clean )
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dtrMatrix.c -o dtrMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
( cd Lib ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile )
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chm_common.c -o chm_common.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_error.c -o cholmod_error.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_aat.c -o cholmod_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dgeMatrix.c -o dgeMatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_complex.c -o cholmod_complex.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_add.c -o cholmod_add.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_common.c -o cholmod_common.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_version.c -o cholmod_version.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_factor.c -o cholmod_factor.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_band.c -o cholmod_band.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_memory.c -o cholmod_memory.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Mutils.c -o Mutils.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^~
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Check/cholmod_read.c -o cholmod_read.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c Csparse.c -o Csparse.o
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     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:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^~
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
In file included from ../Core/cholmod_change_factor.c:118:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^~
In file included from ../Core/cholmod_dense.c:50:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^~
In file included from ../Core/cholmod_dense.c:52:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^~
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^~
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^~
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^~
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^~
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^~
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
                  ^
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^~~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^~
In file included from ../Core/cholmod_triplet.c:110:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
In file included from ../Core/cholmod_triplet.c:112:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^~
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^~
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^~
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^~~~
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^~~~~~~
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:116:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
In file included from ../Core/cholmod_change_factor.c:118:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^~~~~
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^~
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^~
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^~
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^~
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^~~
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:124:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^~
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^~
In file included from ../Core/cholmod_transpose.c:126:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:131:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^~
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^~
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
In file included from ../Core/cholmod_transpose.c:136:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^~~~~~~
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^~~~~~~
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^~~~
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^~~
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     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:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     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 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^~~~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:28:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  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:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^~
In file included from ../Cholesky/cholmod_solve.c:69:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:78:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^~
In file included from ../Supernodal/cholmod_super_numeric.c:80:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^~
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -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:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^~~~~~~~~~
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^~
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^~~
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^~~~~~~
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     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:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:166:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:168:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
In file included from ../Cholesky/cholmod_rowfac.c:172:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:174:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^~
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^~
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^~
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^~
In file included from ../Cholesky/cholmod_rowfac.c:176:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^~~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     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 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^~
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^~
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^~
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^~
In file included from ../MatrixOps/cholmod_sdmult.c:50:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^~~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^~
In file included from ../Cholesky/cholmod_solve.c:69:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^~
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^~~
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/CHOLMOD/Lib'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c colamd_global.c -o colamd_global.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c colamd.c -o colamd.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c colamd.c -o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/COLAMD/Source'
( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile lib )
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_global.c -o amd_i_global.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[5]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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 amd_i_global.o amd_l_global.o 
make[5]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/AMD/Source'
make[4]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/SuiteSparse_config'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER  -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c SuiteSparse_config.c -o SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/SuiteSparse_config'
make[4]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/SuiteSparse_config'
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
make[4]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src/SuiteSparse_config'
make[3]: Entering directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/Matrix/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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  
    matrix-products                         html  
Rd warning: /usr/src/tmp/RtmpaQGeHh/R.INSTALL22f9d64b09f764/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  
    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  
** 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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package mgcv
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package survival
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agmart.c -o agmart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agmart2.c -o agmart2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agscore.c -o agscore.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agsurv4.c -o agsurv4.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agmart3.c -o agmart3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agsurv5.c -o agsurv5.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chinv3.c -o chinv3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cholesky2.c -o cholesky2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chinv2.c -o chinv2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chsolve3.c -o chsolve3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cholesky5.c -o cholesky5.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chsolve2.c -o chsolve2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c chsolve5.c -o chsolve5.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agexact.c -o agexact.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agsurv3.c -o agsurv3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cholesky3.c -o cholesky3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c cox_Rcallback.c -o cox_Rcallback.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c concordance1.c -o concordance1.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxsafe.c -o coxsafe.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxph_wtest.c -o coxph_wtest.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxdetail.c -o coxdetail.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxmart.c -o coxmart.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxmart2.c -o coxmart2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxscho.c -o coxscho.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c dmatrix.c -o dmatrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c doloop.c -o doloop.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxcount1.c -o coxcount1.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxscore.c -o coxscore.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c finegray.c -o finegray.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c concordance3.c -o concordance3.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxfit6.c -o coxfit6.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxexact.c -o coxexact.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pystep.c -o pystep.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survConcordance.c -o survConcordance.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pyears2.c -o pyears2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pyears3b.c -o pyears3b.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survfit4.c -o survfit4.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c pyears1.c -o pyears1.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survdiff2.c -o survdiff2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survpenal.c -o survpenal.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxfit5.c -o coxfit5.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c tmerge.c -o tmerge.o
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survsplit.c -o survsplit.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survreg6.c -o survreg6.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survregc1.c -o survregc1.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survfitci.c -o survfitci.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survregc2.c -o survregc2.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c agfit4.c -o agfit4.o
agfit4.c: In function 'agfit4':
agfit4.c:575:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized]
                     if (tstop[p] < dtime) break; /* no more to add */
                        ^
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
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x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survreg7.c -o survreg7.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include  -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c survfitkm.c -o survfitkm.o
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
make[3]: Entering directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.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 coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
    Survmethods                             html  
    aareg                                   html  
    aeqSurv                                 html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    cipoisson                               html  
Rd warning: /usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpKHscY2/R.INSTALL2506f55e29a84f/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic
    clogit                                  html  
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    concordance                             html  
    concordancefit                          html  
    cox.zph                                 html  
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    flchain                                 html  
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    is.ratetable                            html  
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    levels.Surv                             html  
    lines.survfit                           html  
    logLik.coxph                            html  
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    model.frame.coxph                       html  
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    summary.aareg                           html  
    summary.coxph                           html  
    summary.pyears                          html  
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    summary.survfit                         html  
    survConcordance-deprecated              html  
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    survfit.coxph                           html  
    survfit.formula                         html  
    survfit.matrix                          html  
    survfit.object                          html  
    survfitcoxph.fit                        html  
    survival-internal                       html  
    survobrien                              html  
    survreg                                 html  
    survreg.control                         html  
    survreg.distributions                   html  
    survreg.object                          html  
    survregDtest                            html  
    tcut                                    html  
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    tobin                                   html  
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    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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
begin installing recommended package boot
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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  
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    k3.linear                               html  
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    print.saddle.distn                      html  
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    saddle.distn.object                     html  
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    tilt.boot                               html  
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** 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-3.6.1/src/library/Recommended'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c init.c -o init.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mvn.c -o mvn.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c tprs.c -o tprs.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c coxph.c -o coxph.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c soap.c -o soap.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c matrix.c -o matrix.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c qp.c -o qp.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c misc.c -o misc.o
misc.c: In function 'tweedious':
misc.c:321:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if (j_max>j_hi) j_max = j_hi; if (j_max<j_lo) j_max = j_lo;
     ^~
misc.c:321:35: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
     if (j_max>j_hi) j_max = j_hi; if (j_max<j_lo) j_max = j_lo;
                                   ^~
misc.c:401:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
misc.c:485:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mgcv.c -o mgcv.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c magic.c -o magic.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c sparse-smooth.c -o sparse-smooth.o
sparse-smooth.c: In function 'Rkdnearest':
sparse-smooth.c:996:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   if (!dim_sym) dim_sym = install("dim");if (!dist_sym) dist_sym = install("dist");
   ^~
sparse-smooth.c:996:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   if (!dim_sym) dim_sym = install("dim");if (!dist_sym) dist_sym = install("dist");
                                          ^~
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c discrete.c -o discrete.o
discrete.c: In function 'indReduce':
discrete.c:101:24: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
  i=ka[l+1];j=kb[l];Wij = wl[l];
                    ~~~~^~~~~~~
discrete.c:99:31: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
         i=ka[l];j=kb[l+1];Wij = ws[l];
                           ~~~~^~~~~~~
discrete.c: In function 'XWXijs':
discrete.c:834:9: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
         ^
discrete.c:834:6: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
      ^
discrete.c:1019:27: warning: 'W' may be used uninitialized in this function [-Wmaybe-uninitialized]
     W[*Kik + mim * *Kjk1] += *ps *  *p3;
                           ^~
discrete.c:1050:51: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
          *pwi = *pw * *p0;*psi = *ps * *p0;*pli = *pl * *p2;
                                                   ^~~
discrete.c: In function 'XWXd0':
discrete.c:1288:11: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
   #pragma omp parallel for private(j,kb,kk,r,c,rb,cb,rt,ct,tid,i) num_threads(*nthreads) schedule(dynamic)
           ^~~
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c gdi.c -o gdi.o
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -c mat.c -o mat.o
mat.c: In function 'chol_down':
mat.c:1747:9: warning: unused variable 'j' [-Wunused-variable]
   int i,j,n1;
         ^
mat.c: In function 'chol_up':
mat.c:1872:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
       if (*n>1) R[1] = -2.0;return; /* signals error */
       ^~
mat.c:1872:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
       if (*n>1) R[1] = -2.0;return; /* signals error */
                             ^~~~~~
mat.c: In function 'Rlanczos':
mat.c:3467:15: warning: 'cir' may be used uninitialized in this function [-Wmaybe-uninitialized]
       #pragma omp parallel private(i,ri) num_threads(*nt)
               ^~~
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
make[3]: Entering directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o mgcv.so coxph.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 tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR
make[3]: Leaving directory '/usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/src'
installing to /usr/src/RPM/BUILD/R-3.6.1/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  
    anova.gam                               html  
    bam                                     html  
Rd warning: /usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/man/bam.Rd:14: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/man/bam.Rd:129: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: /usr/src/tmp/RtmpNK8gW2/R.INSTALL2506ee3c1ba39f/mgcv/man/bam.Rd:188: file link 'makeForkCluster' in package 'parallel' does not exist and so has been treated as a topic
    bam.update                              html  
    bandchol                                html  
    bug.reports.mgcv                        html  
    cSplineDes                              html  
    chol.down                               html  
    choose.k                                html  
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    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.models                              html  
    gam.outer                               html  
    gam.reparam                             html  
    gam.scale                               html  
    gam.selection                           html  
    gam.side                                html  
    gam.vcomp                               html  
    gam2objective                           html  
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    gamlss.etamu                            html  
    gamlss.gH                               html  
    gamm                                    html  
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    get.var                                 html  
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
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[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
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[4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4
[15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29]
(Function and variable index) [30] [31] (Concept index) [32] [33] )
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[4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4
[15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29]
(Function and variable index) [30] [31] (Concept index) [32] [33] )
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
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[59] [60] (Function and variable index) [61]
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[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]
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texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] )
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
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@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
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[44] Chapter 8 [45] [46]
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[47] [48] [49] [50] [51] [52]
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[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] )
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[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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[46] [47] [48] [49] [50] (Function and Variable Index) [51]
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[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
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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[46] [47] [48] [49] [50] (Function and Variable Index) [51] [52]
(Concept Index) [53] Appendix A [54] [55] )
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[46] [47] [48] [49] [50] (Function and Variable Index) [51] [52]
(Concept Index) [53] Appendix A [54] [55] )
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[37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47]
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[78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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[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]
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[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] )
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[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] </us
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[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]
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[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]
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[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
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[62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78]
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[81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92]
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" -lpackB[] 
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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[147]
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[148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158]
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[164] [165] [166] [167] [168]
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Chapter 7 [169] [170] Chapter 8 [171] [172] [173]
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[2] [3] [4] [5]
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[]@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]
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[27] [28] [29]
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[][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org
 / std / standing-documents / 
[30]
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11PICFLAGS)")[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45]
[46] [47] [48] [49] [50] [51] [52] [53]
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= "."))[] 

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version 52.0[] 
[54] [55] [56] [57] [58] [59] [60] [61]
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 []@texttt 'register' storage class specifier is deprecated and incompatible wi
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[62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78]
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[]@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi
lename@texttt }[] @textrm and
[79] [80]
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[]@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu
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[81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92]
Chapter 4 [93] [94] [95] [96] [97]
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[]@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by
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[98] [99] [100]
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[][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs 
/ LightningTalks / EuroLLVM%202014%20--%20container%20overflow .
[101] [102]
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[108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118]
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 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de
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[119] [120] [121] [122] [123] [124] [125]
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" -lpackB[] 
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
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[147]
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 []    @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_
NilValue);[] 
[148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158]
[159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163]
[164] [165] [166] [167] [168]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [169] [170] Chapter 8 [171] [172] [173]
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[175] [176] [177] [178] [179] [180]
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[181] [182]
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er-wise, it is \T1/pcr/m/n/10 (double.base

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\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

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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5] [6] [7]
Underfull \hbox (badness 10000) in paragraph at lines 339--342
[][][]\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]
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[]\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] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15]
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 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 

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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
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[]\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] [26]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
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[]\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]
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[]\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]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

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[]\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
[32] [33] [34] [35]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

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[][][]\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
[38]
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[]\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
[39] [40]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 

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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 

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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
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 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

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\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
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 

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 []      \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = NA)[] 

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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-

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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[70] [71] [72]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5430--5438
[]\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
[82] [83] [84] [85] [86] [87] [88] [89]
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[]\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 : / /
[90] [91] [92]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 

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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 

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 []\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}[] 
[93] [94]
Underfull \hbox (badness 1242) in paragraph at lines 6325--6329
\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.

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[]\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

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[]\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
[95]
Underfull \hbox (badness 1308) in paragraph at lines 6402--6410
[]\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
[96] [97]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6556--6556
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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

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\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
[101] [102]
Underfull \hbox (badness 1406) in paragraph at lines 6928--6934
[]\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

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\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

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\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

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\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

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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
Underfull \hbox (badness 1067) in paragraph at lines 6990--6997
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7182--7182
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
Underfull \hbox (badness 1231) in paragraph at lines 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
Underfull \hbox (badness 10000) in paragraph at lines 7518--7520
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7663--7663
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7901--7901
 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting

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[]\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

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[][]\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
[119]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8053--8057
[]\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")
[120] [121] [122] [123] [124] [125]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\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

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\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 =
[126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 8801--8802
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
Underfull \hbox (badness 10000) in paragraph at lines 8987--8991
[]\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
[132] [133]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 

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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 

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 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 

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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
Underfull \hbox (badness 5403) in paragraph at lines 9224--9226
[]\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 9243--9245
[]\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
[136] [137] [138]
Underfull \hbox (badness 1603) in paragraph at lines 9454--9457
[]\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
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10060--10065
[]\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

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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 

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 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
Underfull \hbox (badness 1168) in paragraph at lines 10218--10223
\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
[150]
Underfull \hbox (badness 10000) in paragraph at lines 10257--10263
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as

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[]\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
[151] [152]
Underfull \hbox (badness 2828) in paragraph at lines 10423--10427
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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\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 / Double _

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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10529--10529
 []\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, ..[] 
[155] [156]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10673--10673
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\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

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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11088--11091
[]\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
[163] [164] [165] [166] [167] [168] [169] [170] [171]
Underfull \hbox (badness 5288) in paragraph at lines 11786--11788
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
Underfull \hbox (badness 3039) in paragraph at lines 11796--11801
[]\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

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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
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[]\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

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\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
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12093--12095
[]\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
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12934--12934
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 2221) in paragraph at lines 13380--13389
\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 13380--13389
\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
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
Underfull \hbox (badness 2573) in paragraph at lines 13756--13758
[]\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 =
[200] [201]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13908
[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[202] [203]
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[][][]\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 ,

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
Underfull \hbox (badness 10000) in paragraph at lines 14162--14165
[][][]\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 14172--14172
 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
Underfull \hbox (badness 10000) in paragraph at lines 14238--14241
[]\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 14255--14255
 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 

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[]\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 14308--14315
\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(

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[]\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,
[208] [209] [210]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 14480--14480
 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
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 []\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 14714--14714
 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
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[]\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-

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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
Underfull \hbox (badness 6944) in paragraph at lines 14896--14899
[][][]\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 ,
[216]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
Underfull \hbox (badness 10000) in paragraph at lines 15059--15061
[]\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

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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 

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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
Underfull \hbox (badness 2790) in paragraph at lines 15092--15095
[]\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

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[]\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
[220]
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[]\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 15198--15200
\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this

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[]\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

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[]\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 =
[221]
Underfull \hbox (badness 10000) in paragraph at lines 15232--15236
[]\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

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\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 15237--15245
[]\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
[222]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15345--15345
 []\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 ")[] 

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Overfull \hbox (42.18039pt too wide) in paragraph at lines 15367--15367
 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16184--16184
 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[236]
Underfull \hbox (badness 2418) in paragraph at lines 16293--16297
\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
 ,

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[]\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
[237]
Underfull \hbox (badness 2326) in paragraph at lines 16335--16342
[][][]\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 ,
[238] [239] [240]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[241]
Underfull \hbox (badness 1867) in paragraph at lines 16606--16613
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[242] [243] [244] [245]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 16875--16875
 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

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 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

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Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[247] [248] [249] [250]
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 []\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))) 
[251] [252] [253] [254]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 17574--17574
 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257] [258]
Underfull \hbox (badness 2435) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[259]
Underfull \hbox (badness 2285) in paragraph at lines 17903--17905
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

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 []\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.[] 

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 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
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 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 

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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
[262]
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 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 

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 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[263] [264]
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 []\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 18225--18225
 []\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):[] 
[265] [266] [267]
Underfull \hbox (badness 10000) in paragraph at lines 18430--18432
[]\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
[268]
Underfull \hbox (badness 4217) in paragraph at lines 18514--18523
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 18529--18545
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18948--18951
[]\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 ,
[275] [276]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19071--19071
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
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 []\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 19256--19256
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287] [288]
Underfull \hbox (badness 1975) in paragraph at lines 19834--19837
[]\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
[289] [290] [291] [292] [293] [294]
Underfull \hbox (badness 1077) in paragraph at lines 20229--20234
[]\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
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20250
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[296]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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
[297] [298]
Underfull \hbox (badness 10000) in paragraph at lines 20466--20470
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use

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[][]\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

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[]\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-
[299] [300]
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[][][]\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 ,
[301]
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[]\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
[302]
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[]\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 20793--20798
\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 20793--20798
\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 20793--20798
\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
[303] [304] [305]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[306]
Underfull \hbox (badness 3343) in paragraph at lines 21020--21024
[][][]\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
[307]
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 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[308] [309]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228
 []\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 21231--21231
 []\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 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[310] [311]
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[]\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

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 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[312] [313]
Underfull \hbox (badness 1400) in paragraph at lines 21565--21569
[][][]\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
[314] [315] [316]
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[]\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,

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\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

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\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,
[317] [318] [319] [320] [321] [322] [323] [324] [325]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362
 []\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 22363--22363
 []        \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 22366--22366
 []\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)[] 
[326] [327]
Underfull \hbox (badness 1655) in paragraph at lines 22490--22494
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[328] [329] [330] [331]
Underfull \hbox (badness 2277) in paragraph at lines 22739--22742
[]\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.
[332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 1484) in paragraph at lines 23304--23312
[]\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

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\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 /
[340] [341]
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 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1448) in paragraph at lines 23886--23894
\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 =
[349] [350]
Underfull \hbox (badness 3849) in paragraph at lines 24000--24005
[]\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
[351]
Underfull \hbox (badness 7308) in paragraph at lines 24077--24083
[]\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 24077--24083
\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 24077--24083
[][]\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 24087--24090
[]\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 24087--24090
\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
[352] [353]
Underfull \hbox (badness 10000) in paragraph at lines 24240--24242
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[354] [355] [356]
Underfull \hbox (badness 6188) in paragraph at lines 24459--24462
[]\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
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 2197) in paragraph at lines 24943--24947
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

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\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
[364]
Underfull \hbox (badness 2846) in paragraph at lines 24957--24961
[]\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 24957--24961
\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 24999--24999
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25051--25057
[]\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 25051--25057
\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 25064--25066
[]\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%
[366]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25115--25115
 [] \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:[] 
[367] [368] [369]
Underfull \hbox (badness 8189) in paragraph at lines 25308--25314
[]\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
[][][]
[370] [371] [372]
Underfull \hbox (badness 1694) in paragraph at lines 25530--25533
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[373] [374] [375]
Underfull \hbox (badness 1603) in paragraph at lines 25777--25779
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[376] [377]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[378] [379]
Underfull \hbox (badness 3271) in paragraph at lines 26111--26114
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[380] [381] [382]
Underfull \hbox (badness 3138) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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
[383]
Underfull \hbox (badness 1194) in paragraph at lines 26424--26427
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 1389) in paragraph at lines 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

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[]\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 26503--26506
[]\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
[384]
Underfull \hbox (badness 10000) in paragraph at lines 26519--26522
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26541--26548
[]\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 26541--26548
\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 26541--26548
\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 26541--26548
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[385] [386] [387] [388]
Underfull \vbox (badness 10000) has occurred while \output is active [389]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885
 []\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 26898--26902
[]\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

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\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)] =
[390] [391]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\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

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\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
[392] [393] [394]
Underfull \hbox (badness 10000) in paragraph at lines 27314--27320
[][][]\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 27314--27320
[][]\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
[395]
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 []\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 27348--27348
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[396] [397] [398] [399] [400] [401] [402]
Underfull \hbox (badness 1817) in paragraph at lines 27782--27786
[]\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 =
[403]
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[]\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
[404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 28050--28053
[]\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
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727
 []           \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))[] 
[417] [418] [419] [420]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993
 []\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 29004--29004
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 29010--29010
 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 

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 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 

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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[421]
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[]\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
[422]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[423] [424]
Underfull \hbox (badness 3713) in paragraph at lines 29279--29290
[]\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
[425]
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\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 29423--29430
\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 /
[426] [427]
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[]\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
[428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
[430]
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[]\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
[431] [432]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29848--29848
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 

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 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 

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 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[433] [434] [435] [436] [437]
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

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\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 ,
[438] [439] [440] [441] [442] [443] [444] [445]
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 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 7558) in paragraph at lines 31250--31254
[]\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 31260--31262
[]\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

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[][][]\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
[453]
Underfull \hbox (badness 10000) in paragraph at lines 31269--31271
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31677--31681
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 

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 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469] [470]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[471] [472] [473] [474] [475] [476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[477]
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[]\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
[478]
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

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\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
[479] [480]
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 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[481] [482] [483]
Underfull \hbox (badness 8151) in paragraph at lines 33392--33395
[]\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 .
[484] [485] [486] [487]
Underfull \hbox (badness 1210) in paragraph at lines 33627--33629
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499]
[500] [501]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[502] [503] [504]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34816--34816
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 

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 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[505]
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[][][]\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 34861--34867
[][]\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
[506]
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 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510] [511]
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 []\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)[] 
[512]
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 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[513] [514] [515] [516] [517] [518]
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 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

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 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
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[]\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

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\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 36105--36115
\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 36105--36115
\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 36105--36115
\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
[523]
Underfull \hbox (badness 10000) in paragraph at lines 36149--36155
[]\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 '

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\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 36149--36155
\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

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[]\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 36161--36168
\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 36161--36168
\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
[524] [525] [526] [527]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[528] [529] [530] [531] [532] [533] [534] [535]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 37000--37000
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[536] [537] [538] [539]
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 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[540]
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 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[541] [542] [543] [544] [545] [546]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 37726--37726
 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 

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 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[547]
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[]\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

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\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 ).
[548]
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 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[549] [550] [551] [552]
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 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[553]
Underfull \vbox (badness 10000) has occurred while \output is active [554]
[555]
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 []\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. 
[556]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 

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[]\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

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\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
[557]
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\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

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\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
[558] [559] [560]
Underfull \hbox (badness 10000) in paragraph at lines 38664--38668
[]\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

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[]\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
[561] [562]
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 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[563]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 38881--38881
 []\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 
[564] [565] [566]
Underfull \hbox (badness 1082) in paragraph at lines 39025--39028
[]\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
[567] [568]
Underfull \hbox (badness 1038) in paragraph at lines 39216--39219
[]\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
[569] [570] [571] [572] [573] [574]
Underfull \hbox (badness 1442) in paragraph at lines 39579--39583
\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 =
[575] [576] [577]
Underfull \hbox (badness 4096) in paragraph at lines 39825--39828
[]\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 ,
[578] [579]
Underfull \hbox (badness 7888) in paragraph at lines 39939--39943
[]\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) >
[580] [581]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093
 []            \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1"
, "2"), c("A", "B")))),[] 

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 []            \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),[] 

[582]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097
 []                 \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 40110--40112
[]\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
[583]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[584] [585]
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[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[586]
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[][][]\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 : / /
[587] [588] [589] [590] [591] [592]
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\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 ',

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[]\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-

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\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,

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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-

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\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at

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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[593]
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\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

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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[594]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /

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[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-

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 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[595] [596] [597]
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[]\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
[598] [599]
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 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 

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 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 

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[601] [602] [603] [604]
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[]\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
[605] [606]
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 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[607]
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[]\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

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\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

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[][][]\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;
[608]
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[]\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

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\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 ,
[609] [610] [611] [612] [613]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[614] [615] [616] [617] [618] [619]
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 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[620]
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 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[621]
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[]\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 ),
[622]
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[]\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
[623] [624] [625]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[626]
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 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[627]
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 []\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[] 

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 []\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 ...[] 
[628] [629]
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[]\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,

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\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,
[630]
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[]\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

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\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
[631]
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[]\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
[632]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[633]
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[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[634] [635] [636] [637] [638]
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[]\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
[639]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

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[]\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
[640]) (./compiler-pkg.tex
Chapter 2.
[641]
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[]\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-

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\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
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 

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[652] [653] [654] [655]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
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[]\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.
[660] [661]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
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[]\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 ,

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\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
[669] [670] [671]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681]
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[682] [683] [684] [685] [686]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
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[688]
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[690]
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[691] [692]
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[693]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
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[704]
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[705]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /

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[]\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 /

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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
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[]\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

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[]\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
[725] [726]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

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\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
[727] [728]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
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[]\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
[738] [739]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
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[]\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
[741] [742] [743] [744] [745] [746] [747] [748]
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[]\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

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\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
[749]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

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[]\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-

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\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 ,
[750] [751]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
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\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

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\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

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\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

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\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
[756] [757]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 

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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 

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 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
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[765] [766] [767] [768]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range

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\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-
[772] [773] [774]
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 

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[]\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 ,
[775]
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /

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\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
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[]\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
[793]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 

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[]\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
[794]
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[]\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"
[795]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[796] [797] [798]
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[]\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

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[][][]\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
[799] [800]
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\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 ,

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\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 ,

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\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 ),

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[]\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

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\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
[801]
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[]\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 /
[802] [803]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
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[]\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
[807] [808] [809] [810] [811]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
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 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 

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 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
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[]\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 ,

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\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 ,

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\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
[822]
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 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
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[]\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 :
[824]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
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[]\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

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\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
[827]
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[]\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

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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
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\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 ,
[830]
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[]\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 /
[831] [832]
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[]\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
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.

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[]\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 =
[837] [838] [839]
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[]\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
[840]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
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 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 

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[]\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
[844] [845]
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 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846]
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[]\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

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[][]\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
[847] [848]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 

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 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[849] [850] [851]
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[][][]\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.

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 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 

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 []\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 981--981
 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1265--1265
 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[856] [857] [858]
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\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

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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

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 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
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[][][]\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
[865]
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
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 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 

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\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
[874]
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[][][]\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

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 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
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\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

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 []\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 :[] 

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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[882]
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[][][]\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
[883] [884] [885]
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 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 

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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
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[]\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

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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 

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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[891] [892] [893]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
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 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

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 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 

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 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 

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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
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[][][]\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%
[897]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[898] [899] [900] [901]
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[]\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
[902] [903] [904] [905]
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\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
[906]
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[]\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
[907]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 

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 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[908]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
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\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 ,
[910] [911]
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[]\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.
[912]
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[913 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/mai.pdf>]
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[915 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/oma.pdf>]
[916]
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[]\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
[917]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
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 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5696--5696
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 

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[]\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 =
[924] [925] [926] [927] [928] [929] [930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6181--6181
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 

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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
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[]\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

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[][] 
[939 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/pch.pdf>]
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

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[942]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
Underfull \hbox (badness 2600) in paragraph at lines 7091--7093
[]\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
[944] [945] [946] [947]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710
 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[955] [956] [957] [958] [959]
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[963] [964]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

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[]\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
[965]
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[]\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
[966]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 

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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
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 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[971]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color

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[]\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
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [973]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
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 []\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)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

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\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
[985] [986] [987] [988] [989] [990] [991] [992] [993] [994]
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

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[]\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-
[995] [996] [997] [998]
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[]\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
[999] [1000] [1001] [1002] [1003] [1004]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
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[]\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 ,
[1009]
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[]\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-

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[]\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
[1010] [1011] [1012]
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[]\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
[1013] [1014] [1015]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

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[]\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-
[1016]
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 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1019] [1020] [1021] [1022]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1023] [1024] [1025] [1026] [1027]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281
 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1029]
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[]\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
[1030] [1031]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 

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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 

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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
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[1047]
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[]\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
[1048]
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[]\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-
[1049] [1050] [1051]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\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
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
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[]\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-

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\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")
[1072] [1073] [1074] [1075] [1076]
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[]\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
[1077]
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[][][]\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 ,
[1078] [1079]
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[]\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
[1080] [1081] [1082]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
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\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
[1087] [1088] [1089]
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-
[1090] [1091]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 

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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 

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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[] 

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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 

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 []\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[
] 

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[1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105]
[1106] [1107] [1108]
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
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[]\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
[1111] [1112] [1113]
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[]\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 =
[1114] [1115]
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

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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
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[]\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

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[]\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
[1119]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
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[]\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,

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\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
[1130] [1131]
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[]\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
[1132]
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[]\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

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[]
[1133] [1134]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =

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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =

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[]\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
[1136] [1137] [1138]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
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 ,
[1146] [1147] [1148]
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
[1149] [1150] [1151] [1152]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 

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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

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[1155]
Underfull \hbox (badness 10000) in paragraph at lines 5355--5356
[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
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[]\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
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[]\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
[1167] [1168]
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[]\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,

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\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
[1169]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see

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[][]\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
[1172]
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[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
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 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 

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 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \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
<to be read again> 
                   \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
<to be read again> 
                   \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

<to be read again> 
                   \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
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\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
[1180]
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[]\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 ,

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\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 ,

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\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 ,
[1181] [1182]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see

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[]\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
[1183] [1184]
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
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[]\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
[1196]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
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[] 
[1208] [1209] [1210] [1211]
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[] 
[1212]
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][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
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

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[]\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
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
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
[1227]
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
[1228] [1229]
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[]\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
[1230] [1231] [1232]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\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
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\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 744--753
\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
[1237] [1238]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837
 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026
 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 

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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
Underfull \hbox (badness 5388) in paragraph at lines 1145--1150
[]\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
[1243]
Underfull \hbox (badness 10000) in paragraph at lines 1169--1177
[]\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

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 []\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)[] 
[1244] [1245]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322
 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\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

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[]\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
[1247] [1248]) (./splines-pkg.tex
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 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\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
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
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:[] 

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 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
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[] 
[1269]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466
 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\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
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\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

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\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 1536--1540
\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
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737
 []\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 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966
 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3175--3177
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
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 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

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 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3615--3615
 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 3893--3893
 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4182--4182
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

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 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4589--4589
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
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[]\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 =
[1332] [1333] [1334] [1335] [1336] [1337]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5066--5066
 []\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))[] 

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 []\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))[] 
[1338] [1339] [1340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5289--5289
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

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 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 

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[]\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
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5517--5522
[]\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 5517--5522
\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

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\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 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5882--5882
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
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 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6175--6175
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
Underfull \hbox (badness 10000) in paragraph at lines 6242--6247
[]\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
[1355] [1356] [1357] [1358]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
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[]\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

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[]\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

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\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,

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[][][]\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
[1360]
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 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 

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 []\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):[] 

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 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

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[1362] [1363] [1364]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7270--7274
\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
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7369--7372
[]\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
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7506--7509
[]\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 =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
Underfull \hbox (badness 10000) in paragraph at lines 7918--7923
[]\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 , ...,
[1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 1210) in paragraph at lines 8273--8275
[]\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
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
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 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 

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Overfull \hbox (31.3804pt too wide) in paragraph at lines 8781--8781
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

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 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8922--8922
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 

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 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9529--9531
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9990--9996
[][][]\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);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10203--10206
[]\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
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 

Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
Underfull \hbox (badness 4132) in paragraph at lines 10504--10508
[]\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 10558--10564
[]\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-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10609--10612
[]\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
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:

Underfull \hbox (badness 10000) in paragraph at lines 10948--10954
[][][]\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,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10986--10991
\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 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11119--11122
\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
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436
 []            \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 11449--11453
[]\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
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

Underfull \hbox (badness 1062) in paragraph at lines 11901--11906
[]\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 11918--11920
[]\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
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 12534--12536
[]\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
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12603--12605
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12841--12843
[]\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 12847--12851
[]\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 12847--12851
\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
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13796--13800
[]\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
 ,
[1468] [1469] [1470] [1471] [1472]
Underfull \hbox (badness 1163) in paragraph at lines 14129--14137
\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 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 

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 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779
 []\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 14780--14780
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15279--15282
[]\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 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16136--16141
\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
[1503]
Underfull \hbox (badness 1648) in paragraph at lines 16202--16204
[]\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 16217--16226
\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 16217--16226
\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
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845
 []\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[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996
 []\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 18043--18043
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18581--18584
[]\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 18594--18598
[]\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
[1541]
Underfull \hbox (badness 1478) in paragraph at lines 18602--18606
\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 18660--18662
[]\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
[1542] [1543]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766
 []      \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 [1544]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 

Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\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 18850--18850
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1545]
Underfull \hbox (badness 2564) in paragraph at lines 18888--18899
[]\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 18888--18899
\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
[1546]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1547] [1548] [1549]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1550]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1551] [1552] [1553] [1554] [1555] [1556]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1557]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659
 []       \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 19661--19661
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1558]
Underfull \hbox (badness 10000) in paragraph at lines 19709--19713
[]\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 10000) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for

Underfull \hbox (badness 5260) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1559]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1560] [1561] [1562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1563]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1564]
Underfull \hbox (badness 1107) in paragraph at lines 20064--20066
[]\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

Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1565]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126
 []\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)[] 
[1566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1567] [1568]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1569]
Underfull \hbox (badness 7740) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of

Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570] [1571]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548
 [] \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 20553--20553
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582]
[1583] [1584]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1585]
Underfull \hbox (badness 6859) in paragraph at lines 21474--21481
[][][]\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 21485--21491
[]\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 ,
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1598] [1599] [1600] [1601] [1602]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1603] [1604] [1605] [1606] [1607]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1616] [1617]
Underfull \hbox (badness 1028) in paragraph at lines 23540--23543
[]\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
[1618] [1619]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23705--23707
[]\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 =

[1621]
Underfull \hbox (badness 7944) in paragraph at lines 23767--23769
[]\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 =

[1622] [1623]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1624] [1625] [1626]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1627] [1628]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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] =
[1629]
Underfull \hbox (badness 2134) in paragraph at lines 24287--24291
[][][]\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 24300--24300
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1630] [1631] [1632] [1633] [1634] [1635]
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
[1637]
Underfull \hbox (badness 6268) in paragraph at lines 24777--24782
[][]\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 ,

Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1638] [1639] [1640]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\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 24995--24999
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\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
[1641]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1642] [1643] [1644]
Underfull \hbox (badness 2495) in paragraph at lines 25221--25230
[]\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 .
[1645]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 

Underfull \hbox (badness 1412) in paragraph at lines 25310--25312
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1646]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397
 []\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 25422--25422
 []\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 25425--25425
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1647] [1648] [1649]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 

Underfull \hbox (badness 2547) in paragraph at lines 25651--25657
[]\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
[1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697
 []\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 25718--25718
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1651]
Underfull \hbox (badness 1019) in paragraph at lines 25780--25785
\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
[1652] [1653]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1654] [1655] [1656] [1657] [1658] [1659] [1660]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1661] [1662]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486
 []\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 26487--26487
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1663]
Underfull \hbox (badness 2922) in paragraph at lines 26556--26561
[]\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
[1664]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26593--26593
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 26596--26596
 []                    \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 26605--26605
 []         \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 26606--26606
 []  \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 26610--26610
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1665]
Underfull \hbox (badness 3240) in paragraph at lines 26664--26667
[][][]\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
[1666]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26685--26685
 []  \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 26688--26688
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1667]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26771--26771
 []  \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 26775--26775
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 

Overfull \hbox (58.38037pt too wide) in paragraph at lines 26785--26785
 []  \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 26790--26790
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1668]
Underfull \hbox (badness 2922) in paragraph at lines 26826--26832
[]\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 26848--26848
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1669]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26864--26864
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1670]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26978--26978
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1671]
Underfull \hbox (badness 2922) in paragraph at lines 27040--27045
[]\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
[1672]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27078--27078
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1673]
Underfull \hbox (badness 2922) in paragraph at lines 27127--27132
[]\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 27158--27158
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1674]
Underfull \hbox (badness 2922) in paragraph at lines 27192--27197
[]\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 (25.98041pt too wide) in paragraph at lines 27217--27217
 []\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 27221--27221
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
[1675]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27241--27241
 []  \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 27251--27251
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 

Underfull \hbox (badness 2922) in paragraph at lines 27286--27291
[]\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
[1676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27308--27308
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 27326--27326
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1677]
Underfull \hbox (badness 6493) in paragraph at lines 27378--27383
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion

Overfull \hbox (4.38043pt too wide) in paragraph at lines 27405--27405
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1678]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27407--27407
 []\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 27410--27410
 []\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 27413--27413
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689]
[1690] [1691] [1692]
Underfull \hbox (badness 3396) in paragraph at lines 28337--28339
[]\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
[1693] [1694] [1695]
Underfull \hbox (badness 2237) in paragraph at lines 28514--28516
[]\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
[1696] [1697]
Underfull \hbox (badness 2591) in paragraph at lines 28678--28680
[]\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
[1698]
Underfull \hbox (badness 2237) in paragraph at lines 28724--28727
[]\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
[1699]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28797--28797
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1700] [1701]
Underfull \hbox (badness 3407) in paragraph at lines 28905--28909
[]\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)
[1702] [1703]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\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
[1704] [1705] [1706] [1707]
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en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a
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 []\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:[] 

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[1747]
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[]\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co
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[1748]
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 []\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 "")[] 
[1749]) (./stats4-pkg.tex [1750]
Chapter 11.
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[1754] [1755] [1756]pdfTeX warning (ext4): destination with the same identifier
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(./tcltk-pkg.tex [1760]
Chapter 12.
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on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1780]) (./tools-pkg.tex
Chapter 13.
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mpress == "none")[] 
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efined macros may be given in a sep-a-rate file us-ing
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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
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[1852]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
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\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
[1853] [1854] [1855]) (./utils-pkg.tex [1856]
Chapter 14.

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[1863]
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irefox window[] 

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 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 

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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1864] [1865]
Underfull \hbox (badness 1946) in paragraph at lines 624--628
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1866]
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 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 

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 []\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 681--681
 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 

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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

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[]\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 717--723
\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-
[1867]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1868]
Underfull \hbox (badness 4505) in paragraph at lines 850--856
\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
[1869] [1870] [1871]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1872]
Underfull \hbox (badness 1748) in paragraph at lines 1089--1097
[]\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-

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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1873]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1874]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 

Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825
 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1883] [1884]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1885] [1886]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1887]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1888] [1889] [1890]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344
 []                 \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 2367--2367
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1891] [1892]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1893]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\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
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1894] [1895]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1896] [1897] [1898]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1899] [1900] [1901] [1902]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1903]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1904]
Underfull \hbox (badness 2452) in paragraph at lines 3359--3362
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1905] [1906] [1907] [1908] [1909] [1910]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1911] [1912]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\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 3906--3914
[]\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
[1913]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able

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[]\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 3997--4002
\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 3997--4002
\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1914] [1915]
Underfull \hbox (badness 4660) in paragraph at lines 4119--4122
\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 4143--4145
[]\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
[1916] [1917] [1918]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\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
[1919]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1920]
Underfull \hbox (badness 1931) in paragraph at lines 4446--4453
[]\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)
[1921] [1922] [1923] [1924] [1925]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1927] [1928] [1929]
[1930] [1931] [1932] [1933] [1934]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\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
[1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1943]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\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
[1944]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1945] [1946] [1947]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\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 6258--6267
\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
[1948]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\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 6338--6341
[]\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
[1949] [1950]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[1951] [1952]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\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 5331) in paragraph at lines 6644--6650
[]\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 6644--6650
\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 6644--6650
\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 6658--6665
[]\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")
[1953]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\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

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\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 6716--6719
\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.,
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,

Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\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-

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\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 6792--6799
\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 6800--6803
[]\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
[1955]
Underfull \hbox (badness 1314) in paragraph at lines 6879--6886
[]\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
[1956]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1957]
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[]\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 7009--7012
[]\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

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1958] [1959]
Underfull \hbox (badness 4132) in paragraph at lines 7176--7178
[]\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
[1960] [1961] [1962]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1965]
Underfull \hbox (badness 10000) in paragraph at lines 7526--7528
[]\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
[1966] [1967]
Underfull \hbox (badness 10000) in paragraph at lines 7711--7713
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if

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[]\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 class
[1968] [1969] [1970] [1971]
Underfull \hbox (badness 1859) in paragraph at lines 7939--7942
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1972]
Underfull \hbox (badness 1655) in paragraph at lines 8032--8035
[]\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 8043--8043
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1973] [1974]
Underfull \hbox (badness 1917) in paragraph at lines 8134--8136
[]\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 ,
[1975] [1976] [1977] [1978]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 

Overfull \hbox (18.78088pt too wide) in paragraph at lines 8407--8407
 []            \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 8408--8408
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 

Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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
[1979]
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[]\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 8458--8463
[]\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,

Overfull \hbox (9.78043pt too wide) in paragraph at lines 8504--8504
 []          \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 8505--8505
 []                                   \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[] 
[1980] [1981]
Underfull \hbox (badness 10000) in paragraph at lines 8634--8639
[]\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

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[][]\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

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\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion

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\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
[1982] [1983]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1984] [1985]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8929--8929
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1986] [1987]
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[]\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
[1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]
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[]\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
[1996] [1997] [1998]
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\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
[1999]
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 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[2000] [2001]
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 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2002] [2003]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10225--10225
 []\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[] 
[2004] [2005]
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 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

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 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

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 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2006]
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[]\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
[2007] [2008] [2009]
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 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 

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 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2010]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are

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\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 .

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\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
[2011] [2012] [2013]
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 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2014] [2015] [2016] [2017]
Underfull \hbox (badness 10000) in paragraph at lines 11165--11169
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2018]
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 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 

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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2019] [2020]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11372--11372
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2021] [2022]
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[]\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-


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\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
[2023]
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 []\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 '[] 
[2024]
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[]\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

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\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,

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\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-

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\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,

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\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
[2025] [2026]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2027]
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 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2028] [2029] [2030]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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

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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2031] [2032]
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 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

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[]\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
[2033]
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[]\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

[2034]
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[]\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
[2035] [2036] [2037] [2038]
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[]\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

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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2039]
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 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 

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[]\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
[2040]
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 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
[2041] [2042]
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[]\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
[2043] [2044]
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[]\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-
[2045] [2046] [2047]
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 

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[]\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 = <S>) \T1/ptm/m/n/10 will not have

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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2048]
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 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2049]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 

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 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 

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[2050] [2051]
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[]\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
[2052] [2053] [2054]
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[]\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

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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
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\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
[2055] [2056]
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\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),

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\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
[2057] [2058]
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[]\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

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2059] [2060] [2061]
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 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2062] [2063] [2064] [2065] [2066] [2067]
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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[]\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

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\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

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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =

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[]\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

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\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 ,

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\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[][][]

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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
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[2068]
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\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 =

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[]\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

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[][][]\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 ,
[2069]
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 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2070] [2071] [2072]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;

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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2073]
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 []\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:[]
 
[2074]
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ata = DAT)))[] 

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[2075] [2076]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2077]
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[]\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.
[2078] [2079]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2080]
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[]\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

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[]\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 =
[2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex
Chapter 15.
[2087]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2088] [2089] [2090] [2091] [2092]
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 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2093] [2094] [2095] [2096]) (./MASS-pkg.tex
Chapter 16.
[2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107]
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 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118]
[2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129]
[2130]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2131] [2132] [2133] [2134]
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[]\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
[2135] [2136] [2137]
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\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 ,

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\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 ,
[2138] [2139]
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[]\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
[2140] [2141] [2142]
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2143]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154]
[2155]
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[]\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
[2156] [2157] [2158] [2159] [2160] [2161] [2162]
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 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2163] [2164] [2165]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176]
[2177] [2178] [2179]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2180]
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 []\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") 
[2181] [2182]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...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
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2183]
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[]\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
[2184] [2185] [2186] [2187]
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2189]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2190] [2191] [2192] [2193] [2194] [2195]
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 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2196]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

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[]\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 ) =
[2197]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2198] [2199]
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\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
[2200] [2201]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2202]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2203] [2204] [2205] [2206] [2207] [2208]
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[]\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
[2209] [2210]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

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[]\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
[2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221]
[2222] [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2231]
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[]\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 ,

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[]\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),
[2232]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243]
[2244] [2245]) (./Matrix-pkg.tex [2246]
Chapter 17.

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[]\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

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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2247]
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[]\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
[2248]
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[]\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

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\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
[2249]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

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[]\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
[2250] [2251]
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 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2252]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2253] [2254]
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 []\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:[] 

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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  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 '[] 

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 []\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}"}.[] 

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 []        \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?[] 

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 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 

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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2255]
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[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2256] [2257] [2258]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- '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
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2261pdfTeX 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.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2262]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2263]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 

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[]\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
[2264]
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[]\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
[2265]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

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 []\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(<UTF-8>) gives bad plots[] 

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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2266]
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[]\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

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\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

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[]\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

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\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
[2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2268]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\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 1710--1714
\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 1721--1724
[][][]\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
[2269] [2270]
Underfull \hbox (badness 3547) in paragraph at lines 1875--1878
[]\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
[2271] [2272] [2273] [2274] [2275]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2276]
Underfull \hbox (badness 7379) in paragraph at lines 2330--2332
[]\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
[2277] [2278] [2279]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\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 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble

Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\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 ;
[2280]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\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 2677--2682
[]\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 2677--2682
[][]\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
[2281]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\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 2713--2718
[][]\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
[2282]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\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 2983--2985
[]\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 2986--2990
[]\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 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2283]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\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 3012--3016
[][][]\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
[2284] [2285]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\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 3243--3245
[][][]\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)
[2286]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\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
[2287] [2288]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\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 3528--3532
\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 ,
[2289]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2290] [2291]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2292]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3815
[]\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
[2293] [2294] [2295]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\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 4091--4095
[]\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
[2296]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\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 4100--4103
\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 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2297] [2298]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2299] [2300] [2301] [2302]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \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 4534--4534
 []\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 4537--4537
 []\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 4547--4547
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2303] [2304] [2305] [2306]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2307]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\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 4932--4932
 []  \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 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2308]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \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 '[] 
[2309] [2310]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\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 5124--5124
 []\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 5130--5130
 [] \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 5131--5131
 [] \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 5134--5134
 []\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 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2311]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\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 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2312]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\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 5277--5279
[]\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 5279--5282
[]\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 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2313]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2314]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2315] [2316] [2317]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\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[] 
[2318]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2319]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2320]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\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 5819--5819
 []          \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 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2321]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2322]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\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
[2323]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2325]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\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
[2326]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\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.,
[2327]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\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.,

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 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2328]
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[]\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

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[][]\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,

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[]\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
[2329]
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 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2330] [2331]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),

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[]\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,

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\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
[2332] [2333]pdfTeX warning (ext4): destination with the same identifier (name{
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                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2334]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
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                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7152 ...A{crossprod}{matrix-products}{crossprod}
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                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
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\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
[2335] [2336pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
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 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    ]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;

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\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 =

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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-tures (use

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\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-

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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit
to for sev-eral other

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\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

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[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2337] [2338]
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[]\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

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[]\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
[2339]
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[]\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
[2340]
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[]\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
[2341] [2342]
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 

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[]\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 .

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\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

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[]\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.,
[2344]
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[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2345]
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[]\T1/ptm/m/n/10 fast sim-
[2346]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \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
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                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2347]
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 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 

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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 

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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 

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[]\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 ,
[2348]
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[]\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
[2349]
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[]\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.,
[2350]
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[]\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.,
[2351]
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 

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[2352]
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[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use

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[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal

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[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2353] [2354]
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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[]\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

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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
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Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2357]
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 []\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![] 

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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 

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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 

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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 

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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 

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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

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[]\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
[2359]
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 []\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"[] 
[2360]
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 

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 []\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
<to be read again> 
                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2361] [2362]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2363] [2364]
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably

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[]\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

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\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
[2365] [2366]
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[]\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
[2367]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
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ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2369]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a

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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via

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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (

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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (

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\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,
[2370]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's

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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines

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[]\T1/ptm/m/n/10 works via

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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

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[]\T1/ptm/m/n/10 all work via

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[][][]\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

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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2371]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

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[]\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,

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[]\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co-
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rasts to be ap-plied to the

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


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\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
[2372]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a

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[]\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-
[2373]
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 []  \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 10259--10259
 []  \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 10260--10260
 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2374] [2375]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444
 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445
 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2376]
Underfull \hbox (badness 4621) in paragraph at lines 10485--10489
[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2377]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573
 []\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 10577--10577
 []\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 10578--10578
 []\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 10583--10583
 []\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 10586--10586
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2378]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609
 []\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 10610--10610
 []\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 10636--10636
 []\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 10638--10638
 []   \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 10640--10640
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2379]
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2380]
Underfull \hbox (badness 10000) in paragraph at lines 10784--10788
[][][]\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
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2381] [2382]
Underfull \hbox (badness 10000) in paragraph at lines 10954--10956
[]\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 10982--10982
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 

Underfull \hbox (badness 5036) in paragraph at lines 11010--11012
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2383]
Underfull \hbox (badness 2970) in paragraph at lines 11143--11149
[]\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 11143--11149
\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 ,
[2384]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\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
[2385]
Underfull \hbox (badness 10000) in paragraph at lines 11234--11239
[]\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 11249--11251
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2386] [2387]
Underfull \hbox (badness 2698) in paragraph at lines 11374--11380
[][][]\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,
[2388]
Underfull \hbox (badness 10000) in paragraph at lines 11467--11469
[]\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 11485--11490
[]\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 11485--11490
\T1/pcr/m/n/10 list(NULL,<character>)\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

Underfull \hbox (badness 2591) in paragraph at lines 11493--11498
\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
[2389]
Underfull \hbox (badness 2057) in paragraph at lines 11565--11567
[]\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.,
[2390] [2391]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\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 11691--11695
[]\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 11691--11695
\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
[2392]
Underfull \hbox (badness 7649) in paragraph at lines 11798--11800
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2393] [2394] [2395]
Underfull \hbox (badness 7362) in paragraph at lines 11999--12001
[]\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
[2396]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037
 []\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 12038--12038
 []\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)[] 
[2397] [2398]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2399] [2400] [2401]) (./boot-pkg.tex [2402]
Chapter 18.
[2403] [2404] [2405] [2406] [2407] [2408] [2409]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2410]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\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 583--588
[]\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-
[2411] [2412] [2413]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\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 851--855
[][][]\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 ,
[2414]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\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 [2415]
[2416]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\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 1066--1070
\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 1066--1070
\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"
[2417]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\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 1082--1091
\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2418] [2419] [2420] [2421]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2422] [2423] [2424] [2425] [2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2427] [2428] [2429]
Underfull \vbox (badness 10000) has occurred while \output is active [2430]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2431]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2432] [2433] [2434]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
[2435]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\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 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2436] [2437]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2438] [2439] [2440] [2441] [2442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\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 2894--2894
 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2443] [2444] [2445]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2446]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2447] [2448] [2449]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2450] [2451] [2452] [2453] [2454] [2455] [2456]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2457] [2458]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2459] [2460] [2461]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2462]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2463] [2464]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f

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\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
[2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2474] [2475] [2476] [2477]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2478]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2487]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2488]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2489] [2490] [2491] [2492]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2493] [2494]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\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 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2495] [2496] [2497]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2498] [2499]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex
[2508]
Chapter 19.
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519]
[2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex
Chapter 20.
[2525]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\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 133--142
\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 133--142
\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 133--142
\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
[2526] [2527]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2528] [2529]
Underfull \vbox (badness 10000) has occurred while \output is active [2530]
[2531]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2532] [2533]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2534]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2535] [2536]
Underfull \hbox (badness 2941) in paragraph at lines 779--782
[][][]\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 
,

Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2537]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2538]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2539]
Underfull \hbox (badness 4872) in paragraph at lines 975--977
[]\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 989--993
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2540]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2541]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2542]
Underfull \hbox (badness 4144) in paragraph at lines 1190--1194
[]\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
[2543]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266
 []          \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 1272--1272
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2544] [2545]
Underfull \hbox (badness 10000) in paragraph at lines 1411--1416
[]\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

Underfull \hbox (badness 10000) in paragraph at lines 1459--1462

[2546]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1480
[][][]\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 1500--1500
 []\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 1510--1510
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2547]
Underfull \hbox (badness 5741) in paragraph at lines 1550--1553
[]\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
[2548]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2549]
Underfull \hbox (badness 1540) in paragraph at lines 1733--1741
\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 =
[2550] [2551]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824
 []\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 1843--1843
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2552] [2553] [2554] [2555]
Underfull \hbox (badness 10000) in paragraph at lines 2162--2165

[2556]
Underfull \hbox (badness 3179) in paragraph at lines 2176--2182
[][][]\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.
[2557] [2558]
Underfull \hbox (badness 10000) in paragraph at lines 2334--2337
[][][]\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 ,
[2559]
Underfull \hbox (badness 1292) in paragraph at lines 2402--2405
[]\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

Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\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 2434--2437
[][][]\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 ,
[2560] [2561] [2562] [2563]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650
 []\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 ):[] 
[2564] [2565] [2566]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2567] [2568]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2569] [2570] [2571]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572]
Underfull \hbox (badness 10000) in paragraph at lines 3286--3289
[]\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
[2573]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2574] [2575] [2576]
Underfull \hbox (badness 10000) in paragraph at lines 3522--3525
[]\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
[2577]
Underfull \hbox (badness 10000) in paragraph at lines 3585--3590
[][][]\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 ,
[2578]
Underfull \hbox (badness 3884) in paragraph at lines 3647--3652
\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 3659--3662
[][][]\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 ,
[2579] [2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 3844--3847
[][][]\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 3875--3878
[][][]\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 ,
[2582]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3939--3941
[]\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
[2583] [2584] [2585] [2586]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132
 []     \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 4134--4134
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2587] [2588]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272
 []\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 4281--4281
 []   \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 4283--4283
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

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 []\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 4288--4288
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 

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 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2589] [2590] [2591] [2592] [2593] [2594]
Underfull \hbox (badness 10000) in paragraph at lines 4668--4674
[]\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 4684--4686
[]\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
[2595]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 4697--4697
 []\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 4699--4699
 []\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 4709--4709
 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 

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 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2596]) (./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,[] 

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 []           \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,[] 
[2597]
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[]\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
[2598]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2599] [2600] [2601]) (./foreign-pkg.tex [2602]
Chapter 22.
[2603]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2604] [2605]
Underfull \hbox (badness 3601) in paragraph at lines 235--243
[]\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 ,
[2606]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2607] [2608] [2609]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2610]
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 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 

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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

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\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

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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to

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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,

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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-

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\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
[2611]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]

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[]\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
[2612]
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 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 

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 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2613]
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 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 

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 []\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 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2614] [2615]
Underfull \hbox (badness 10000) in paragraph at lines 813--814


Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2616] [2617]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2618]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2619] [2620]
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[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2621] [2622]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2623]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\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
[2624]) (./lattice-pkg.tex
Chapter 23.
[2625] [2626] [2627]
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2628]
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 []        \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"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

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 []       \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"),[] 
[2629] [2630] [2631] [2632]
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
[2633] [2634] [2635] [2636]
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[]\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

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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2637]
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
[2638] [2639]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2640] [2641] [2642]
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 ,
[2643]
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 ,
[2644]
Underfull \vbox (badness 10000) has occurred while \output is active [2645]
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
[2646]
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

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[]\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
[2647] [2648] [2649] [2650]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2651]
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
[2652] [2653] [2654]
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"),[] 
[2655] [2656] [2657] [2658] [2659]
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")[] 

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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2660] [2661]
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

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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


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\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 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2662]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\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 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

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\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

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[]\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
[2663] [2664]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 

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 []      \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 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2665]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\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 3143--3150
\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
[2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2670]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496
 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2671] [2672] [2673] [2674] [2675]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2676]
Underfull \hbox (badness 2277) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by

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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2677] [2678]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

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[]\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

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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

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\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
[2679]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\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 4170--4174
\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
[2680] [2681]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\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 ,

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\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 ,

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\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

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\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

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\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

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[]\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 ,

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[]\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
[2682] [2683] [2684] [2685] [2686] [2687]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2688] [2689]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2690] [2691]
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[]\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
[2692] [2693] [2694] [2695] [2696] [2697]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\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

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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2698]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

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\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
[2699]
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[]\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
[2700]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2701]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 5693--5693
 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of


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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2702] [2703]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\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

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[]\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

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\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
[2704] [2705]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\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 ,
[2706] [2707]
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
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[]\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

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\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
[2710]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2711] [2712]
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\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
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2714] [2715] [2716] [2717] [2718] [2719]
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[]\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-

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\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
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2721]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

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\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
[2722]
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\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
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2725]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2726] [2727]
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to

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[]\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
[2728]
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2729]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 

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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2730] [2731] [2732]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2733]
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[]\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
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se

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\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
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 

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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2744]
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[]\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
[2745]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2746]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2747] [2748]
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2749] [2750]
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2751]
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[]\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

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\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
[2752] [2753] [2754] [2755] [2756] [2757] [2758]
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[]\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 ,

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\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 ,
[2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2762] [2763] [2764]
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\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

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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2765] [2766]) (./mgcv-pkg.tex
Chapter 24.
[2767] [2768]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2769]
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2770] [2771] [2772] [2773]
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[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
[2774]
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 []\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)+[] 
[2775] [2776] [2777]
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[]\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
[2778] [2779] [2780]
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[]\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
[2781]
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[]\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).
[2782]
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[2784] [2785] [2786] [2787]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2788]
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 

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 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 

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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 

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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 

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 []\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)[] 

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[2790]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 

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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 

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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 

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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2800] [2801] [2802] [2803] [2804] [2805]
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\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

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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

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[]\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

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2806]
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2807] [2808]
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\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
[2809] [2810]
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[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
[2811]
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[2815] [2816] [2817] [2818] [2819] [2820] [2821]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2822] [2823] [2824] [2825] [2826] [2827]
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[]\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
[2828] [2829]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2833] [2834] [2835] [2836] [2837] [2838] [2839]
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 []  \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)+[] 
[2840] [2841] [2842]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2843]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
[2844]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2845]
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[]\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
[2846] [2847]
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[][][]\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 ,

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[][]\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 .
[2848]
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[2850] [2851]
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[]\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 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2852] [2853] [2854] [2855] [2856] [2857] [2858]
Underfull \hbox (badness 6708) in paragraph at lines 5453--5454
[]\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
[2859]
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 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2860]
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 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 

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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 

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 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2862] [2863] [2864] [2865] [2866] [2867]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 

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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2868] [2869] [2870] [2871] [2872] [2873]
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 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 

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 []\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) 
[2874] [2875] [2876] [2877]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2891] [2892]
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 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2893] [2894]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 

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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 

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[2914]
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[]\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 ,

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\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 ,

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\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 .
[2915]
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[]\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 ,

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\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
[2916] [2917] [2918]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 

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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2919] [2920] [2921]
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\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
[2922] [2923] [2924] [2925]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2926] [2927]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2928] [2929] [2930] [2931]
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 []  \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[] 
[2933]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

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[]\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
[2934]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2935]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

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[][]\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,
[2936] [2937]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\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,
[2938] [2939] [2940] [2941]
Underfull \hbox (badness 1946) in paragraph at lines 10247--10254
[]\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

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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method

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\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

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[]\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 10255--10258
\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.
[2942]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

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[]\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 ,
[2943] [2944] [2945] [2946] [2947]
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 []\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) 
[2948] [2949] [2950] [2951] [2952] [2953]
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[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if

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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 

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[]\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-
[2954]
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[]\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-
[2955] [2956] [2957]
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 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 

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[]\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
[2958]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\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 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\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 11296--11300
\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 ,
[2959] [2960] [2961]
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Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2965] [2966]
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 []  \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))+[] 

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 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 

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 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 

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 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2967]
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 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 

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 []  \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:[] 
[2968]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a

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\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
[2969] [2970]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2971]
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 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data)  ## first 
deriv penalty[] 

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 []\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[] 
[2972] [2973] [2974]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2975] [2976] [2977] [2978]
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 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2979]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2980] [2981]
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Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\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-

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\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 12627--12630
\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"
[2983]
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 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2984]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

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\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-
[2985] [2986] [2987]
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 []\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...[] 


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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2990]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2991] [2992] [2993] [2994]
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[][][]\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
[2995]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2996] [2997] [2998] [2999]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-

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\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
[3000]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\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 ,

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[][]\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 13660--13664
[][]\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 ,
[3001] [3002] [3003] [3004] [3005]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3006]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3007] [3008]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3009] [3010]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\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
[3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021]
[3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3031] [3032] [3033] [3034] [3035]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\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 15778--15778
 []\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 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3036] [3037] [3038]) (./nlme-pkg.tex
Chapter 25.
[3039]
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\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
[3040]
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
[3041] [3042] [3043] [3044] [3045]
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,[] 
[3046] [3047]
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 ---------------------------
---------------[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055]
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"),[] 
[3056]
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
[3057] [3058] [3059] [3060] [3061] [3062] [3063]
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 ,
[3064]
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
[3065] [3066] [3067] [3068] [3069]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3071]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3072] [3073]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\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 ,
[3074]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\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 ,
[3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093]
[3094]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\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 ,
[3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105]
[3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116]
[3117] [3118]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\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 ,
[3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3135]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3136]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\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 ,
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\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 6339--6339
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3142]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\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 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3143]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3144]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3145] [3146] [3147]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\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 ,
[3148]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 

Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\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
[3149] [3150] [3151]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\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 ,
[3152] [3153] [3154]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial
-iza-

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\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 7406--7414
\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 7429--7432
[][][]\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 ,
[3155] [3156] [3157]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\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 8156--8173
[][]\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 ,

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 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3166] [3167] [3168] [3169] [3170]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 

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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3171]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\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
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179] [3180] [3181] [3182] [3183]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\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 ,

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 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3184]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\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
[3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...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
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3189]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s

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[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite

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\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
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\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
[3198] [3199] [3200]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3201]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3202] [3203] [3204]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3205] [3206]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 

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[]\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[][][]
[3207]
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[]\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=

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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3208] [3209] [3210] [3211]
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 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3212] [3213] [3214] [3215] [3216] [3217]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3218] [3219] [3220] [3221] [3222] [3223]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\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 ,
[3224] [3225] [3226] [3227]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\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 ,
[3228] [3229] [3230] [3231] [3232]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\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
[3233] [3234]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\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 ,
[3235]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\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 ,
[3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3245] [3246] [3247] [3248] [3249]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\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
[3251]
Underfull \hbox (badness 1838) in paragraph at lines 13734--13741
[]\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 13734--13741
\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 13791--13791
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3252]
Underfull \hbox (badness 10000) in paragraph at lines 13798--13801
[]\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 13798--13801
\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 13826--13829
[]\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 13826--13829
\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
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\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
[3254]
Underfull \hbox (badness 1472) in paragraph at lines 13931--13938
\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 ,
[3255]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\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 ,
[3256] [3257] [3258] [3259]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3260] [3261] [3262] [3263]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...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
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3273] [3274] [3275]
[3276] [3277] [3278] [3279] [3280] [3281] [3282]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\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
[3283] [3284] [3285]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3286] [3287] [3288] [3289] [3290]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\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 ,
[3291]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3292] [3293] [3294] [3295] [3296] [3297] [3298]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3299] [3300] [3301] [3302] [3303]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\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 17171--17180
\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 17171--17180
\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 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for

Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\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
[3304]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance

Underfull \hbox (badness 10000) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for

Underfull \hbox (badness 1694) in paragraph at lines 17235--17243
\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3305] [3306] [3307] [3308]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3309] [3310] [3311] [3312] [3313] [3314] [3315]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\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 18017--18027
[][]\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 ,
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\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
[3317]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\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
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\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
[3319]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\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

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\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
[3320]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\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 18341--18350
[][][]\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 18341--18350
[][]\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 ,
[3321]
Underfull \hbox (badness 3579) in paragraph at lines 18380--18385
\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
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\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
[3324] [3325]
Underfull \hbox (badness 1009) in paragraph at lines 18658--18667
\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
[3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \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
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3335]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70
 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3336] [3337] [3338]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3339]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\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 429--429
 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3340] [3341]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3342]) (./rpart-pkg.tex
Chapter 27.
[3343] [3344] [3345] [3346]
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, ...)[] 
[3347] [3348] [3349] [3350]
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
[3351] [3352]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3353] [3354]
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[] 
[3355]
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"), ...)[] 
[3356] [3357] [3358]
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, ...)[] 
[3359]
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
[3360]
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[] 

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 []\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,[] 
[3361] [3362] [3363] [3364] [3365] [3366]
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 ',
[3367] [3368]
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,[] 
[3369] [3370] [3371]) (./spatial-pkg.tex [3372]
Chapter 28.
[3373] [3374] [3375] [3376] [3377] [3378]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389]
[3390] [3391]) (./survival-pkg.tex [3392]
Chapter 29.
[3393] [3394]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

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 []\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.[] 
[3395] [3396]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... 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
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3397] [3398]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3399]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3400] [3401]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3403] [3404]
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 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3405] [3406] [3407]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.

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 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3408] [3409]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
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on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3411]
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3412] [3413]
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 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3414] [3415] [3416] [3417] [3418]
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[][][]\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 ,
[3419]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3420] [3421] [3422] [3423] [3424] [3425] [3426]
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 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 

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 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3427] [3428] [3429]
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 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3430] [3431] [3432] [3433]
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 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3434]
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 []           \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre
ssion", "death")))[] 

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[]\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
[3435]
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[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3436]
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 []                 \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 )))[] 

[3437] [3438]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3441] [3442] [3443] [3444] [3445]
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 []                    \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 )))[] 
[3446]
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[3448] [3449] [3450] [3451] [3452]
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 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3453] [3454]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3455]
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 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3456]
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 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3457]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3458] [3459]
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[]\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
[3460] [3461]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 

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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3462] [3463] [3464]
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 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3465]
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 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

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 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50
,60,70,100)) +[] 

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 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3466] [3467] [3468] [3469] [3470]
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[3472] [3473]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

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\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
[3474] [3475] [3476] [3477] [3478]
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 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

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 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
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<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3479] [3480]
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 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3481] [3482] [3483] [3484] [3485]
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 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 

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 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3486] [3487] [3488] [3489]
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 []    \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 ),[] 
[3490] [3491] [3492]
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[]\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
[3493] [3494]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form

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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3495]
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 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3496]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3497]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3498]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3499] [3500] [3501]
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[][][]\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 ,
[3502]
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3503] [3504]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
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[]\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-

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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-

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\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-

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\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
[3508]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3509] [3510] [3511] [3512]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3513]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3514] [3515]
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\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 .

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\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 ,

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\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
[3516]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3517] [3518] [3519]
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 []                 \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 )[] 
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

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\T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] 
[3522] [3523] [3524] [3525]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 

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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3526]
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 

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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3527] [3528] [3529] [3530] [3531] [3532] [3533]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3534] [3535] [3536])
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(/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6]
[7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
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[2] (./base-pkg.tex
Chapter 1.
[3] [4]
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[]\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 .

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\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

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\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 ^

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[]\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

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\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

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\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

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\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

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[]\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, 
it is equal to
[5] [6] [7]
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[][][]\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 534--540
[]\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] (/usr/share/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [13] [14] [15]
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 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 

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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
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[]\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] [26]
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 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
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[]\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]
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[]\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]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

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[]\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
[32] [33] [34] [35]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

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[][][]\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
[38]
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[]\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
[39] [40]
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 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 

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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 

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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
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 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

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\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
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
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 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 

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 []      \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = NA)[] 

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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-

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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
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[]\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
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[]\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
[82] [83] [84] [85] [86] [87] [88] [89]
Underfull \hbox (badness 1796) in paragraph at lines 5993--6001
[]\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 : / /
[90] [91] [92]
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 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 

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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 

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 []\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}[] 
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\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.

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[]\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

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[]\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
[95]
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[]\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
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 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
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[]\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 : 
[99] [100]
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[]\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

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\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
[101] [102]
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[]\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

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\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

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\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

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\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

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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
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\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
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 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
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[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
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 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
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 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting

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[]\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

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[][]\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
[119]
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[]\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")
[120] [121] [122] [123] [124] [125]
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[]\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

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\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 =
[126] [127] [128]
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[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
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[]\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
[132] [133]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 

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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 

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 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 

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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
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[]\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

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[]\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
[136] [137] [138]
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[]\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
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10060--10065
[]\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

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 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE
RS)))) # recycling[] 

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 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
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\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
[150]
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[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as

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[]\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
[151] [152]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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\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 / Double _

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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
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 []\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, ..[] 
[155] [156]
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 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
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[]\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

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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11088--11091
[]\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
[163] [164] [165] [166] [167] [168] [169] [170] [171]
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[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
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[]\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

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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
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[]\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

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\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
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12093--12095
[]\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
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
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 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
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\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

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\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
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
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[]\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 =
[200] [201]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[202] [203]
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[][][]\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 ,

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
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[][][]\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 ,

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 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
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[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class

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 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 

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[]\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

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\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(

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[]\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,
[208] [209] [210]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

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 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 

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 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
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[]\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-

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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
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[][][]\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 ,
[216]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
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[]\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

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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 

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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
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[]\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

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[]\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
[220]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

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\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this

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[]\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

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[]\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 =
[221]
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[]\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

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\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 .

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[]\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
[222]
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 []\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 ")[] 

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 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235]
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 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[236]
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\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
 ,

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[]\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
[237]
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[][][]\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 ,
[238] [239] [240]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[241]
Underfull \hbox (badness 1867) in paragraph at lines 16606--16613
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[242] [243] [244] [245]
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 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

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 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

Underfull \vbox (badness 10000) has occurred while \output is active [246]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[247] [248] [249] [250]
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 []\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))) 
[251] [252] [253] [254]
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 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257] [258]
Underfull \hbox (badness 2435) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[259]
Underfull \hbox (badness 2285) in paragraph at lines 17903--17905
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

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 []\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.[] 

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 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 18075--18075
 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 

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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
[262]
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 []\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 18090--18090
 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[263] [264]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 18217--18217
 []\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 18225--18225
 []\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):[] 
[265] [266] [267]
Underfull \hbox (badness 10000) in paragraph at lines 18430--18432
[]\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
[268]
Underfull \hbox (badness 4217) in paragraph at lines 18514--18523
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 18529--18545
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18948--18951
[]\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 ,
[275] [276]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19071--19071
 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 19255--19255
 []\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 19256--19256
 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287] [288]
Underfull \hbox (badness 1975) in paragraph at lines 19834--19837
[]\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
[289] [290] [291] [292] [293] [294]
Underfull \hbox (badness 1077) in paragraph at lines 20229--20234
[]\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
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20250
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[296]
Underfull \hbox (badness 10000) in paragraph at lines 20317--20321
[]\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
[297] [298]
Underfull \hbox (badness 10000) in paragraph at lines 20466--20470
[]\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 20466--20470
[][]\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 20471--20478
[]\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-
[299] [300]
Underfull \hbox (badness 10000) in paragraph at lines 20602--20609
[][][]\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 ,
[301]
Underfull \hbox (badness 10000) in paragraph at lines 20723--20727
[]\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
[302]
Underfull \hbox (badness 5161) in paragraph at lines 20793--20798
[]\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 20793--20798
\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 20793--20798
\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 20793--20798
\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
[303] [304] [305]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 20960--20960
 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[306]
Underfull \hbox (badness 3343) in paragraph at lines 21020--21024
[][][]\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
[307]
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 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[308] [309]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228
 []\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 21231--21231
 []\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 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[310] [311]
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[]\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/
ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of

Overfull \hbox (4.38043pt too wide) in paragraph at lines 21397--21397
 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[312] [313]
Underfull \hbox (badness 1400) in paragraph at lines 21565--21569
[][][]\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
[314] [315] [316]
Underfull \hbox (badness 2469) in paragraph at lines 21735--21741
[]\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,

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\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 21735--21741
\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,
[317] [318] [319] [320] [321] [322] [323] [324] [325]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362
 []\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 22363--22363
 []        \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 22366--22366
 []\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)[] 
[326] [327]
Underfull \hbox (badness 1655) in paragraph at lines 22490--22494
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[328] [329] [330] [331]
Underfull \hbox (badness 2277) in paragraph at lines 22739--22742
[]\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.
[332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 1484) in paragraph at lines 23304--23312
[]\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 23304--23312
\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 /
[340] [341]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23381--23381
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1448) in paragraph at lines 23886--23894
\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 =
[349] [350]
Underfull \hbox (badness 3849) in paragraph at lines 24000--24005
[]\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
[351]
Underfull \hbox (badness 7308) in paragraph at lines 24077--24083
[]\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

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\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 24077--24083
[][]\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 24087--24090
[]\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 24087--24090
\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
[352] [353]
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[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[354] [355] [356]
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[]\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
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 2197) in paragraph at lines 24943--24947
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

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\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
[364]
Underfull \hbox (badness 2846) in paragraph at lines 24957--24961
[]\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-

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\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 24999--24999
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25051--25057
[]\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 25051--25057
\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 25064--25066
[]\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%
[366]
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 [] \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:[] 
[367] [368] [369]
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[]\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
[][][]
[370] [371] [372]
Underfull \hbox (badness 1694) in paragraph at lines 25530--25533
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[373] [374] [375]
Underfull \hbox (badness 1603) in paragraph at lines 25777--25779
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[376] [377]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[378] [379]
Underfull \hbox (badness 3271) in paragraph at lines 26111--26114
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[380] [381] [382]
Underfull \hbox (badness 3138) in paragraph at lines 26411--26417
[]\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 ,

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\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 26411--26417
\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
[383]
Underfull \hbox (badness 1194) in paragraph at lines 26424--26427
[]\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

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[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

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[]\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

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[]\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
[384]
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[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

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[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26541--26548
[]\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 26541--26548
\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 26541--26548
\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 26541--26548
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[385] [386] [387] [388]
Underfull \vbox (badness 10000) has occurred while \output is active [389]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885
 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec,
 300X faster[] 

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[]\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

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\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)] =
[390] [391]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\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

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\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
[392] [393] [394]
Underfull \hbox (badness 10000) in paragraph at lines 27314--27320
[][][]\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 27314--27320
[][]\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
[395]
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 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as
 the longest input.[] 

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 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[396] [397] [398] [399] [400] [401] [402]
Underfull \hbox (badness 1817) in paragraph at lines 27782--27786
[]\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 =
[403]
Underfull \hbox (badness 1796) in paragraph at lines 27850--27853
[]\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
[404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 28050--28053
[]\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
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727
 []           \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))[] 
[417] [418] [419] [420]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993
 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3
\u147b\u203c")[] 

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 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 

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 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm
l#Literal-constants[] 

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 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 

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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[421]
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[]\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
[422]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[423] [424]
Underfull \hbox (badness 3713) in paragraph at lines 29279--29290
[]\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
[425]
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\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 29423--29430
\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 /
[426] [427]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
[430]
Underfull \hbox (badness 1038) in paragraph at lines 29704--29715
[]\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
[431] [432]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 29848--29848
 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 

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 []\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 29851--29851
 []\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 29852--29852
 []\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 29853--29853
 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 29860--29860
 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[433] [434] [435] [436] [437]
Underfull \hbox (badness 4048) in paragraph at lines 30207--30212
[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

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\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 ,
[438] [439] [440] [441] [442] [443] [444] [445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30748--30748
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 7558) in paragraph at lines 31250--31254
[]\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 31260--31262
[]\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

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[][][]\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
[453]
Underfull \hbox (badness 10000) in paragraph at lines 31269--31271
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31677--31681
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 

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 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469] [470]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[471] [472] [473] [474] [475] [476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[477]
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[]\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
[478]
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

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\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
[479] [480]
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 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[481] [482] [483]
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[]\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 .
[484] [485] [486] [487]
Underfull \hbox (badness 1210) in paragraph at lines 33627--33629
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499]
[500] [501]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[502] [503] [504]
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 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 

Overfull \hbox (42.78088pt too wide) in paragraph at lines 34818--34818
 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[505]
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[][][]\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

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[][]\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
[506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34972--34972
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510] [511]
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 []\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)[] 
[512]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 35315--35315
 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[513] [514] [515] [516] [517] [518]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 35756--35756
 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 35757--35757
 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
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[]\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

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\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

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\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

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\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

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\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
[523]
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[]\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 '

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\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,

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\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

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[]\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

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\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

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\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
[524] [525] [526] [527]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[528] [529] [530] [531] [532] [533] [534] [535]
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 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[536] [537] [538] [539]
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 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[540]
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 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[541] [542] [543] [544] [545] [546]
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 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 

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 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[547]
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[]\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

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\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 ).
[548]
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 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[549] [550] [551] [552]
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 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[553]
Underfull \vbox (badness 10000) has occurred while \output is active [554]
[555]
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 []\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. 
[556]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 

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[]\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

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\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
[557]
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\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

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\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
[558] [559] [560]
Underfull \hbox (badness 10000) in paragraph at lines 38664--38668
[]\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

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[]\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
[561] [562]
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 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[563]
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 []\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 
[564] [565] [566]
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[]\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
[567] [568]
Underfull \hbox (badness 1038) in paragraph at lines 39216--39219
[]\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
[569] [570] [571] [572] [573] [574]
Underfull \hbox (badness 1442) in paragraph at lines 39579--39583
\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 =
[575] [576] [577]
Underfull \hbox (badness 4096) in paragraph at lines 39825--39828
[]\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 ,
[578] [579]
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[]\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) >
[580] [581]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093
 []            \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 40095--40095
 []            \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),[] 

[582]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097
 []                 \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 40110--40112
[]\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
[583]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[584] [585]
Underfull \hbox (badness 3872) in paragraph at lines 40308--40311
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[586]
Underfull \hbox (badness 5475) in paragraph at lines 40374--40378
[][][]\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 : / /
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 40792--40799
\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 40848--40857
[]\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-

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\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,

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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-

Underfull \hbox (badness 10000) in paragraph at lines 40858--40866
\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at

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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[593]
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\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

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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[594]
Underfull \hbox (badness 3460) in paragraph at lines 40987--40990
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /

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[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-

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 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[595] [596] [597]
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[]\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
[598] [599]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 41339--41339
 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 

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 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 

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[601] [602] [603] [604]
Underfull \hbox (badness 6542) in paragraph at lines 41703--41705
[]\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
[605] [606]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 41822--41822
 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[607]
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[]\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

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\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

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[][][]\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;
[608]
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[]\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

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\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 ,
[609] [610] [611] [612] [613]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[614] [615] [616] [617] [618] [619]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 42772--42772
 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[620]
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 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[621]
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[]\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 ),
[622]
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[]\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
[623] [624] [625]
Underfull \hbox (badness 3668) in paragraph at lines 43125--43127
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[626]
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 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[627]
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 []\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[] 

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 []\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 ...[] 
[628] [629]
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[]\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,

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\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,
[630]
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[]\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

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\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
[631]
Underfull \hbox (badness 2818) in paragraph at lines 43553--43559
[]\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
[632]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[633]
Underfull \hbox (badness 1622) in paragraph at lines 43682--43684
[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[634] [635] [636] [637] [638]
Underfull \hbox (badness 2846) in paragraph at lines 44045--44049
[]\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
[639]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

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[]\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
[640]) (./compiler-pkg.tex
Chapter 2.
[641]
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[]\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-

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\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
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 

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[652] [653] [654] [655]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
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[]\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.
[660] [661]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
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[]\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 ,

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\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
[669] [670] [671]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681]
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[682] [683] [684] [685] [686]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
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[688]
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[690]
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[691] [692]
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[693]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
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[704]
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[705]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /

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[]\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 /

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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
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[]\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

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[]\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
[725] [726]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

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\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
[727] [728]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
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[]\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
[738] [739]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
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[]\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
[741] [742] [743] [744] [745] [746] [747] [748]
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[]\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

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\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
[749]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

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[]\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-

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\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 ,
[750] [751]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[752] [753]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
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\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

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\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

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\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

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\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
[756] [757]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 

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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 

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 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
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[765] [766] [767] [768]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range

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\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-
[772] [773] [774]
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 

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[]\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 ,
[775]
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /

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\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
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[]\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
[793]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 

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[]\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
[794]
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[]\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"
[795]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[796] [797] [798]
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[]\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

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[][][]\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
[799] [800]
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\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 ,

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\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 ,

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\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 ),

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[]\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

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\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
[801]
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[]\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 /
[802] [803]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
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[]\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
[807] [808] [809] [810] [811]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
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 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 

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 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
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[]\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 ,

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\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 ,

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\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
[822]
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 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
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[]\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 :
[824]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
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[]\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

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\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
[827]
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[]\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

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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
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\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 ,
[830]
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[]\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 /
[831] [832]
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[]\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
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.

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[]\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 =
[837] [838] [839]
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[]\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
[840]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
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 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 

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[]\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
[844] [845]
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 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846]
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[]\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

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[][]\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
[847] [848]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 

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 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[849] [850] [851]
Underfull \hbox (badness 10000) in paragraph at lines 960--964
[][][]\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.

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 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 

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 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 

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 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1265--1265
 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[856] [857] [858]
Underfull \hbox (badness 1024) in paragraph at lines 1427--1435
\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

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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

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 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
Underfull \hbox (badness 10000) in paragraph at lines 1839--1845
[][][]\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
[865]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1876--1876
 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 2378--2378
 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 

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\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
[874]
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[][][]\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

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 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
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\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

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 []\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 :[] 

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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[882]
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[][][]\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
[883] [884] [885]
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 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 

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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
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[]\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

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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 

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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[891] [892] [893]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
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 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

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 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 

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 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 

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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
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[][][]\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%
[897]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[898] [899] [900] [901]
Underfull \hbox (badness 3930) in paragraph at lines 4215--4217
[]\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
[902] [903] [904] [905]
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\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
[906]
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[]\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
[907]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 

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 []      \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma
=c(2,2,3,2))[] 
[908]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
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\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 ,
[910] [911]
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[]\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.
[912]
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[913 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/mai.pdf>]
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[915 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/oma.pdf>]
[916]
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[]\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
[917]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5329--5329
 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5695--5695
 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 5696--5696
 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 

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[]\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 =
[924] [925] [926] [927] [928] [929] [930]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6181--6181
 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 

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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
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[]\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

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[][] 
[939 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/pch.pdf>]
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

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[942]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
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[]\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
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
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[955] [956] [957] [958] [959]
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
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[963] [964]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

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[]\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
[965]
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[]\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
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 

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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
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 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[971]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color

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[]\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
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [973]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
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 []\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)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

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\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
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

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[]\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-
[995] [996] [997] [998]
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[]\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
[999] [1000] [1001] [1002] [1003] [1004]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
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[]\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 ,
[1009]
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[]\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-

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[]\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
[1010] [1011] [1012]
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[]\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
[1013] [1014] [1015]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

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[]\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-
[1016]
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 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
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[1019] [1020] [1021] [1022]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1029]
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[]\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
[1030] [1031]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 

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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 

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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046]
[1047]
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[]\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
[1048]
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[]\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-
[1049] [1050] [1051]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061]
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[]\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
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
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[]\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-

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\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")
[1072] [1073] [1074] [1075] [1076]
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[]\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
[1077]
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[][][]\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 ,
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[]\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
[1080] [1081] [1082]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
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\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
[1087] [1088] [1089]
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[][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo
r-ma-tion about group generic func-tions; [][]Meth-
[1090] [1091]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 

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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 

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 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th
e default method[] 

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 []\T1/pcr/m/n/9 ## call f() with 1 argument:  the default "B0" is not passed b
y callNextMethod[] 

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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 

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 []\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[
] 

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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
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[]\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
[1111] [1112] [1113]
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[]\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 =
[1114] [1115]
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[]\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

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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
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[]\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

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[]\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
[1119]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
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[]\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,

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\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
[1130] [1131]
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[]\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
[1132]
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[]\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

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[]
[1133] [1134]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =

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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =

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[]\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
[1136] [1137] [1138]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
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 ,
[1146] [1147] [1148]
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
[1149] [1150] [1151] [1152]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 

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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

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[1155]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
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[]\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
[1161] [1162] [1163] [1164] [1165] [1166]
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[]\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
[1167] [1168]
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[]\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,

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\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
[1169]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
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
[1172]
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[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
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 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 

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 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \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
<to be read again> 
                   \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
<to be read again> 
                   \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

<to be read again> 
                   \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
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\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
[1180]
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[]\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 ,

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\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 ,

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\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 ,
[1181] [1182]
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

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[]\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
[1183] [1184]
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
[1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195]
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[]\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
[1196]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1208] [1209] [1210] [1211]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1212]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 

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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
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[]\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

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[]\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.,

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\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
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
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
[1227]
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[]\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
[1228] [1229]
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[]\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
[1230] [1231] [1232]
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[]\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
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\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

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\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
[1237] [1238]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 

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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
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[]\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
[1243]
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[]\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

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 []\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)[] 
[1244] [1245]
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 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\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

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[]\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
[1247] [1248]) (./splines-pkg.tex
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 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
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 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
Underfull \hbox (badness 1424) in paragraph at lines 594--596
[]\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
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
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 ,

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 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 

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 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1269]
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\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
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\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

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\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 1536--1540
\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
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737
 []\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 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
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 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3175--3177
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
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 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

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 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
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 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
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 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4182--4182
 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

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 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4589--4589
 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\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 =
[1332] [1333] [1334] [1335] [1336] [1337]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5066--5066
 []\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))[] 

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 []\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))[] 
[1338] [1339] [1340]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 5289--5289
 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

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 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 

Underfull \hbox (badness 2680) in paragraph at lines 5334--5336
[]\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
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5517--5522
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances

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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

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\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 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 5882--5882
 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
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 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
Overfull \hbox (84.78088pt too wide) in paragraph at lines 6175--6175
 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
Underfull \hbox (badness 10000) in paragraph at lines 6242--6247
[]\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
[1355] [1356] [1357] [1358]
Underfull \hbox (badness 5954) in paragraph at lines 6438--6440
[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
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[]\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

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[]\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 6527--6532
\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,

Underfull \hbox (badness 7238) in paragraph at lines 6563--6566
[][][]\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
[1360]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6598--6598
 []\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 6613--6613
 []\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):[] 

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 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1361]
[1362] [1363] [1364]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872
 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7270--7274
\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
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7369--7372
[]\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
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7506--7509
[]\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 =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
Underfull \hbox (badness 10000) in paragraph at lines 7918--7923
[]\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 , ...,
[1381] [1382] [1383] [1384] [1385]
Underfull \hbox (badness 1210) in paragraph at lines 8273--8275
[]\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
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 8736--8736
 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1393]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8781--8781
 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

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 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8922--8922
 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349
 []           \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 9350--9350
 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9529--9531
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9990--9996
[][][]\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);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10203--10206
[]\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
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 

Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
Underfull \hbox (badness 4132) in paragraph at lines 10504--10508
[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od

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[]\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-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10609--10612
[]\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
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:

Underfull \hbox (badness 10000) in paragraph at lines 10948--10954
[][][]\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,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10986--10991
\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 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11119--11122
\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
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436
 []            \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 
0.1),[] 

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[]\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
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

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[]\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-

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[]\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
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 12534--12536
[]\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
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12603--12605
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12841--12843
[]\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

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[]\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 12847--12851
\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
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13796--13800
[]\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
 ,
[1468] [1469] [1470] [1471] [1472]
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\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 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435
 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 

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 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779
 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 

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 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15279--15282
[]\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 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16136--16141
\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
[1503]
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[]\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 16217--16226
\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 16217--16226
\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
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845
 []\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[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996
 []\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 18043--18043
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18581--18584
[]\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 18594--18598
[]\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
[1541]
Underfull \hbox (badness 1478) in paragraph at lines 18602--18606
\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 18660--18662
[]\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
[1542] [1543]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766
 []      \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 [1544]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 

Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\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 18850--18850
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1545]
Underfull \hbox (badness 2564) in paragraph at lines 18888--18899
[]\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 18888--18899
\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
[1546]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1547] [1548] [1549]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1550]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1551] [1552] [1553] [1554] [1555] [1556]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1557]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659
 []       \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 19661--19661
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1558]
Underfull \hbox (badness 10000) in paragraph at lines 19709--19713
[]\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 10000) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for

Underfull \hbox (badness 5260) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1559]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1560] [1561] [1562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1563]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1564]
Underfull \hbox (badness 1107) in paragraph at lines 20064--20066
[]\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

Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1565]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126
 []\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)[] 
[1566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1567] [1568]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1569]
Underfull \hbox (badness 7740) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of

Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570] [1571]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548
 [] \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 20553--20553
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582]
[1583] [1584]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1585]
Underfull \hbox (badness 6859) in paragraph at lines 21474--21481
[][][]\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 21485--21491
[]\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 ,
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1598] [1599] [1600] [1601] [1602]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1603] [1604] [1605] [1606] [1607]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1616] [1617]
Underfull \hbox (badness 1028) in paragraph at lines 23540--23543
[]\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
[1618] [1619]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23705--23707
[]\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 =

[1621]
Underfull \hbox (badness 7944) in paragraph at lines 23767--23769
[]\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 =

[1622] [1623]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1624] [1625] [1626]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1627] [1628]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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] =
[1629]
Underfull \hbox (badness 2134) in paragraph at lines 24287--24291
[][][]\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 24300--24300
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1630] [1631] [1632] [1633] [1634] [1635]
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
[1637]
Underfull \hbox (badness 6268) in paragraph at lines 24777--24782
[][]\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 ,

Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1638] [1639] [1640]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\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 24995--24999
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\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
[1641]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1642] [1643] [1644]
Underfull \hbox (badness 2495) in paragraph at lines 25221--25230
[]\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 .
[1645]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 

Underfull \hbox (badness 1412) in paragraph at lines 25310--25312
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1646]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397
 []\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 25422--25422
 []\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 25425--25425
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1647] [1648] [1649]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 

Underfull \hbox (badness 2547) in paragraph at lines 25651--25657
[]\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
[1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697
 []\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 25718--25718
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1651]
Underfull \hbox (badness 1019) in paragraph at lines 25780--25785
\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
[1652] [1653]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1654] [1655] [1656] [1657] [1658] [1659] [1660]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1661] [1662]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c
ol = 3, n = 1001)[] 

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 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

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Underfull \hbox (badness 2922) in paragraph at lines 26556--26561
[]\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
[1664]
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 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 

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 []                    \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^
{-e^{phi[3]}*~x}}))[] 

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 []         \T1/pcr/m/n/9 c(0  ,  1   ), 1, length = 0.08, angle = 25); text(0.
5, 1, quote(1))[] 

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 []  \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3
 # (Asym + R0)/2[] 

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 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1665]
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[][][]\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
[1666]
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 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log(
0.4), c0 = 3/4)) )[] 

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 = c(-1, 8),[] 
[1667]
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 []  \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log
(log(2)))) )[] 

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 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 

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 []  \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)[] 

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 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1668]
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[]\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

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 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1669]
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 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1670]
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 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1671]
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[]\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
[1672]
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 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1673]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\
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 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1674]
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[]\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

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 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number 
of iter...: 0" :[] 

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 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
[1675]
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 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] 
== "scal")))[] 

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 []  \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[] 

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[]\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
[1676]
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 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

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 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1677]
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[]\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

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 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1678]
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 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 

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 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul
l() fit to Chick.6")[] 

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 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
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[]\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
[1693] [1694] [1695]
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[]\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
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[]\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
[1698]
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[]\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
[1699]
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 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1700] [1701]
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[]\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)
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[]\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
[1704] [1705] [1706] [1707]
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 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, 
main = t.tit,[] 

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 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1708]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1709]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1710]
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 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1711] [1712]
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[]\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
[1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721]
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 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 

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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1722] [1723] [1724] [1725] [1726]
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 []        \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con
v = FALSE,[] 

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 []        \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace
 = 0)[] 
[1727] [1728]
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 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature
s: --------------[] 

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 []\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:[] 

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[]\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
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[]\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
[1741] [1742] [1743] [1744] [1745] [1746]
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 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F
ALSE, 
[1747]
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[]\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
[1748]
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 []\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 "")[] 
[1749]) (./stats4-pkg.tex [1750]
Chapter 11.
[1751] [1752] [1753]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1754] [1755] [1756]pdfTeX warning (ext4): destination with the same identifier
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                   \relax 
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                                                   [1757] [1758] [1759])
(./tcltk-pkg.tex [1760]
Chapter 12.
[1761] [1762] [1763] [1764]
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
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[]\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
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[][][]\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
[1780]) (./tools-pkg.tex
Chapter 13.
[1781]
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
[1782]
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[]\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

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[]\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
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[1783]
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 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch
ing warning)[] 
[1784]
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[]\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

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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
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\T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1
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[1785]
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 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta
ngle = TRUE, 

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[]\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
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[1793] [1794]
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 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", "
xz"),[] 

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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
[1795] [1796] [1797]
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 []                              \T1/pcr/m/n/10 outputs = FALSE, sources = FALS
E, ...)[] 

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 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU
E, ...)[] 

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\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:

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[1798]
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[]\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

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
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tm/m/n/10 and
[1799]
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[]\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
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[]\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
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 []              \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking
To"),[] 

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 []              \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En
hances"))[] 

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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1807] [1808] [1809]pdfTeX warning (ext4): destination with the same identifier
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[1813]
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[]\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

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 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1814]
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 []                  \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi
dth=0.5in}}}"),[] 

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[]\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-

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\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-

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\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
[1815]
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\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
[1816]
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 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb
ose"))[] 

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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of

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\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 .
[1817]
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 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster"
, "codetools")[] 

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 []                    \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo
", "Suggests"),[] 

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 []    \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations
 = TRUE)[] 
[1818] [1819] [1820] [1821]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2705--2705
 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system.
Rd"),[] 
[1822]
Underfull \hbox (badness 2486) in paragraph at lines 2750--2758
[]\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
[1823] [1824] [1825] [1826] [1827]
Underfull \hbox (badness 1072) in paragraph at lines 3128--3130
[]\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
[1828] [1829] [1830] [1831] [1832]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 3464--3464
 []             \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro
s", "system.Rd"))[] 
[1833] [1834] [1835] [1836]
Underfull \hbox (badness 4108) in paragraph at lines 3712--3719
[]\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
[1837] [1838]
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 []                      \T1/pcr/m/n/10 types = c("examples", "tests", "vignett
es"),[] 

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 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter
net"))[] 

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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,

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[]\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in
-stalled. This should be run with
[1839] [1840]
Underfull \hbox (badness 7832) in paragraph at lines 3971--3974
[]\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
[1841]
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 []                     \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg
ests"))[] 
[1842]
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[]\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
[1843] [1844] [1845]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4258--4258
 []  \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry
run),[] 
[1846] [1847]
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 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, 
bugs) 

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[]\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright
\T1/ptm/m/n/10 ' and
[1848]
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[]\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

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[]\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

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\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
[1849] [1850] [1851]
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 []               \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F
ALSE,[] 

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 []               \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr
ess = "xz")[] 

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[]\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 ',

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\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 4706--4712
[]\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

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\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 ',
[1852]
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[]\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

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\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
[1853] [1854] [1855]) (./utils-pkg.tex [1856]
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 ',
[1857] [1858] [1859] [1860]
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 []\T1/pcr/m/n/9 find("cor", numeric = TRUE)                     # numbers with
 these names[] 
[1861]
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\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1862]
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[]\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
[1863]
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 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 

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 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 

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 []         \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No
", "Cancel"))),[] 
[1864] [1865]
Underfull \hbox (badness 1946) in paragraph at lines 624--628
\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1866]
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 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc
es"), 

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 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l
ist(),[] 

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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

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 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l
ist(),[] 

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 []                       \T1/pcr/m/n/10 program = NULL, dictionaries = charact
er())[] 

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[]\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 ,

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\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-
[1867]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1868]
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\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
[1869] [1870] [1871]
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 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1872]
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[]\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-

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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\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.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1873]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1874]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882]
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 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 

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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1883] [1884]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1885] [1886]
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 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1887]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1888] [1889] [1890]
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 []                 \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")[] 


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 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1891] [1892]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1893]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\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
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1894] [1895]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1896] [1897] [1898]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1899] [1900] [1901] [1902]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1903]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1904]
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[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1905] [1906] [1907] [1908] [1909] [1910]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1911] [1912]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\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

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[]\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
[1913]
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able

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[]\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

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\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

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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1914] [1915]
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\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

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[]\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
[1916] [1917] [1918]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\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
[1919]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1920]
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[]\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)
[1921] [1922] [1923] [1924] [1925]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1927] [1928] [1929]
[1930] [1931] [1932] [1933] [1934]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\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
[1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942]
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 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1943]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\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
[1944]
Underfull \hbox (badness 1502) in paragraph at lines 6085--6090
[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1945] [1946] [1947]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\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 6258--6267
\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
[1948]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\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 6338--6341
[]\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
[1949] [1950]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[1951] [1952]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\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

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[]\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 6644--6650
\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 6644--6650
\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 6658--6665
[]\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")
[1953]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\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

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\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 6716--6719
\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.,
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,

Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\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 6792--6799
\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 6792--6799
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

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[]\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
[1955]
Underfull \hbox (badness 1314) in paragraph at lines 6879--6886
[]\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
[1956]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1957]
Underfull \hbox (badness 5133) in paragraph at lines 6995--6999
[]\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 7009--7012
[]\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

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1958] [1959]
Underfull \hbox (badness 4132) in paragraph at lines 7176--7178
[]\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
[1960] [1961] [1962]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1965]
Underfull \hbox (badness 10000) in paragraph at lines 7526--7528
[]\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
[1966] [1967]
Underfull \hbox (badness 10000) in paragraph at lines 7711--7713
[]\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 7716--7718
[]\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 class
[1968] [1969] [1970] [1971]
Underfull \hbox (badness 1859) in paragraph at lines 7939--7942
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1972]
Underfull \hbox (badness 1655) in paragraph at lines 8032--8035
[]\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 8043--8043
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1973] [1974]
Underfull \hbox (badness 1917) in paragraph at lines 8134--8136
[]\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 ,
[1975] [1976] [1977] [1978]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 

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 []            \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 8408--8408
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 

Underfull \hbox (badness 10000) in paragraph at lines 8436--8438
[]\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
[1979]
Underfull \hbox (badness 10000) in paragraph at lines 8450--8452
[]\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 8458--8463
[]\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,

Overfull \hbox (9.78043pt too wide) in paragraph at lines 8504--8504
 []          \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 8505--8505
 []                                   \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[] 
[1980] [1981]
Underfull \hbox (badness 10000) in paragraph at lines 8634--8639
[]\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 8634--8639
[][]\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 8634--8639
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion

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\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
[1982] [1983]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1984] [1985]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8929--8929
 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1986] [1987]
Underfull \hbox (badness 1789) in paragraph at lines 9060--9062
[]\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
[1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]
Underfull \hbox (badness 5203) in paragraph at lines 9633--9636
[]\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
[1996] [1997] [1998]
Underfull \hbox (badness 1394) in paragraph at lines 9859--9866
\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
[1999]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 9883--9883
 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[2000] [2001]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 10044--10044
 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2002] [2003]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 10225--10225
 []\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[] 
[2004] [2005]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 10311--10311
 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 10314--10314
 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 10319--10319
 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2006]
Underfull \hbox (badness 2027) in paragraph at lines 10391--10394
[]\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
[2007] [2008] [2009]
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 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 

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 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2010]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are

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\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 10672--10677
\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
[2011] [2012] [2013]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10905--10905
 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2014] [2015] [2016] [2017]
Underfull \hbox (badness 10000) in paragraph at lines 11165--11169
\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2018]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11183--11183
 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 

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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2019] [2020]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11372--11372
 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2021] [2022]
Underfull \hbox (badness 1917) in paragraph at lines 11496--11499
[]\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-


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\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
[2023]
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 []\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 '[] 
[2024]
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[]\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

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\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,

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\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-

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\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,

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\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
[2025] [2026]
Underfull \hbox (badness 3646) in paragraph at lines 11758--11760
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2027]
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 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2028] [2029] [2030]
Underfull \hbox (badness 10000) in paragraph at lines 11977--11981
[]\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 12008--12014
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2031] [2032]
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 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

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[]\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
[2033]
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[]\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

[2034]
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[]\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
[2035] [2036] [2037] [2038]
Underfull \hbox (badness 1888) in paragraph at lines 12575--12578
[]\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 12590--12593
[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2039]
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 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 

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[]\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
[2040]
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 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf
fix)) 
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[]\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
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[]\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-
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
 TRUE, ...))[] 

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[]\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 = <S>) \T1/ptm/m/n/10 will not have

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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
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 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2049]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 

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 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 

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 # "1 is 1" here[] 
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[]\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
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[]\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

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\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

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\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
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\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),

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\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
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[]\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

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
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 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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[]\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

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\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

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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =

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[]\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

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\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 ,

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\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[][][]

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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2068]
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\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 =

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\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

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[]\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

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[][][]\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 ,
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 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2070] [2071] [2072]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;

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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2073]
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 []\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:[]
 
[2074]
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 []                      \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d
ata = DAT)))[] 

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 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2075] [2076]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2077]
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[]\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.
[2078] [2079]
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 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep =
 " ", 
[2080]
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[]\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

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[]\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 =
[2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex
Chapter 15.
[2087]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2088] [2089] [2090] [2091] [2092]
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 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2093] [2094] [2095] [2096]) (./MASS-pkg.tex
Chapter 16.
[2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107]
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 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
[2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118]
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[2130]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
[2131] [2132] [2133] [2134]
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[]\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
[2135] [2136] [2137]
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\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 ,

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\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 ,
[2138] [2139]
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[]\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
[2140] [2141] [2142]
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2143]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
[2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154]
[2155]
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[]\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
[2156] [2157] [2158] [2159] [2160] [2161] [2162]
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 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
[2163] [2164] [2165]
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
[2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176]
[2177] [2178] [2179]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2180]
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 []\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") 
[2181] [2182]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...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
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2183]
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[]\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
[2184] [2185] [2186] [2187]
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2189]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
[2190] [2191] [2192] [2193] [2194] [2195]
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 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2196]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

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[]\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 ) =
[2197]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
[2198] [2199]
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\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
[2200] [2201]
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2202]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2203] [2204] [2205] [2206] [2207] [2208]
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[]\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
[2209] [2210]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

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[]\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
[2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221]
[2222] [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230]
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2231]
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[]\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 ,

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[]\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),
[2232]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243]
[2244] [2245]) (./Matrix-pkg.tex [2246]
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
[2247]
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
[2248]
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
[2249]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

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[]\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
[2250] [2251]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488
 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2252]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2253] [2254]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660
 []\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:[] 

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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  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 662--662
 []\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}"}.[] 

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 []        \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?[] 

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 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 

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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2255]
Underfull \hbox (badness 3189) in paragraph at lines 732--736
[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2256] [2257] [2258]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- '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
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2261pdfTeX 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.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2262]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2263]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 

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[]\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
[2264]
Underfull \hbox (badness 1609) in paragraph at lines 1435--1439
[]\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
[2265]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

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 []\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(<UTF-8>) gives bad plots[] 

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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2266]
Underfull \hbox (badness 10000) in paragraph at lines 1531--1538
[]\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 1531--1538
\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

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[]\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

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\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
[2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... 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
<to be read again> 
                   \relax 
l.1623 ... 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
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2268]
Underfull \hbox (badness 2922) in paragraph at lines 1710--1714
[]\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

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\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

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[][][]\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
[2269] [2270]
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[]\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
[2271] [2272] [2273] [2274] [2275]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2276]
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[]\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
[2277] [2278] [2279]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\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

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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble

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[]\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 ;
[2280]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix.
 If miss-ing,

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[]\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

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[][]\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
[2281]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\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 2713--2718
[][]\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
[2282]
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[]\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

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[]\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

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[]\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou
p meth-ods re-turn a

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[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2283]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec
t of S3 class

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[][][]\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
[2284] [2285]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th
is group con-tains

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[][][]\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)
[2286]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\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
[2287] [2288]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\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 3528--3532
\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 ,
[2289]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2290] [2291]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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

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[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2292]
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[]\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
[2293] [2294] [2295]
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 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim 
= c(5L, 5L),[] 

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[]\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
[2296]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\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 4100--4103
\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 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2297] [2298]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2299] [2300] [2301] [2302]
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 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

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 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 

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 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary 
dir./folder:[] 

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 []\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)[] 

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 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2303] [2304] [2305] [2306]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2307]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\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 4932--4932
 []  \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 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2308]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \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 '[] 
[2309] [2310]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\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 5124--5124
 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col
/row) indices:[] 

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 [] \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 5131--5131
 [] \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 5134--5134
 []\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 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2311]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\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 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2312]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\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 5277--5279
[]\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 5279--5282
[]\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 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2313]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2314]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2315] [2316] [2317]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\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[] 
[2318]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2319]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2320]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\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 5819--5819
 []          \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 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2321]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2322]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\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
[2323]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2325]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\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
[2326]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\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.,
[2327]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\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 6485--6485
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2328]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\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 6524--6530
[][]\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 6545--6548
[]\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
[2329]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2330] [2331]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),

Underfull \hbox (badness 5036) in paragraph at lines 6775--6779
[]\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 6775--6779
\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
[2332] [2333]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.det}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
Underfull \hbox (badness 10000) in paragraph at lines 6971--6974


Underfull \hbox (badness 10000) in paragraph at lines 6981--6983
[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
[2334]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
cent.*.Rpcent.}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.crossprod}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.7152 ...A{crossprod}{matrix-products}{crossprod}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.tcrossprod}) has been already used, du
plicate ignored
<to be read again> 
                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
Underfull \hbox (badness 1881) in paragraph at lines 7350--7356
\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
[2335] [2336pdfTeX warning (ext4): destination with the same identifier (name{R
fn.crossprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
                    ]
Underfull \hbox (badness 10000) in paragraph at lines 7423--7426
[]\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 7423--7426
\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 7426--7431
[]\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 7426--7431
\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 7431--7435
[]\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 7431--7435
\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 7441--7442
[]\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth
er sig-na-
[2337] [2338]
Underfull \hbox (badness 1009) in paragraph at lines 7577--7579
[]\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 7622--7625
[]\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
[2339]
Underfull \hbox (badness 6063) in paragraph at lines 7656--7659
[]\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
[2340]
Underfull \hbox (badness 10000) in paragraph at lines 7708--7710
[]\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
[2341] [2342]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847
 []\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 [2343]
Underfull \hbox (badness 2635) in paragraph at lines 7912--7917
[]\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 7912--7917
\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 7920--7923
[]\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.,
[2344]
Underfull \hbox (badness 3482) in paragraph at lines 7994--8000
[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2345]
Underfull \hbox (badness 1867) in paragraph at lines 8114--8116
[]\T1/ptm/m/n/10 fast sim-
[2346]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor
m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \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
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2347]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241
 []\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 8242--8242
 []\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 8243--8243
 []\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 8356--8366
[]\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 ,
[2348]
Underfull \hbox (badness 3179) in paragraph at lines 8427--8430
[]\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
[2349]
Underfull \hbox (badness 10000) in paragraph at lines 8517--8520
[]\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.,
[2350]
Underfull \hbox (badness 10000) in paragraph at lines 8593--8596
[]\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.,
[2351]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609
 []\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
[2352]
Underfull \hbox (badness 10000) in paragraph at lines 8719--8721
[]\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 8721--8724
[]\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 8727--8734
[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
[2353] [2354]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820
 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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[]\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

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\T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro
m
[2355] [2356]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2357]
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 []\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![] 

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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 

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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 

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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 

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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 

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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

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[]\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
[2359]
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 []\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"[] 
[2360]
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 

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 []\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
<to be read again> 
                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2361] [2362]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
[2363] [2364]
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably

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[]\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

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\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
[2365] [2366]
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[]\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
[2367]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
[2368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol
ve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2369]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a

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[]\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via

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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (

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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 (

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\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,
[2370]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's

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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines

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[]\T1/ptm/m/n/10 works via

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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

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[]\T1/ptm/m/n/10 all work via

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[][][]\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

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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
 [FIXME ??] only[] 
[2371]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

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[]\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,

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[]\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)

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\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

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


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\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
[2372]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a

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[]\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-
[2373]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 

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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 

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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2374] [2375]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 

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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2376]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2377]
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 

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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 

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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 

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 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims
 = c(10,20)))[] 

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 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2378]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

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 []\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)[] 

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 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep
resentations.[] 

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 []   \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack
age = "SparseM"))) {[] 

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 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2379]
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2380]
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[][][]\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
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2381] [2382]
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[]\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

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 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 

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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2383]
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[]\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-

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\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 ,
[2384]
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[]\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
[2385]
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[]\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

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[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2386] [2387]
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[][][]\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,
[2388]
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[]\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/
n/10 : and many

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[]\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

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\T1/pcr/m/n/10 list(NULL,<character>)\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

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\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
[2389]
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[]\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.,
[2390] [2391]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\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

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[]\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

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\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
[2392]
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[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2393] [2394] [2395]
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[]\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
[2396]
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 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted
 if necessary:[] 

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 []\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)[] 
[2397] [2398]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2399] [2400] [2401]) (./boot-pkg.tex [2402]
Chapter 18.
[2403] [2404] [2405] [2406] [2407] [2408] [2409]
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 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2410]
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[]\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

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[]\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-
[2411] [2412] [2413]
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[]\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.

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[][][]\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 ,
[2414]
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 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, 
data = nuke)[] 

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[2416]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues

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\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"
[2417]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\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 1082--1091
\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2418] [2419] [2420] [2421]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2422] [2423] [2424] [2425] [2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2427] [2428] [2429]
Underfull \vbox (badness 10000) has occurred while \output is active [2430]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2431]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2432] [2433] [2434]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
[2435]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\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 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2436] [2437]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2438] [2439] [2440] [2441] [2442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 

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 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2443] [2444] [2445]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2446]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2447] [2448] [2449]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2450] [2451] [2452] [2453] [2454] [2455] [2456]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2457] [2458]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2459] [2460] [2461]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2462]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2463] [2464]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\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 4368--4372
\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
[2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2474] [2475] [2476] [2477]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2478]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2487]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2488]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2489] [2490] [2491] [2492]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2493] [2494]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\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 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2495] [2496] [2497]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2498] [2499]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex
[2508]
Chapter 19.
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519]
[2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex
Chapter 20.
[2525]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\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 133--142
\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 133--142
\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 133--142
\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
[2526] [2527]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2528] [2529]
Underfull \vbox (badness 10000) has occurred while \output is active [2530]
[2531]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2532] [2533]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2534]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2535] [2536]
Underfull \hbox (badness 2941) in paragraph at lines 779--782
[][][]\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 
,

Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2537]
Underfull \hbox (badness 10000) in paragraph at lines 864--866
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2538]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2539]
Underfull \hbox (badness 4872) in paragraph at lines 975--977
[]\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 989--993
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2540]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2541]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2542]
Underfull \hbox (badness 4144) in paragraph at lines 1190--1194
[]\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
[2543]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266
 []          \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 1272--1272
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2544] [2545]
Underfull \hbox (badness 10000) in paragraph at lines 1411--1416
[]\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

Underfull \hbox (badness 10000) in paragraph at lines 1459--1462

[2546]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1480
[][][]\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 1500--1500
 []\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 1510--1510
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2547]
Underfull \hbox (badness 5741) in paragraph at lines 1550--1553
[]\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
[2548]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2549]
Underfull \hbox (badness 1540) in paragraph at lines 1733--1741
\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 =
[2550] [2551]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824
 []\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 1843--1843
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2552] [2553] [2554] [2555]
Underfull \hbox (badness 10000) in paragraph at lines 2162--2165

[2556]
Underfull \hbox (badness 3179) in paragraph at lines 2176--2182
[][][]\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.
[2557] [2558]
Underfull \hbox (badness 10000) in paragraph at lines 2334--2337
[][][]\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 ,
[2559]
Underfull \hbox (badness 1292) in paragraph at lines 2402--2405
[]\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

Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\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 2434--2437
[][][]\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 ,
[2560] [2561] [2562] [2563]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650
 []\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 ):[] 
[2564] [2565] [2566]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2567] [2568]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2569] [2570] [2571]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572]
Underfull \hbox (badness 10000) in paragraph at lines 3286--3289
[]\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
[2573]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2574] [2575] [2576]
Underfull \hbox (badness 10000) in paragraph at lines 3522--3525
[]\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
[2577]
Underfull \hbox (badness 10000) in paragraph at lines 3585--3590
[][][]\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 ,
[2578]
Underfull \hbox (badness 3884) in paragraph at lines 3647--3652
\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 3659--3662
[][][]\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 ,
[2579] [2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 3844--3847
[][][]\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 3875--3878
[][][]\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 ,
[2582]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3939--3941
[]\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
[2583] [2584] [2585] [2586]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132
 []     \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 4134--4134
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2587] [2588]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272
 []\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 4281--4281
 []   \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 4283--4283
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

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 []\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 4288--4288
 []   \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k),
 do.n.k=FALSE,[] 

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 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2589] [2590] [2591] [2592] [2593] [2594]
Underfull \hbox (badness 10000) in paragraph at lines 4668--4674
[]\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

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[]\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
[2595]
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 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 

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 []\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[] 

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 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 

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 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2596]) (./codetools-pkg.tex
Chapter 21.

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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 

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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 

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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2597]
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[]\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
[2598]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2599] [2600] [2601]) (./foreign-pkg.tex [2602]
Chapter 22.
[2603]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2604] [2605]
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[]\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 ,
[2606]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2607] [2608] [2609]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2610]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463
 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 

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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

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\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

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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to

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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,

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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-

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\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
[2611]
Underfull \hbox (badness 10000) in paragraph at lines 551--559
[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]

Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\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
[2612]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624
 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 

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 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2613]
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 []\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 662--662
 []\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 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2614] [2615]
Underfull \hbox (badness 10000) in paragraph at lines 813--814


Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823
 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2616] [2617]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899
 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2618]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2619] [2620]
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[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2621] [2622]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2623]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\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
[2624]) (./lattice-pkg.tex
Chapter 23.
[2625] [2626] [2627]
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 []       \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"),[] 
[2628]
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 []        \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul
t.dotplot"),[] 

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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.barchart"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

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 []       \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"),[] 
[2629] [2630] [2631] [2632]
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
[2633] [2634] [2635] [2636]
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[]\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

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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2637]
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
[2638] [2639]
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[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2640] [2641] [2642]
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 ,
[2643]
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 ,
[2644]
Underfull \vbox (badness 10000) has occurred while \output is active [2645]
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
[2646]
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

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[]\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
[2647] [2648] [2649] [2650]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2651]
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
[2652] [2653] [2654]
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"),[] 
[2655] [2656] [2657] [2658] [2659]
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")[] 

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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2660] [2661]
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

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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


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\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 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2662]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\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,

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\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

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\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 2959--2963
[]\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
[2663] [2664]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \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 3061--3061
 []      \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 3062--3062
 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2665]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\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.

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\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
[2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2670]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2671] [2672] [2673] [2674] [2675]
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 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2676]
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by

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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2677] [2678]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

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[]\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

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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

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\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
[2679]
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[]\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 4170--4174
\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
[2680] [2681]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\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 ,

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\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 ,

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\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

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\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

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\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

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[]\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 ,

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[]\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
[2682] [2683] [2684] [2685] [2686] [2687]
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 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2688] [2689]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2690] [2691]
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[]\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
[2692] [2693] [2694] [2695] [2696] [2697]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\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

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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2698]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

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\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
[2699]
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[]\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
[2700]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2701]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of


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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2702] [2703]
Underfull \hbox (badness 2538) in paragraph at lines 5846--5850
\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

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[]\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

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\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
[2704] [2705]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\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 ,
[2706] [2707]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2708] [2709]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\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

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\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
[2710]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2711] [2712]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\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
[2713]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
[2714] [2715] [2716] [2717] [2718] [2719]
Underfull \hbox (badness 1320) in paragraph at lines 6955--6962
[]\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-

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\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
[2720]
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 []                 \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = 
NULL,[] 
[2721]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

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\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
[2722]
Underfull \hbox (badness 10000) in paragraph at lines 7160--7163
\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
[2723] [2724]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2725]
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
[2726] [2727]
Underfull \hbox (badness 2644) in paragraph at lines 7513--7517
\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 7526--7529
[]\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
[2728]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596
 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
[2729]
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 []        \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam
e.type)[] 

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 []      \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident
ifier, name.type)[] 
[2730] [2731] [2732]
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
[2733]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\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
[2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\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 8470--8473
\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
[2742] [2743]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645
 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

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 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin
t, ...)[] 

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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2744]
Underfull \hbox (badness 3118) in paragraph at lines 8677--8680
[]\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
[2745]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2746]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
[2747] [2748]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966
 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
[2749] [2750]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105
 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
[2751]
Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168
[]\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 9164--9168
\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
[2752] [2753] [2754] [2755] [2756] [2757] [2758]
Underfull \hbox (badness 7238) in paragraph at lines 9622--9626
[]\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 9622--9626
\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 ,
[2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2762] [2763] [2764]
Underfull \hbox (badness 10000) in paragraph at lines 10015--10020
\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

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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2765] [2766]) (./mgcv-pkg.tex
Chapter 24.
[2767] [2768]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

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 []    \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret
e=FALSE,[] 
[2769]
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2770] [2771] [2772] [2773]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
[2774]
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 []\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)+[] 
[2775] [2776] [2777]
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[]\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
[2778] [2779] [2780]
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[]\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
[2781]
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[]\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).
[2782]
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[2784] [2785] [2786] [2787]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2788]
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 

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 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 

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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 

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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 

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 []\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)[] 

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[2790]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 

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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 

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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 

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[2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799]
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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
[2800] [2801] [2802] [2803] [2804] [2805]
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\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

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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

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[]\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

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2806]
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2807] [2808]
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\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
[2809] [2810]
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[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
[2811]
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[2815] [2816] [2817] [2818] [2819] [2820] [2821]
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2822] [2823] [2824] [2825] [2826] [2827]
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[]\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
[2828] [2829]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701
 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

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[2831] [2832]
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2833] [2834] [2835] [2836] [2837] [2838] [2839]
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 []  \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)+[] 
[2840] [2841] [2842]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2843]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
[2844]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2845]
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[]\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
[2846] [2847]
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[][][]\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 ,

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[][]\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 .
[2848]
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[2850] [2851]
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[]\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

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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2852] [2853] [2854] [2855] [2856] [2857] [2858]
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[]\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
[2859]
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 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2860]
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 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 

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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 

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Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609
 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2862] [2863] [2864] [2865] [2866] [2867]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 

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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2868] [2869] [2870] [2871] [2872] [2873]
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 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 

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 []\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) 
[2874] [2875] [2876] [2877]
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[2880] [2881]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
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[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2891] [2892]
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 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2893] [2894]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 

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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 

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[2914]
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[]\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 ,

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\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 ,

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\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 .
[2915]
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[]\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 ,

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\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
[2916] [2917] [2918]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 

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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
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\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
[2922] [2923] [2924] [2925]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2926] [2927]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
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 []  \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[] 
[2933]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

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[]\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
[2934]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2935]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

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[][]\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,
[2936] [2937]
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[]\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,
[2938] [2939] [2940] [2941]
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[]\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

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\T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre
s-sion terms. This method

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\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

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[]\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:

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\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.
[2942]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

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[]\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 ,
[2943] [2944] [2945] [2946] [2947]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637
 []\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) 
[2948] [2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if

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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 

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[]\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-
[2954]
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[]\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-
[2955] [2956] [2957]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179
 [] \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 11190--11195
[]\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
[2958]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\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 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\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 11296--11300
\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 ,
[2959] [2960] [2961]
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Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2965] [2966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703
 []  \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 11715--11715
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727
 []  \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 11732--11732
 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2967]
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 []  \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 11739--11739
 []  \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:[] 
[2968]
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[]\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 11808--11810
\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
[2969] [2970]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2971]
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 []\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 12018--12018
 []\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[] 
[2972] [2973] [2974]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2975] [2976] [2977] [2978]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407
 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2979]
Underfull \hbox (badness 10000) in paragraph at lines 12468--12470
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2980] [2981]
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Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\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 12627--12630
\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 12627--12630
\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"
[2983]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709
 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2984]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\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 12754--12760
\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-
[2985] [2986] [2987]
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Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968
 []\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...[] 


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Underfull \hbox (badness 10000) in paragraph at lines 13071--13079
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2990]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2991] [2992] [2993] [2994]
Underfull \hbox (badness 3396) in paragraph at lines 13358--13361
[][][]\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
[2995]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2996] [2997] [2998] [2999]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\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 13627--13630
\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
[3000]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\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 13660--13664
[][]\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 13660--13664
[][]\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 ,
[3001] [3002] [3003] [3004] [3005]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3006]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029
 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3007] [3008]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163
 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3009] [3010]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\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
[3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021]
[3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3031] [3032] [3033] [3034] [3035]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\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 15778--15778
 []\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 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3036] [3037] [3038]) (./nlme-pkg.tex
Chapter 25.
[3039]
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
[3040]
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
[3041] [3042] [3043] [3044] [3045]
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,[] 
[3046] [3047]
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 ---------------------------
---------------[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055]
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"),[] 
[3056]
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
[3057] [3058] [3059] [3060] [3061] [3062] [3063]
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 ,
[3064]
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
[3065] [3066] [3067] [3068] [3069]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3071]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3072] [3073]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\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 ,
[3074]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\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 ,
[3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093]
[3094]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\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 ,
[3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105]
[3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116]
[3117] [3118]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\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 ,
[3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3135]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3136]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\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 ,
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3142]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\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 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3143]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3144]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3145] [3146] [3147]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\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 ,
[3148]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 

Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\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
[3149] [3150] [3151]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\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 ,
[3152] [3153] [3154]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\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 7406--7414
\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 7406--7414
\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 7429--7432
[][][]\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 ,
[3155] [3156] [3157]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\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 8156--8173
[][]\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 8199--8199
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3166] [3167] [3168] [3169] [3170]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 

Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3171]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\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
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179] [3180] [3181] [3182] [3183]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\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 9335--9335
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3184]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\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
[3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...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
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3189]
Underfull \hbox (badness 10000) in paragraph at lines 9706--9709
[]\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 9750--9753
[]\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 9750--9753
\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
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\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
[3198] [3199] [3200]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3201]
Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3202] [3203] [3204]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3205] [3206]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 

Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\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[][][]
[3207]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\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 10838--10840
[]\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 10874--10874
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3208] [3209] [3210] [3211]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3212] [3213] [3214] [3215] [3216] [3217]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3218] [3219] [3220] [3221] [3222] [3223]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\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 ,
[3224] [3225] [3226] [3227]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\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 ,
[3228] [3229] [3230] [3231] [3232]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\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
[3233] [3234]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\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 ,
[3235]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\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 ,
[3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3245] [3246] [3247] [3248] [3249]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\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
[3251]
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[]\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 13734--13741
\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 13791--13791
 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3252]
Underfull \hbox (badness 10000) in paragraph at lines 13798--13801
[]\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 13798--13801
\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 13826--13829
[]\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 13826--13829
\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
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\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
[3254]
Underfull \hbox (badness 1472) in paragraph at lines 13931--13938
\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 ,
[3255]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\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 ,
[3256] [3257] [3258] [3259]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3260] [3261] [3262] [3263]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...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
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3273] [3274] [3275]
[3276] [3277] [3278] [3279] [3280] [3281] [3282]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\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
[3283] [3284] [3285]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3286] [3287] [3288] [3289] [3290]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\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 ,
[3291]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3292] [3293] [3294] [3295] [3296] [3297] [3298]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3299] [3300] [3301] [3302] [3303]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\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 ,

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\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

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\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 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for

Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\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
[3304]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance

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\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for

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\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3305] [3306] [3307] [3308]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3309] [3310] [3311] [3312] [3313] [3314] [3315]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\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 18017--18027
[][]\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 ,
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\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
[3317]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\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
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\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
[3319]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\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 18245--18250
\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
[3320]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\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 18341--18350
[][][]\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 18341--18350
[][]\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 ,
[3321]
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\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
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\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
[3324] [3325]
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\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
[3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \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
<to be read again> 
                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3335]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3336] [3337] [3338]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3339]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\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)),[] 

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 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3340] [3341]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3342]) (./rpart-pkg.tex
Chapter 27.
[3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3347] [3348] [3349] [3350]
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
[3351] [3352]
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 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3353] [3354]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3355]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3356] [3357] [3358]
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, ...)[] 
[3359]
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
[3360]
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[] 

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 []\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,[] 
[3361] [3362] [3363] [3364] [3365] [3366]
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 ',
[3367] [3368]
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,[] 
[3369] [3370] [3371]) (./spatial-pkg.tex [3372]
Chapter 28.
[3373] [3374] [3375] [3376] [3377] [3378]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389]
[3390] [3391]) (./survival-pkg.tex [3392]
Chapter 29.
[3393] [3394]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

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 []\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.[] 
[3395] [3396]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... 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
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3397] [3398]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3399]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3400] [3401]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3403] [3404]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805
 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3405] [3406] [3407]
Underfull \hbox (badness 1097) in paragraph at lines 975--977
[]\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 995--995
 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3408] [3409]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110
 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3410]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3411]
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3412] [3413]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3414] [3415] [3416] [3417] [3418]
Underfull \hbox (badness 1337) in paragraph at lines 1799--1803
[][][]\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 ,
[3419]
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 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3420] [3421] [3422] [3423] [3424] [3425] [3426]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 

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 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3427] [3428] [3429]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3430] [3431] [3432] [3433]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3434]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894
 []           \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 2908--2910
[]\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
[3435]
Underfull \hbox (badness 1048) in paragraph at lines 2963--2965
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3436]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037
 []                 \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 )))[] 

[3437] [3438]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3441] [3442] [3443] [3444] [3445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560
 []                    \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 )))[] 
[3446]
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[3448] [3449] [3450] [3451] [3452]
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 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3453] [3454]
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 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3455]
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 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3456]
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 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3457]
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 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3458] [3459]
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[]\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
[3460] [3461]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668
 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 

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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3462] [3463] [3464]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3465]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

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 []\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 4958--4958
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3466] [3467] [3468] [3469] [3470]
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[3472] [3473]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

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\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
[3474] [3475] [3476] [3477] [3478]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

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 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3479] [3480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3481] [3482] [3483] [3484] [3485]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333
 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r
r =expected,[] 

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 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3486] [3487] [3488] [3489]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626
 []    \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 ),[] 
[3490] [3491] [3492]
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[]\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
[3493] [3494]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form

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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3495]
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 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3496]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3497]
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 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3498]
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 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3499] [3500] [3501]
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[][][]\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 ,
[3502]
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 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3503] [3504]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3505] [3506] [3507]
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[]\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-

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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-

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\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-

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\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
[3508]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3509] [3510] [3511] [3512]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3513]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3514] [3515]
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\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 .

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\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 ,

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\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
[3516]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3517] [3518] [3519]
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 []                 \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 )[] 
[3520] [3521]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

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 []                 \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 )[] 
[3522] [3523] [3524] [3525]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 

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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3526]
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 

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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3527] [3528] [3529] [3530] [3531] [3532] [3533]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3534] [3535] [3536]) (./fullrefman.ind [3537] [3538] [3539] [3540] [3541]
[3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550] [3551] [3552]
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[3563]
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[3564]
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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 
[3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572]
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 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean 
rel.diff.=",[] 

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 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F
ALSE) 
[16] [17] [18] [19] [20]
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[]\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] [26]
Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670
 []              \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em
pty.names = TRUE,[] 
[27]
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[]\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]
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[]\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]
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 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 

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[]\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
[32] [33] [34] [35]
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 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla
ss "POSIXlt"[] 
[36] [37]
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

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[][][]\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
[38]
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[]\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
[39] [40]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627
 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt
ick=FALSE), 
[41] [42] [43] [44] [45] [46] [47] [48] [49] [50]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295
 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, 
lwd = 1, bty="n")[] 

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 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = ""
, type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  J_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 
[51]
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 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab =
 "", type = "n",[] 

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 []     \T1/pcr/m/n/9 main = "Bessel Functions  K_nu(x)  near 0\n log - log  sc
ale") ; axis(2, at=1)[] 

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 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5,
 sep = ", ")),[] 
[52] [53] [54] [55] [56] [57]
Underfull \hbox (badness 10000) in paragraph at lines 3771--3773
[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
[58] [59] [60] [61]
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 []   \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
[62] [63] [64]
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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an 
ob-ject

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\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
[65] [66] [67]
Underfull \hbox (badness 4595) in paragraph at lines 4411--4414
[]\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par
-i-son[][][] and
[68] [69]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566
 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{
", 1:10, "}:"))[] 

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 []      \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e
xclude = NA)[] 

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[]\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na
med ar-gu-

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[]\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu
e and valid
[70] [71] [72]
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 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna
mes (default)[] 
[73] [74] [75]
Underfull \hbox (badness 2521) in paragraph at lines 5033--5035
[]\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
[76] [77] [78] [79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5430--5438
[]\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
[82] [83] [84] [85] [86] [87] [88] [89]
Underfull \hbox (badness 1796) in paragraph at lines 5993--6001
[]\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 : / /
[90] [91] [92]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 6187--6187
 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile
r, math-library:[] 

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 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 

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 []\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}[] 
[93] [94]
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\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.

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[]\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

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[]\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
[95]
Underfull \hbox (badness 1308) in paragraph at lines 6402--6410
[]\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
[96] [97]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 6556--6556
 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e
ncoding"))[] 
[98]
Overfull \hbox (89.35893pt too wide) in paragraph at lines 6598--6600
[]\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 : 
[99] [100]
Underfull \hbox (badness 10000) in paragraph at lines 6746--6749
[]\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

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\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
[101] [102]
Underfull \hbox (badness 1406) in paragraph at lines 6928--6934
[]\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

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\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

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\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

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\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

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[]\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in
g from
[103]
Underfull \hbox (badness 1067) in paragraph at lines 6990--6997
\T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar
ds . freedesktop . org / clipboards-[]spec /
[104] [105]
Underfull \vbox (badness 10000) has occurred while \output is active [106]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7182--7182
 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE"))
; close(con)[] 
[107]
Underfull \hbox (badness 1231) in paragraph at lines 7307--7313
\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
[108] [109] [110] [111]
Underfull \hbox (badness 10000) in paragraph at lines 7518--7520
[]\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th
e call to
[112] [113]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 7663--7663
 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org")   ## this redirect
s to https://[] 
[114] [115] [116]
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 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng
th.out = 24)[] 
[117] [118]
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[]\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors
? The

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\T1/ptm/m/n/10 `factory-fresh' de-fault is \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , 
but this can be changed by set-ting

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[]\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 8021--8031
[][]\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
[119]
Overfull \hbox (4.63962pt too wide) in paragraph at lines 8053--8057
[]\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")
[120] [121] [122] [123] [124] [125]
Underfull \hbox (badness 1629) in paragraph at lines 8539--8551
[]\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

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\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 =
[126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 8801--8802
[][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / 
index . html #
[129] [130] [131]
Underfull \hbox (badness 10000) in paragraph at lines 8987--8991
[]\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
[132] [133]
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 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]:  --------
-------------[] 

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 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO
!\n"); pi+2})[] 

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 []        \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "(
", "function"),[] 

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 []        \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh
owAttributes"),[] 
[134] [135]
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[]\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 9243--9245
[]\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
[136] [137] [138]
Underfull \hbox (badness 1603) in paragraph at lines 9454--9457
[]\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
[139] [140] [141] [142] [143] [144] [145] [146] [147]
Underfull \hbox (badness 1917) in paragraph at lines 10060--10065
[]\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

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 []\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 10116--10116
 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling
 on both levels[] 
[148] [149]
Underfull \hbox (badness 1168) in paragraph at lines 10218--10223
\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
[150]
Underfull \hbox (badness 10000) in paragraph at lines 10257--10263
[]\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m
/n/10 ..<n> \T1/ptm/m/n/10 and ba-si-cally the same as

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[]\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
[151] [152]
Underfull \hbox (badness 2828) in paragraph at lines 10423--10427
[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19
85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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\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 / Double _

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 []     \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA
ttributes"))[] 
[153] [154]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10529--10529
 []\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, ..[] 
[155] [156]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 10673--10673
 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon
th.abb[5:9])) 
[157] [158] [159]
Underfull \hbox (badness 6396) in paragraph at lines 10862--10870
[]\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

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[]\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t
o but faster than
[160] [161] [162]
Underfull \hbox (badness 10000) in paragraph at lines 11088--11091
[]\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
[163] [164] [165] [166] [167] [168] [169] [170] [171]
Underfull \hbox (badness 5288) in paragraph at lines 11786--11788
[]\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val
ue of
[172]
Underfull \hbox (badness 3039) in paragraph at lines 11796--11801
[]\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

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[]\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for
[173] [174]
Underfull \hbox (badness 4569) in paragraph at lines 11978--11982
[]\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

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\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
[175] [176]
Underfull \hbox (badness 10000) in paragraph at lines 12093--12095
[]\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
[177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12934--12934
 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes.   Could provide 
a constructor[] 
[188] [189] [190] [191] [192] [193]
Underfull \hbox (badness 2221) in paragraph at lines 13380--13389
\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

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\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
[194] [195] [196] [197]
Underfull \hbox (badness 2253) in paragraph at lines 13641--13643
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[198] [199]
Underfull \hbox (badness 2573) in paragraph at lines 13756--13758
[]\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 =
[200] [201]
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[]\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See

[202] [203]
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[][][]\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 ,

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia .

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 []                     \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B 
as it exists already[] 
[204]
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 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode
 = "0777")[] 
[205]
Underfull \hbox (badness 10000) in paragraph at lines 14162--14165
[][][]\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 ,

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 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu
rsive = TRUE)[] 
[206]
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[]\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di-
tion ob-ject of class

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 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio
ns it is found:[] 
[207]
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 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F
ALSE, 

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[]\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 14308--14315
\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(

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[]\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,
[208] [209] [210]
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 []       \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING) 

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 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO
DING)[] 
[211] [212] [213]
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 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have 
type symbol (aka name).[] 

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 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions.  Use it in co
mbination with[] 
[214]
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[]\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-

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\T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger 
penalty (see
[215]
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[][][]\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 ,
[216]
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 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1
0,100,1000),[] 
[217] [218]
Underfull \hbox (badness 10000) in paragraph at lines 15059--15061
[]\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

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 []          \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = 
decimal.mark,[] 

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 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric
(x)),[] 
[219]
Underfull \hbox (badness 2790) in paragraph at lines 15092--15095
[]\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

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[]\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
[220]
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[]\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

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\T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this

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[]\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

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[]\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 =
[221]
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[]\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

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\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 .

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[]\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
[222]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15345--15345
 []\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 ")[] 

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Overfull \hbox (42.18039pt too wide) in paragraph at lines 15367--15367
 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you 
want see the effect[] 
[224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235]
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 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil
l a DLLInfoList[] 
[236]
Underfull \hbox (badness 2418) in paragraph at lines 16293--16297
\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
 ,

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[]\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
[237]
Underfull \hbox (badness 2326) in paragraph at lines 16335--16342
[][][]\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 ,
[238] [239] [240]
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 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F
ALSE, 
[241]
Underfull \hbox (badness 1867) in paragraph at lines 16606--16613
[]\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][]
[] (or char-ac-ter string for
[242] [243] [244] [245]
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 []  \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around 
"checking hack"[] 

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 []\T1/pcr/m/n/9 name.rex <- "(?<first>[[:upper:]][[:lower:]]+) (?<last>[[:uppe
r:]][[:lower:]]+)"[] 

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Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955
 []        \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F
ALSE)[] 
[247] [248] [249] [250]
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 []\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))) 
[251] [252] [253] [254]
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 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F
ALSE) 
[255] [256] [257] [258]
Underfull \hbox (badness 2435) in paragraph at lines 17837--17839
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[259]
Underfull \hbox (badness 2285) in paragraph at lines 17903--17905
[]\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1
0 http : / / userguide . icu-[]project . org /

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 []\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.[] 

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 []    \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p
rint(sort(x))[] 

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 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se
t = TRUE, 
[260] [261]
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 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------
----------------[] 

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 []\T1/pcr/m/n/9 identical(f, g)                        # TRUE, as bytecode is 
ignored by default[] 
[262]
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 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share
 an environment:[] 

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 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi
ng "srcref" :[] 
[263] [264]
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 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u
se ifelse(),[] 

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 []\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):[] 
[265] [266] [267]
Underfull \hbox (badness 10000) in paragraph at lines 18430--18432
[]\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
[268]
Underfull \hbox (badness 4217) in paragraph at lines 18514--18523
[][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[]
[][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/
pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm
/m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam
es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 2057) in paragraph at lines 18529--18545
[][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 ,
[269] [270] [271] [272] [273] [274]
Underfull \hbox (badness 4699) in paragraph at lines 18948--18951
[]\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 ,
[275] [276]
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 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = "
GMT")[] 
[277] [278]
Underfull \hbox (badness 4739) in paragraph at lines 19206--19208
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[279]
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 []\T1/pcr/m/n/9 isSymmetric(D3)                         # FALSE (as row and co
lumn names differ)[] 

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 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE  (as names are 
not checked)[] 
[280] [281] [282] [283] [284] [285] [286] [287] [288]
Underfull \hbox (badness 1975) in paragraph at lines 19834--19837
[]\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
[289] [290] [291] [292] [293] [294]
Underfull \hbox (badness 1077) in paragraph at lines 20229--20234
[]\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
[295]
Underfull \hbox (badness 10000) in paragraph at lines 20243--20250
[][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se /
[296]
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[]\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
[297] [298]
Underfull \hbox (badness 10000) in paragraph at lines 20466--20470
[]\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use

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[][]\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

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[]\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-
[299] [300]
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[][][]\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 ,
[301]
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[]\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
[302]
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[]\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 20793--20798
\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 20793--20798
\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

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\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
[303] [304] [305]
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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 

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 []           \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = 
FALSE)[] 
[306]
Underfull \hbox (badness 3343) in paragraph at lines 21020--21024
[][][]\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
[307]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 21106--21106
 []          \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments 
as for lists[] 

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 []              \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1,
 pr = 0.2))),[] 
[308] [309]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228
 []\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 21231--21231
 []\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 21276--21281
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-
[310] [311]
Underfull \hbox (badness 2564) in paragraph at lines 21367--21370
[]\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

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 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8")  # Linux, macOS, other
 Unix-alikes[] 
[312] [313]
Underfull \hbox (badness 1400) in paragraph at lines 21565--21569
[][][]\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
[314] [315] [316]
Underfull \hbox (badness 2469) in paragraph at lines 21735--21741
[]\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 21735--21741
\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 21735--21741
\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,
[317] [318] [319] [320] [321] [322] [323] [324] [325]
Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362
 []\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 22363--22363
 []        \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 22366--22366
 []\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)[] 
[326] [327]
Underfull \hbox (badness 1655) in paragraph at lines 22490--22494
[]\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion 
(also known as a `clo-sure'):
[328] [329] [330] [331]
Underfull \hbox (badness 2277) in paragraph at lines 22739--22742
[]\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.
[332] [333] [334] [335] [336] [337] [338] [339]
Underfull \hbox (badness 1484) in paragraph at lines 23304--23312
[]\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

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\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 /
[340] [341]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 23381--23381
 []      \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y =
 all,[] 
[342] [343] [344] [345] [346] [347] [348]
Underfull \hbox (badness 1448) in paragraph at lines 23886--23894
\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 =
[349] [350]
Underfull \hbox (badness 3849) in paragraph at lines 24000--24005
[]\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
[351]
Underfull \hbox (badness 7308) in paragraph at lines 24077--24083
[]\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 24077--24083
\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 24077--24083
[][]\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 24087--24090
[]\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 24087--24090
\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
[352] [353]
Underfull \hbox (badness 10000) in paragraph at lines 24240--24242
[]\T1/ptm/m/n/10 character string: par-tial match-ing to one of
[354] [355] [356]
Underfull \hbox (badness 6188) in paragraph at lines 24459--24462
[]\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
[357] [358] [359] [360] [361] [362] [363]
Underfull \hbox (badness 2197) in paragraph at lines 24943--24947
[]\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s
tartup mes-sages given by

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\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
[364]
Underfull \hbox (badness 2846) in paragraph at lines 24957--24961
[]\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 24957--24961
\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 24999--24999
 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ
e.only) 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003
 []              \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk
gs"))[] 
[365]
Underfull \hbox (badness 10000) in paragraph at lines 25051--25057
[]\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 25051--25057
\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 25064--25066
[]\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%
[366]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25115--25115
 [] \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:[] 
[367] [368] [369]
Underfull \hbox (badness 8189) in paragraph at lines 25308--25314
[]\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
[][][]
[370] [371] [372]
Underfull \hbox (badness 1694) in paragraph at lines 25530--25533
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings
 (see `De-tails');
[373] [374] [375]
Underfull \hbox (badness 1603) in paragraph at lines 25777--25779
[]\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a
re con-verted by
[376] [377]
Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912
\T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T
1/ptm/m/n/10 .
[378] [379]
Underfull \hbox (badness 3271) in paragraph at lines 26111--26114
[]\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men
t vari-able
[380] [381] [382]
Underfull \hbox (badness 3138) in paragraph at lines 26411--26417
[]\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 26411--26417
\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 26411--26417
\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
[383]
Underfull \hbox (badness 1194) in paragraph at lines 26424--26427
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 1389) in paragraph at lines 26450--26452
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see

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[]\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by

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[]\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 26503--26506
[]\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
[384]
Underfull \hbox (badness 10000) in paragraph at lines 26519--26522
[]\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle
d -- see

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
[]\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-

Underfull \hbox (badness 10000) in paragraph at lines 26527--26532
\T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1
0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26541--26548
[]\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 26541--26548
\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 26541--26548
\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 26541--26548
\T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran";
[385] [386] [387] [388]
Underfull \vbox (badness 10000) has occurred while \output is active [389]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885
 []\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 26898--26902
[]\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

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\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)] =
[390] [391]
Underfull \hbox (badness 10000) in paragraph at lines 27045--27048
[]\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 27045--27048
\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
[392] [393] [394]
Underfull \hbox (badness 10000) in paragraph at lines 27314--27320
[][][]\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 27314--27320
[][]\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
[395]
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 []\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 27348--27348
 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha
t you wanted[] 
[396] [397] [398] [399] [400] [401] [402]
Underfull \hbox (badness 1817) in paragraph at lines 27782--27786
[]\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 =
[403]
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[]\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
[404] [405] [406]
Underfull \hbox (badness 10000) in paragraph at lines 28050--28053
[]\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
[407] [408] [409] [410] [411] [412] [413] [414] [415] [416]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727
 []           \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))[] 
[417] [418] [419] [420]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993
 []\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 29004--29004
 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\
U147b\U203c"[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 29010--29010
 []\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 29011--29011
 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug
.cgi?id=16098[] 

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 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow
ed (parse errors)[] 
[421]
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[]\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
[422]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110
 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu
l bottom-right note[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156
 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind =
 NULL)[] 
[423] [424]
Underfull \hbox (badness 3713) in paragraph at lines 29279--29290
[]\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
[425]
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\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 29423--29430
\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 /
[426] [427]
Underfull \hbox (badness 1533) in paragraph at lines 29541--29544
[]\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
[428] [429]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686
 []     \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m
ax", "min"))[] 
[430]
Underfull \hbox (badness 1038) in paragraph at lines 29704--29715
[]\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
[431] [432]
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 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide
ntical(X, X.))[] 

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 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument
 of deparse()[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "list")[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 

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 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character",                      h
ow = "unlist")[] 

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 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h
ow = "unlist")[] 
[433] [434] [435] [436] [437]
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[]\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor
 to

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\T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the
 mode:

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\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 ,
[438] [439] [440] [441] [442] [443] [444] [445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 30748--30748
 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene
d as needed.[] 
[446] [447] [448] [449] [450] [451] [452]
Underfull \hbox (badness 7558) in paragraph at lines 31250--31254
[]\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 31260--31262
[]\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

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[][][]\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
[453]
Underfull \hbox (badness 10000) in paragraph at lines 31269--31271
[]\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la
urikari . net / tre / documentation /

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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs /
[454] [455] [456] [457] [458]
Underfull \hbox (badness 10000) in paragraph at lines 31677--31681
[][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] []
[]NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple
x_[][][]
[459] [460] [461] [462] [463]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021
 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"))[] 

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 []      \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y
ears"),[] 
[464] [465] [466] [467] [468] [469] [470]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408
 []           \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/
2 && n > 1e7))[] 
[471] [472] [473] [474] [475] [476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843
 []     \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul =
 FALSE)[] 
[477]
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[]\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
[478]
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[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

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\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
[479] [480]
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 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data
", sep = "\n") 
[481] [482] [483]
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[]\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 .
[484] [485] [486] [487]
Underfull \hbox (badness 1210) in paragraph at lines 33627--33629
[]\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp
ly(nvec,seq_len)) \T1/ptm/m/n/10 and it
[488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499]
[500] [501]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564
 []         \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index
.return = FALSE)[] 
[502] [503] [504]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 34816--34816
 []              \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length 
= Inf,[] 

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 []              \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes"
, "keepNA"),[] 
[505]
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[][][]\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

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[][]\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
[506]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 34972--34972
 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments
 should print:)[] 
[507] [508] [509] [510] [511]
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 []\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)[] 
[512]
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 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is
 being added[] 
[513] [514] [515] [516] [517] [518]
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 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un
known") 

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 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile =
 FALSE)[] 
[519] [520] [521]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021
 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS
E, nowadays often three 
[522]
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[]\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

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\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

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\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

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\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

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\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
[523]
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[]\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 '

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\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,

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\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

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[]\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 36161--36168
\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

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\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
[524] [525] [526] [527]
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 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e
xprs = exprs))) 
[528] [529] [530] [531] [532] [533] [534] [535]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 37000--37000
 []            \T1/pcr/m/n/10 add the string to the left of the match to the ou
tput.[] 
[536] [537] [538] [539]
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 []        \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p
refix)[] 
[540]
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 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll
apse = "\n")[] 
[541] [542] [543] [544] [545] [546]
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 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e
verything gets added.[] 

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 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also
 missing, ....[] 
[547]
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[]\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

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\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 ).
[548]
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 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau
lt precision 
[549] [550] [551] [552]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 38134--38134
 []    \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw
ise: last"),"\n")[] 
[553]
Underfull \vbox (badness 10000) has occurred while \output is active [554]
[555]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 38299--38299
 []\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. 
[556]
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 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, 
macOS, FreeBSD:[] 

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[]\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

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\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
[557]
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\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

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\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
[558] [559] [560]
Underfull \hbox (badness 10000) in paragraph at lines 38664--38668
[]\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

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[]\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
[561] [562]
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 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths
), keepNA=TRUE))[] 
[563]
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 []\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 
[564] [565] [566]
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[]\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
[567] [568]
Underfull \hbox (badness 1038) in paragraph at lines 39216--39219
[]\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
[569] [570] [571] [572] [573] [574]
Underfull \hbox (badness 1442) in paragraph at lines 39579--39583
\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 =
[575] [576] [577]
Underfull \hbox (badness 4096) in paragraph at lines 39825--39828
[]\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 ,
[578] [579]
Underfull \hbox (badness 7888) in paragraph at lines 39939--39943
[]\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) >
[580] [581]
Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093
 []            \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 40095--40095
 []            \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),[] 

[582]
Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097
 []                 \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 40110--40112
[]\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
[583]
Underfull \hbox (badness 10000) in paragraph at lines 40190--40193
[][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer .
[584] [585]
Underfull \hbox (badness 3872) in paragraph at lines 40308--40311
[]\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call
-backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer .
[586]
Underfull \hbox (badness 5475) in paragraph at lines 40374--40378
[][][]\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 : / /
[587] [588] [589] [590] [591] [592]
Underfull \hbox (badness 10000) in paragraph at lines 40792--40799
\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 ',

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[]\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-

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\T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t
he file sys-tem varies,

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[]\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op
-tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de-

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\T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da
tabase at

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\T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by 
de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 '
[593]
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\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

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[]\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym
-link tar-get name of
[594]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org /

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[][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h
tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol-

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 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET",
 "Eire", ..., but[] 
[595] [596] [597]
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[]\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
[598] [599]
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 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15
g)\n", ncp))),[] 

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 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL)  ##--> showing the ncp
 root finding:[] 

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[601] [602] [603] [604]
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[]\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
[605] [606]
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 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[
 \t\r\n]") 
[607]
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[]\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

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\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

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[][][]\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;
[608]
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[]\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

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\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 ,
[609] [610] [611] [612] [613]
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 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp
ression(1+x))[] 
[614] [615] [616] [617] [618] [619]
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 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local
es and fonts[] 
[620]
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 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little-
endian platform[] 
[621]
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[]\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 ),
[622]
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[]\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
[623] [624] [625]
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[626]
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 []      \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes
sages:\n"),[] 
[627]
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 []\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[] 

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 []\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 ...[] 
[628] [629]
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[]\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,

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\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,
[630]
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[]\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

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\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
[631]
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[]\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
[632]
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 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is
 at least one:[] 
[633]
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[]\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard 
eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer .
[634] [635] [636] [637] [638]
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[]\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
[639]
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 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char
acter vector[] 

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[]\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
[640]) (./compiler-pkg.tex
Chapter 2.
[641]
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[]\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-

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\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
[642] [643] [644]) (./datasets-pkg.tex
Chapter 3.
[645] [646] [647] [648] [649]
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 []  \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang
e", cex = 1.2,[] 
[650]
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 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi
ven = FALSE)[] 

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[652] [653] [654] [655]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[656] [657]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[658] [659]
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[]\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.
[660] [661]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[662] [663] [664] [665] [666]
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 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption
 time (sec)")[] 
[667] [668]
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[]\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 ,

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\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
[669] [670] [671]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[672]
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 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil
y = binomial())[] 

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 []  \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum),
 data = infert)[] 
[673] [674]
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 []                                        \T1/pcr/m/n/9 sub(" W.",".Width", dn
i3[[2]])))),[] 

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 []    \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d
ni3[[3]]))))[] 
[675] [676] [677] [678]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[679] [680] [681]
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[682] [683] [684] [685] [686]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[687]
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[688]
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[690]
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[691] [692]
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[693]
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 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 
1.2, pch = ".")[] 
[694] [695] [696] [697] [698] [699] [700]
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 []          \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t
he monthly one:[] 
[701] [702]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup
edData","groupedData","data.frame")
[703]
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[704]
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[705]
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 []       \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of
 supplement")[] 

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[]\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www
-[]personal . buseco . monash . edu . au /

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[]\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 /

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\T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma
n / sitephotos /
[706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717]
[718] [719]) (./grDevices-pkg.tex [720]
Chapter 4.
[721] [722] [723] [724]
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[]\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

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[]\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
[725] [726]
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[]\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til
e, i.e., close to

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\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
[727] [728]
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 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d
.pdf",[] 
[729] [730] [731] [732] [733] [734] [735] [736] [737]
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[]\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
[738] [739]
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[]\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2
 . com / Lab / Graphics / Colors /

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 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", 
scale.in = 255))[] 
[740]
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[]\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
[741] [742] [743] [744] [745] [746] [747] [748]
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[]\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

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\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
[749]
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 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res 
= 72,[] 

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[]\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-

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\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 ,
[750] [751]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[752] [753]
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[754] [755]
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\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

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\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

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\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

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\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
[756] [757]
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 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r"
, yaxs = "r") {[] 

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 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE) 

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 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N
ULL, rev = FALSE)[] 
[759] [760] [761] [762] [763]
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 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized
 = FALSE)[] 
[769]
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 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", 
scale.in = 255))[] 

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 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv",  to = hexcolor, scale.
out = NULL))[] 
[770] [771]
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[]\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range

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\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-
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 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE,
 fixup = TRUE) 

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[]\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 ,
[775]
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\T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space 
& oldid = 883465135$[][]\T1/ptm/m/n/10 .
[776] [777]
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[]\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[778] [779] [780] [781] [782]
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[]\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 
height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa
mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\
T1/ptm/m/n/10 ,
[783] [784] [785] [786] [787] [788]
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[][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript /

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\T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m
al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat .
[789] [790]
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 []     \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz
w+p", "zip+p"),[] 
[791] [792]
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[]\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
[793]
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 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, 
height = 768)[] 

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[]\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
[794]
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[]\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"
[795]
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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
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[]\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

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[][][]\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
[799] [800]
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\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 ,

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\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 ,

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\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 ),

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[]\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

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\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
[801]
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[]\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 /
[802] [803]
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 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r
eg-tests-1c.R[] 
[804]
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 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100
, ...)[] 
[805] [806]
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[]\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
[807] [808] [809] [810] [811]
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 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15,
 sep = "."))[] 

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[]\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[812] [813] [814] [815] [816] [817]
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 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp
inch, 

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 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize 
= 12,[] 
[818] [819] [820] [821]
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[]\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 ,

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\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 ,

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\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
[822]
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 []\T1/pcr/m/n/9 windows()  # make sure we have the right device type (availabl
e on Windows only)[] 
[823]
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[]\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 :
[824]
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[825]
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[]\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[826]
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[]\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

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\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
[827]
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[]\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

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 []        \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height
 = 6, xpos = 0,[] 
[828] [829]
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\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 ,
[830]
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[]\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 /
[831] [832]
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[]\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
[833] [834] [835]) (./graphics-pkg.tex [836]
Chapter 5.

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[]\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 =
[837] [838] [839]
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[]\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
[840]
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[]\T1/ptm/m/n/10 Friendly, M. (1992), Graph-i-cal meth-ods for cat-e-gor-i-cal 
data. \T1/ptm/m/it/10 SAS User Group In-ter-na-
[841] [842] [843]
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 []  \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] 

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[]\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
[844] [845]
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 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t
he axis labels drawn[] 
[846]
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[]\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

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[][]\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
[847] [848]
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 []                 \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n
intLog = 5))[] 

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 []        \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = 
NULL, ...)[] 
[849] [850] [851]
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[][][]\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.

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 []        \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = "
# {passengers}", legend = TRUE)[] 

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 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset 
= Age=="Adult"))[] 

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 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur
vived, *)", color=TRUE)[] 
[852] [853] [854] [855]
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 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. 
outside hinges"):[] 
[856] [857] [858]
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\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

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[]\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/
n/10 ),
[859] [860]
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 []\T1/pcr/m/n/9 boxplot(z,   col.axis = "skyblue3", main = "boxplot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main =    "plot(*, col.axi
s=..,main=..)")[] 

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 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill
 = "grey40",[] 

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 []              \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl
ty = 1, outpch = NA)[] 
[861] [862] [863] [864]
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[][][]\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
[865]
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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 

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 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = ""
, ylab = "")[] 
[866] [867]
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 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col
umns, 
[868]
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 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept
h, rows = 1)[] 
[869]
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 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c(
TRUE, FALSE))[] 
[870] [871] [872] [873]
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 []               \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO
rRd", rev = TRUE),[] 

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\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
[874]
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[][][]\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

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 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n
, "terrain"),[] 
[875] [876] [877] [878]
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 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks:  par(lab = c
(mx, my, 7))[] 
[879] [880] [881]
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\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

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 []\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 :[] 

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 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a 
suggestion only"[] 
[882]
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[][][]\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
[883] [884] [885]
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 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL
SE, pch = 19, ...)[] 

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 []        \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel)
, n = 1, plot = plot, ...)[] 
[886] [887]
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[]\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

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[][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the 
grid is reg-u-lar and ei-ther

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[][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/
n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is
[888] [889] [890]
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 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 
0, horiz = TRUE)[] 

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 []       \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = 
par("fg"),[] 

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 []       \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace =
 FALSE,[] 
[891] [892] [893]
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 []  \T1/pcr/m/n/9 text  (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c
ex = 0.8, adj = 0)[] 

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 []  \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce
x = cexv[i])[] 
[894]
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 []                      \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj
 = c(0, 0.3))[] 

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 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c
ol = "blue")[] 

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 []\T1/pcr/m/n/9 legend("topleft",     "(x,y)", pch=1, title= "topleft, inset =
 .05", inset = .05)[] 

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 []\T1/pcr/m/n/9 legend("topright",    "(x,y)", pch=1, title= "topright, inset 
= .02",inset = .02)[] 

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 []   \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste
("text.font =",i))[] 
[896]
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[][][]\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%
[897]
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 []        \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb
ose"))[] 
[898] [899] [900] [901]
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[]\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
[902] [903] [904] [905]
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\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
[906]
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[]\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
[907]
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 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel 
= panel.cor,[] 

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=c(2,2,3,2))[] 
[908]
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 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = "
blue")  # hmm...[] 
[909]
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\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 ,
[910] [911]
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[]\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.
[912]
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[913 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/mai.pdf>]
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[915 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/oma.pdf>]
[916]
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[]\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
[917]
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 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, 
physicians = 9,[] 

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 []  \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t
eachers = 4,[] 
[918] [919] [920] [921] [922]
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 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p
yramid" = 5),[] 
[923]
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 []    \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow
3"), border = FALSE)[] 

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[]\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 =
[924] [925] [926] [927] [928] [929] [930]
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 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth)           # numeric v
ector ~ factor[] 

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 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes")  # ext
remely silly[] 
[931] [932] [933] [934] [935] [936]
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[]\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see
[937] [938]
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[]\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

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[][] 
[939 </usr/src/RPM/BUILD/R-3.6.1/library/graphics/help/figures/pch.pdf>]
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 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b
lue", cex = .6,[] 
[940]
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 []    \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes  =  FALSE, xlab = "", ylab =
 "", main = main)[] 

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[942]
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[]\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev
in Buhr

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 []  \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b
order = "red")[] 

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 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats::
rnorm(n)))))[] 
[943]
Underfull \hbox (badness 2600) in paragraph at lines 7091--7093
[]\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
[944] [945] [946] [947]
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 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7
, end = 0.1))[] 
[948] [949] [950] [951] [952] [953]
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 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp
ace = "Lab")[] 

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 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit
h obs.number):[] 
[954]
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 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0
, add = TRUE),[] 
[955] [956] [957] [958] [959]
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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

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 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi
us  =  FALSE,[] 

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 []      \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10
, key.loc =  0:1,[] 
[960] [961] [962]
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 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = 
NULL, ...) 

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 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont =
 NULL, ...)[] 
[963] [964]
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 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL,
 ...,[] 

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[]\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
[965]
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[]\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
[966]
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 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035
, seg.lwd = .8)[] 

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 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, 
lambda = 2),[] 
[967] [968]
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 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll
apse = ","),[] 
[969] [970]
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 []     \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: 
Règles, Liberté, Egalité, Fraternité...")[] 
[971]
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color

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[]\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
[972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit
s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8918 \HeaderA{units}{Graphical Units}{units}
                                               [973]
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[]\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th
e poly-gon. See
[974] [975]
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 []\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)[] 
[976]) (./grid-pkg.tex
Chapter 6.
[977] [978] [979] [980] [981] [982] [983] [984]
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\T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo
r ex-am-ple,

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\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
[985] [986] [987] [988] [989] [990] [991] [992] [993] [994]
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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="B"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="C"),[] 

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 []                                       \T1/pcr/m/n/9 just=c("left", "bottom"
), name="D")),[] 

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[]\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-
[995] [996] [997] [998]
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[]\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
[999] [1000] [1001] [1002] [1003] [1004]
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 []  \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75)
, list(...)))[] 
[1005] [1006] [1007]
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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla
ck"), name="r1")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey"
), name="r2")[] 

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 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi
te"), name="r3")[] 
[1008]
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[]\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 ,
[1009]
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[]\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-

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[]\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
[1010] [1011] [1012]
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[]\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
[1013] [1014] [1015]
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 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = 
FALSE)[] 

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[]\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-
[1016]
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 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs =
 FALSE,[] 
[1017] [1018]
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 []                          \T1/pcr/m/n/9 children=gList(grob(name="child", vp
="vp1::vp2")),[] 

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 []           \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp =
 NULL)[] 
[1019] [1020] [1021] [1022]
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 []  \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1
, "inches"),[] 
[1023] [1024] [1025] [1026] [1027]
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 []                                       \T1/pcr/m/n/9 children=vpList(viewpor
t(name="vp2"))))[] 
[1028]
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 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left",
 "bottom")))[] 
[1029]
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[]\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
[1030] [1031]
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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 

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 []          \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border =
 NULL,[] 
[1032] [1033] [1034]
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 []                \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant
i-clockwise")[] 

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 []                \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other 
anti-clockwise")[] 

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 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s
ame path, thus[] 
[1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046]
[1047]
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[]\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
[1048]
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[]\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-
[1049] [1050] [1051]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\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
[1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071]
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[]\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-

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\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")
[1072] [1073] [1074] [1075] [1076]
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[]\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
[1077]
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[][][]\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 ,
[1078] [1079]
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[]\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
[1080] [1081] [1082]
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 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp
ar(col="red"))))[] 
[1083]) (./methods-pkg.tex [1084]
Chapter 7.
[1085] [1086]
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\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
[1087] [1088] [1089]
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-
[1090] [1091]
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 []\T1/pcr/m/n/9 ## vector.  The next method will always be the default, usuall
y a primitive.[] 

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 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w
ith no arguments[] 
[1092]
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 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho
ut arguments[] 

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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[] 

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 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the
 "B0" method[] 

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 []\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[
] 

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[1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105]
[1106] [1107] [1108]
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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N
umber" method[] 

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 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE))
) # the default[] 
[1109] [1110]
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[]\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
[1111] [1112] [1113]
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[]\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 =
[1114] [1115]
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[]\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

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 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F
ALSE}:[] 
[1116] [1117] [1118]
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[]\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

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[]\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
[1119]
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 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin
g(where))[] 
[1120] [1121] [1122]
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 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers
ions visible:[] 
[1123] [1124] [1125] [1126] [1127] [1128] [1129]
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[]\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,

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\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
[1130] [1131]
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[]\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
[1132]
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[]\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

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[]
[1133] [1134]
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[] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 =

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[]\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) {
[1135]
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[]\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit =

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[]\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
[1136] [1137] [1138]
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e
x-ists for
[1139] [1140] [1141]
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 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char
acter(), 

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 []                        \T1/pcr/m/n/10 prototype=NULL, package, validity, ac
cess,[] 
[1142]
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 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w
here) 
[1143] [1144] [1145]
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[]\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 ,
[1146] [1147] [1148]
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
[1149] [1150] [1151] [1152]
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 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate
 inheritance[] 
[1153]
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 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli
er fails here)[] 

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 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho
d for classB[] 

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[1155]
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[]\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...)
[1156] [1157]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1158] [1159] [1160]
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[]\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
[1161] [1162] [1163] [1164] [1165] [1166]
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[]\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
[1167] [1168]
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[]\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,

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\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
[1169]
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[]\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func-
tion re-turned by
[1170] [1171]
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[]\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen
se as any S4 class (see

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[][]\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
[1172]
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[1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
                               [1176]
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 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement 
version of as().[] 
[1177] [1178]
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 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data =
 datasets::iris)[] 

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 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con
tains = "mlm")[] 
[1179]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com
plex}) has been already used, duplicate ignored
<to be read again> 
                   \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
<to be read again> 
                   \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
<to be read again> 
                   \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

<to be read again> 
                   \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
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                
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[]\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
[1180]
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[]\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 ,

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\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 ,

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\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 ,
[1181] [1182]
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[]\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t
ion ob-ject (see

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[]\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
[1183] [1184]
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
[1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195]
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[]\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
[1196]
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 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact
er(), 
[1197]
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 []      \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class
Def =,[] 
[1198] [1199] [1200] [1201]
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 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col
umn matrices[] 
[1202] [1203] [1204]
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 []  \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns),
 "setCount")[] 
[1205] [1206] [1207]
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 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo
rmal arguments[] 
[1208] [1209] [1210] [1211]
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 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre
es of freedom[] 
[1212]
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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 

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 []\T1/pcr/m/n/9 ## Not run:   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1
0] [,11] [,12][] 
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222]
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[]\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

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[]\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.,

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\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
[1223] [1224] [1225]) (./parallel-pkg.tex [1226]
Chapter 8.

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[]\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
[1227]
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[]\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
[1228] [1229]
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[]\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
[1230] [1231] [1232]
Underfull \hbox (badness 10000) in paragraph at lines 443--445
[]\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
[1233] [1234] [1235] [1236]
Underfull \hbox (badness 1917) in paragraph at lines 744--753
[]\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

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\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
[1237] [1238]
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 []         \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini
ty.list = NULL)[] 
[1239] [1240] [1241]
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 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit
y.list = affL)[] 

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 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch
eduled to suitable CPUs[] 
[1242]
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[]\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
[1243]
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[]\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

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 []\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)[] 
[1244] [1245]
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 []                 \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif
(N, 1, 28)))[] 

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 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct,  format = 
"%Y-%m-%d")))[] 
[1246]
Underfull \hbox (badness 1577) in paragraph at lines 1365--1368
[]\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

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[]\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
[1247] [1248]) (./splines-pkg.tex
Chapter 9.

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[]\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495
 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height,  women, bSpl
ine = TRUE))[] 
[1257]
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[]\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
[1258] [1259]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709
 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, 
sparse = TRUE)))[] 
[1260] [1261] [1262]) (./stats-pkg.tex
Chapter 10.
[1263]
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 ,

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 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $
 Species" with 3 levels:[] 

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 []  \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named
 list, as no factors[] 
[1264] [1265] [1266] [1267] [1268]
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 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea
rson Chi-square[] 
[1269]
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 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = 
FALSE) 
[1270] [1271] [1272] [1273] [1274] [1275]
Underfull \hbox (badness 1024) in paragraph at lines 875--877
[]\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
[1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\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

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\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

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\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
[1285] [1286] [1287] [1288]
Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737
 []\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 :[
] 
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726
 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F
ALSE) 
[1302] [1303] [1304] [1305]
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 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co
l = "green")[] 
[1306] [1307] [1308]
Underfull \hbox (badness 10000) in paragraph at lines 3175--3177
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge
neity of
[1309]
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 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 

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 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = 
FALSE)[] 
[1310] [1311] [1312] [1313] [1314] [1315]
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 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = "
log density",[] 
[1316] [1317] [1318] [1319]
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 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit
df = 0) 
[1320] [1321] [1322] [1323] [1324]
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 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 

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 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p 
= FALSE)[] 
[1325] [1326] [1327]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421
 []\T1/pcr/m/n/9 chisq.test(x, p = p)            #               maybe doubtful
, but is ok![] 
[1328] [1329] [1330]
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 []  \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df =
 df, ncp = L)),[] 
[1331]
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[]\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 =
[1332] [1333] [1334] [1335] [1336] [1337]
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 []\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))[] 

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 []\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))[] 
[1338] [1339] [1340]
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 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works
 with these :[] 

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 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil
ter")) 

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[]\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
[1341] [1342] [1343]
Underfull \hbox (badness 1436) in paragraph at lines 5517--5522
[]\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i
ng co-vari-ances

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\T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi
-a-tion of)

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\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 ,
[1344] [1345] [1346]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715
 []         \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE,
 ...)[] 
[1347] [1348] [1349]
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 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center =
 TRUE, 
[1350] [1351] [1352]
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 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter =
 NULL) 
[1353]
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 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en
v = parent.frame())[] 
[1354]
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[]\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
[1355] [1356] [1357] [1358]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn
, see
[1359]
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[]\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

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[]\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

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\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,

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[][][]\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
[1360]
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 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, 
type = "tr")[] 

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 []\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):[] 

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 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h
oriz = TRUE)[] 

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[1362] [1363] [1364]
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 []                     \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker
n = TRUE))))[] 
[1365] [1366] [1367] [1368] [1369] [1370]
Underfull \hbox (badness 10000) in paragraph at lines 7270--7274
\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
[1371]
Underfull \hbox (badness 6493) in paragraph at lines 7369--7372
[]\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
[1372] [1373]
Underfull \hbox (badness 10000) in paragraph at lines 7506--7509
[]\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 =
[1374] [1375] [1376] [1377] [1378] [1379] [1380]
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[]\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 , ...,
[1381] [1382] [1383] [1384] [1385]
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[]\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
[1386] [1387] [1388] [1389] [1390] [1391] [1392]
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 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q
uasipoisson())[] 

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 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link 
= "log")) # fails[] 

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 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit
"), start = c(0,1))[] 
[1394] [1395]
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 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2),
 .90)  # ~= 7e-9[] 
[1396] [1397] [1398] [1399] [1400] [1401]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349
 []           \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4
0k", "> 40k"),[] 

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 []                     \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod
erateS", "VeryS")))[] 
[1402] [1403] [1404]
Underfull \hbox (badness 7291) in paragraph at lines 9529--9531
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of
 homogeneity of
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 6944) in paragraph at lines 9990--9996
[][][]\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);
[1411] [1412] [1413]
Underfull \hbox (badness 3758) in paragraph at lines 10203--10206
[]\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
[1414] [1415] [1416] [1417]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439
 []    \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL
, ...)[] 

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[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1418]
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[]\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth
od

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[]\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-
[1419]
Underfull \hbox (badness 10000) in paragraph at lines 10609--10612
[]\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
[1420] [1421] [1422]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\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 ^^@
[1423] [1424]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:

Underfull \hbox (badness 10000) in paragraph at lines 10948--10954
[][][]\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,
[1425]
Underfull \hbox (badness 1418) in paragraph at lines 10986--10991
\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 (=
[1426]
Underfull \hbox (badness 2635) in paragraph at lines 11119--11122
\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
[1427] [1428] [1429]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1430]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403
 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col
SideColors = cc,[] 
[1431]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436
 []            \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 11449--11453
[]\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
[1432] [1433] [1434]
Underfull \hbox (badness 7379) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of
[1435] [1436]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768
 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4)
, DEV.FUN = nD)[] 
[1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat
}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                             
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836
 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA
LSE),[] 
[1438]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848
 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE),
 ...)[] 

Underfull \hbox (badness 1062) in paragraph at lines 11901--11906
[]\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 11918--11920
[]\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
[1439] [1440] [1441] [1442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168
 []                 \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = 
TRUE,[] 
[1443] [1444]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261
 []  \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label
 = "tobacco",[] 
[1445] [1446] [1447] [1448]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\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 12534--12536
[]\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
[1449]
Underfull \hbox (badness 2753) in paragraph at lines 12603--12605
[]\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https :
 / / bugs . r-[]project . org / bugzilla3 /
[1450] [1451] [1452] [1453]
Underfull \hbox (badness 6910) in paragraph at lines 12841--12843
[]\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 12847--12851
[]\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 12847--12851
\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
[1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554
 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep
t", "slope"))[] 
[1464]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1465] [1466] [1467]
Underfull \hbox (badness 10000) in paragraph at lines 13796--13800
[]\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
 ,
[1468] [1469] [1470] [1471] [1472]
Underfull \hbox (badness 1163) in paragraph at lines 14129--14137
\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 ,
[1473]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1474] [1475] [1476]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435
 []\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 14436--14436
 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
[1477] [1478] [1479] [1480] [1481]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779
 []\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 14780--14780
 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = 
FALSE)[] 
[1482] [1483]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873
 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra
nge(x))) 
[1484] [1485] [1486] [1487] [1488] [1489]
Underfull \hbox (badness 2726) in paragraph at lines 15279--15282
[]\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 ,
[1490]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373
 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i
n R <= 3.5.0[] 
[1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998
 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc
gp, data = esoph) 
[1501] [1502]
Underfull \hbox (badness 1490) in paragraph at lines 16136--16141
\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
[1503]
Underfull \hbox (badness 1648) in paragraph at lines 16202--16204
[]\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 16217--16226
\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 16217--16226
\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
[1504]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287
 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b 
= contr.poly))[] 
[1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845
 []\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[] 
[1514] [1515] [1516]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073
 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, 
s, prob = 0.4)),[] 
[1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526]
Underfull \vbox (badness 10000) has occurred while \output is active [1527]
Underfull \vbox (badness 10000) has occurred while \output is active [1528]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833
 []              \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21
), th = b[1]))[] 
[1529] [1530] [1531]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996
 []\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 18043--18043
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1532]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090
 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens
ity), DNase.2 )[] 
[1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540]
Underfull \hbox (badness 1248) in paragraph at lines 18581--18584
[]\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 18594--18598
[]\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
[1541]
Underfull \hbox (badness 1478) in paragraph at lines 18602--18606
\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 18660--18662
[]\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
[1542] [1543]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766
 []      \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 [1544]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809
 []     \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", 
axes = FALSE)[] 

Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827
 []\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 18830--18830
 []\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 18850--18850
 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max
(interval), 

Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853
 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max
(interval),[] 
[1545]
Underfull \hbox (badness 2564) in paragraph at lines 18888--18899
[]\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 18888--18899
\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
[1546]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951
 []\T1/pcr/m/n/9 f  <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 
1)), 10), 10)[] 
[1547] [1548] [1549]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176
 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 
1, lty = 1:6,[] 
[1550]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\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
[1551] [1552] [1553] [1554] [1555] [1556]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571
 []      \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 
1.5),[] 
[1557]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659
 []       \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 19661--19661
 []              \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else 
points,[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663
 []     \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact
ive(),[] 
[1558]
Underfull \hbox (badness 10000) in paragraph at lines 19709--19713
[]\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 10000) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su
ch it-er-a-tions for

Underfull \hbox (badness 5260) in paragraph at lines 19709--19713
[][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa
r-tic-u-larly de-sir-able for
[1559]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\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
[1560] [1561] [1562]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996
 []                    \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3,
 ...)[] 
[1563]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1564]
Underfull \hbox (badness 1107) in paragraph at lines 20064--20066
[]\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

Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119
 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange
") # all colors[] 
[1565]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126
 []\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)[] 
[1566]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220
 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma
r..., oma...)")[] 
[1567] [1568]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345
 []    \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE)  # no 
cancellation[] 
[1569]
Underfull \hbox (badness 7740) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of

Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456
 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = 
FALSE) 
[1570] [1571]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548
 [] \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 20553--20553
 []\T1/pcr/m/n/9 ## poly(<matrix>, df) --- used to fail till July 14 (vive la F
rance!), 2017:[] 
[1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582]
[1583] [1584]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407
 []          \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly
 equal typically[] 
[1585]
Underfull \hbox (badness 6859) in paragraph at lines 21474--21481
[][][]\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 21485--21491
[]\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 ,
[1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596]
[1597]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223
 []         \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign
 = TRUE, ...)[] 
[1598] [1599] [1600] [1601] [1602]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507
 []             \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x
)) &&[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508
 []                          \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr("
, "p-v"),[] 
[1603] [1604] [1605] [1606] [1607]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\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
[1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615]
Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399
 []  \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1616] [1617]
Underfull \hbox (badness 1028) in paragraph at lines 23540--23543
[]\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
[1618] [1619]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by
[1620]
Underfull \hbox (badness 7944) in paragraph at lines 23705--23707
[]\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 =

[1621]
Underfull \hbox (badness 7944) in paragraph at lines 23767--23769
[]\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 =

[1622] [1623]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869
 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 
10:1, mean)")[] 
[1624] [1625] [1626]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089
 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide
", v.names = "x")[] 
[1627] [1628]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\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] =
[1629]
Underfull \hbox (badness 2134) in paragraph at lines 24287--24291
[][][]\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 24300--24300
 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi
ans Example")[] 
[1630] [1631] [1632] [1633] [1634] [1635]
Underfull \vbox (badness 10000) has occurred while \output is active [1636]
[1637]
Underfull \hbox (badness 6268) in paragraph at lines 24777--24782
[][]\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 ,

Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805
 []    \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As
ym", "xmid", "scal")])[] 
[1638] [1639] [1640]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\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 24995--24999
\T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\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
[1641]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031
 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165  = "Residual standard error"  printed fr
om summary(lm1)[] 
[1642] [1643] [1644]
Underfull \hbox (badness 2495) in paragraph at lines 25221--25230
[]\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 .
[1645]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303
 []       \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends
 = FALSE)[] 

Underfull \hbox (badness 1412) in paragraph at lines 25310--25312
[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui
red; de-faults to
[1646]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397
 []\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 25422--25422
 []\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 25425--25425
 []              \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee
p.stuff = FALSE)[] 
[1647] [1648] [1649]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648
 []    \T1/pcr/m/n/10 nx <- length(x)  -  sum(duplicated( round((x - mean(x)) /
 tol) ))[] 

Underfull \hbox (badness 2547) in paragraph at lines 25651--25657
[]\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
[1650]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697
 []\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 25718--25718
 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # =
= unique(cars$speed)[] 
[1651]
Underfull \hbox (badness 1019) in paragraph at lines 25780--25785
\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
[1652] [1653]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911
 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na.
fail, 
[1654] [1655] [1656] [1657] [1658] [1659] [1660]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290
 []          \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC"
, "hyman"),[] 
[1661] [1662]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471
 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi
 * x) + rnorm(30)/10, 3)[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477
 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean)  f
or when x has ties")[] 

Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486
 []\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 26487--26487
 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman")   (x), add = TRUE, c
ol = 4, n = 1001)[] 

Underfull \vbox (badness 10000) has occurred while \output is active [1663]
Underfull \hbox (badness 2922) in paragraph at lines 26556--26561
[]\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
[1664]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 26593--26593
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim
 = c(-.3, 5),[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 26596--26596
 []                    \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 26605--26605
 []         \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 26606--26606
 []  \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 26610--26610
 []  \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi
[1]+phi[2],2), phi[1]),[] 
[1665]
Underfull \hbox (badness 3240) in paragraph at lines 26664--26667
[][][]\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
[1666]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 26685--26685
 []  \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 26688--26688
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim
 = c(-1, 8),[] 
[1667]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 26771--26771
 []  \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 26775--26775
 []  \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim =
 c(-1/4, 5),[] 

Overfull \hbox (58.38037pt too wide) in paragraph at lines 26785--26785
 []  \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 26790--26790
 []       \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 
[1668]
Underfull \hbox (badness 2922) in paragraph at lines 26826--26832
[]\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 26848--26848
 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat
a = Indo.1),[] 
[1669]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 26864--26864
 []  \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 
1.5 * exp(-x)"),[] 
[1670]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 26978--26978
 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK
a)*input)) 
[1671]
Underfull \hbox (badness 2922) in paragraph at lines 27040--27045
[]\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
[1672]
Overfull \hbox (69.18036pt too wide) in paragraph at lines 27078--27078
 []  \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm
id", phi[4] == "scal")))[] 
[1673]
Underfull \hbox (badness 2922) in paragraph at lines 27127--27132
[]\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 27158--27158
 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = "
red", lwd=2)[] 
[1674]
Underfull \hbox (badness 2922) in paragraph at lines 27192--27197
[]\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 (25.98041pt too wide) in paragraph at lines 27217--27217
 []\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 27221--27221
 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR
UE), trace = TRUE)[] 
[1675]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27241--27241
 []  \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 27251--27251
 []  \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0,  2.5,3.5),   # NB.  SSlogis(x = 
xmid = 2) = 2.5[] 

Underfull \hbox (badness 2922) in paragraph at lines 27286--27291
[]\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
[1676]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27308--27308
 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt),
 digits = 3)[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 27326--27326
 []       \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS
micmen model")[] 
[1677]
Underfull \hbox (badness 6493) in paragraph at lines 27378--27383
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion

Overfull \hbox (4.38043pt too wide) in paragraph at lines 27405--27405
 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat
a = Chick.6)[] 
[1678]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 27407--27407
 []\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 27410--27410
 []\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 27413--27413
 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f
m1)[["Drop"]]), lty = 3)[] 
[1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689]
[1690] [1691] [1692]
Underfull \hbox (badness 3396) in paragraph at lines 28337--28339
[]\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
[1693] [1694] [1695]
Underfull \hbox (badness 2237) in paragraph at lines 28514--28516
[]\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
[1696] [1697]
Underfull \hbox (badness 2591) in paragraph at lines 28678--28680
[]\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
[1698]
Underfull \hbox (badness 2237) in paragraph at lines 28724--28727
[]\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
[1699]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 28797--28797
 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t
race = FALSE) 
[1700] [1701]
Underfull \hbox (badness 3407) in paragraph at lines 28905--28909
[]\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)
[1702] [1703]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\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
[1704] [1705] [1706] [1707]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 29286--29286
 []\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 29314--29314
 []         \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com
mon",[] 
[1708]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1709]
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 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s
pan.smth = 1/4)[] 
[1710]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 29496--29496
 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = 
TRUE,[] 
[1711] [1712]
Underfull \hbox (badness 2205) in paragraph at lines 29585--29590
[]\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
[1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 30180--30180
 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE) 

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 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p =
 FALSE)[] 
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v = FALSE,[] 

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s: --------------[] 

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 []\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:[] 

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[]\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
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[]\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
[1741] [1742] [1743] [1744] [1745] [1746]
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[1747]
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[]\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
[1748]
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 []\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 "")[] 
[1749]) (./stats4-pkg.tex [1750]
Chapter 11.
[1751] [1752] [1753]
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 []    \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf))
, log = TRUE))[] 
[1754] [1755] [1756]pdfTeX warning (ext4): destination with the same identifier
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(./tcltk-pkg.tex [1760]
Chapter 12.
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 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback
 ref in here[] 
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[]\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
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[][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept 
on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 (
whose
[1780]) (./tools-pkg.tex
Chapter 13.
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 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for
 new methods.[] 
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[]\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion
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\T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1
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[]\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co
mpress == "none")[] 
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[]\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
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[]\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
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hances"))[] 

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[1813]
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[]\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

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ogo.svg}{options: width=100}",[] 
[1814]
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dth=0.5in}}}"),[] 

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[]\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user
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\T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1
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\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
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\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
[1816]
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ose"))[] 

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[1817]
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[1822]
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[]\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
[1823] [1824] [1825] [1826] [1827]
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r of links, as re-turned by
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s", "system.Rd"))[] 
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[]\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
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[]\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
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ests"))[] 
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
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\T1/ptm/m/n/10 ' and
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[]\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
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po
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he

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\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
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ALSE,[] 

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ess = "xz")[] 

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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T
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\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 ,

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\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 ',
[1852]
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[]\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

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\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
[1853] [1854] [1855]) (./utils-pkg.tex [1856]
Chapter 14.

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[]\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 ',
[1857] [1858] [1859] [1860]
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 these names[] 
[1861]
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\T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore")
[1862]
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[]\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
[1863]
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 []\T1/pcr/m/n/9 # This default is useful only in SDI mode:  it will tile any F
irefox window[] 

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 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("",
 "Firefox"))[] 

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[1864] [1865]
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\T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org 
/ archive / 2011-[]2 / RJournal _ 2011-[]2 _
[1866]
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ist(),[] 

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er())[] 

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ist(),[] 

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er())[] 

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[]\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 ,

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\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-
[1867]
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 []                   \T1/pcr/m/n/10 ignore_repo_cache =  FALSE, max_repo_cache
_age,[] 
[1868]
Underfull \hbox (badness 4505) in paragraph at lines 850--856
\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
[1869] [1870] [1871]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024
 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer =
 NULL, 
[1872]
Underfull \hbox (badness 1748) in paragraph at lines 1089--1097
[]\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-

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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\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 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
[1873]
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[]\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org 
/ wiki / Digital _ Object _
[1874]
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 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790
 []                                     \T1/pcr/m/n/9 data = infert, family = b
inomial())))[] 

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 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b
efore$timestamp,[] 
[1883] [1884]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971
 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp"
), md5sum=TRUE)[] 
[1885] [1886]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123
 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1887]
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 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind =
 NULL, 
[1888] [1889] [1890]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344
 []                 \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 2367--2367
 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after =
 NULL,[] 
[1891] [1892]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487
 []     \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi
nkley [aut]"),[] 
[1893]
Underfull \hbox (badness 1082) in paragraph at lines 2561--2565
[][][]\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
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                  
Underfull \hbox (badness 1163) in paragraph at lines 2597--2599
[]\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats:
 see e.g. [][]$\T1/pcr/m/n/10 https : / / docs .
[1894] [1895]
Underfull \hbox (badness 10000) in paragraph at lines 2685--2687
[]\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/
phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see
[1896] [1897] [1898]
Underfull \hbox (badness 10000) in paragraph at lines 2902--2904
[]\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see
[1899] [1900] [1901] [1902]
Underfull \hbox (badness 1762) in paragraph at lines 3196--3199
[]\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re
c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package =
[1903]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283
 []\T1/pcr/m/n/9 data(USArrests, "VADeaths")    # load the data sets \TS1/pcr/m
/n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 
'\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] 
[1904]
Underfull \hbox (badness 2452) in paragraph at lines 3359--3362
[]\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1
/pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources
[1905] [1906] [1907] [1908] [1909] [1910]
Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768
 []  \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf
orm$r_arch, "stats.dll"))[] 
[1911] [1912]
Underfull \hbox (badness 10000) in paragraph at lines 3849--3853
[]\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 3906--3914
[]\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
[1913]
Underfull \hbox (badness 1231) in paragraph at lines 3983--3995
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able

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[]\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 3997--4002
\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

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\T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in
 brack-ets are op-tional. See
[1914] [1915]
Underfull \hbox (badness 4660) in paragraph at lines 4119--4122
\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 4143--4145
[]\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
[1916] [1917] [1918]
Underfull \hbox (badness 1565) in paragraph at lines 4328--4332
[]\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
[1919]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411
 []        \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F
ALSE,[] 
[1920]
Underfull \hbox (badness 1931) in paragraph at lines 4446--4453
[]\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)
[1921] [1922] [1923] [1924] [1925]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770
 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o
ne is in the[] 
[1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for
mat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4841 ...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
<to be read again> 
                   \relax 
l.4841 ...mat Unordered and Ordered Lists}{format}
                                                   [1927] [1928] [1929]
[1930] [1931] [1932] [1933] [1934]
Underfull \hbox (badness 1622) in paragraph at lines 5360--5364
[]\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
[1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952
 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h
elp(dgamma):[] 
[1943]
Underfull \hbox (badness 10000) in paragraph at lines 6036--6038
[]\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
[1944]
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[]\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 6085--6090
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1945] [1946] [1947]
Underfull \hbox (badness 10000) in paragraph at lines 6258--6267
[]\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 6258--6267
\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
[1948]
Underfull \hbox (badness 2150) in paragraph at lines 6322--6325
[]\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 6338--6341
[]\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
[1949] [1950]
Underfull \hbox (badness 3118) in paragraph at lines 6460--6462
[]\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
[1951] [1952]
Underfull \hbox (badness 5091) in paragraph at lines 6628--6630
[]\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 5331) in paragraph at lines 6644--6650
[]\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 6644--6650
\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 6644--6650
\T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/
m/n/10 . 

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[]\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")
[1953]
Underfull \hbox (badness 1270) in paragraph at lines 6673--6683
\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

Underfull \hbox (badness 10000) in paragraph at lines 6716--6719
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

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\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.,
[1954]
Underfull \hbox (badness 10000) in paragraph at lines 6778--6782
[]\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu
r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T
1/ptm/m/n/10 ,

Underfull \hbox (badness 2376) in paragraph at lines 6792--6799
[]\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-

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\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 6792--6799
\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 6800--6803
[]\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
[1955]
Underfull \hbox (badness 1314) in paragraph at lines 6879--6886
[]\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
[1956]
Underfull \hbox (badness 10000) in paragraph at lines 6936--6941
[][][]\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 ,

Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959
 []  \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc
lude/udunits2"))[] 
[1957]
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[]\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 7009--7012
[]\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

Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056
 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields
 = "License")[] 
[1958] [1959]
Underfull \hbox (badness 4132) in paragraph at lines 7176--7178
[]\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
[1960] [1961] [1962]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343
 []\T1/pcr/m/n/9 ls.str(mode = "list")   #- what are the structured objects I h
ave defined?[] 
[1963] [1964]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486
 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F
ALSE) 
[1965]
Underfull \hbox (badness 10000) in paragraph at lines 7526--7528
[]\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
[1966] [1967]
Underfull \hbox (badness 10000) in paragraph at lines 7711--7713
[]\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if

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[]\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 class
[1968] [1969] [1970] [1971]
Underfull \hbox (badness 1859) in paragraph at lines 7939--7942
[]\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br
owser (by
[1972]
Underfull \hbox (badness 1655) in paragraph at lines 8032--8035
[]\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 8043--8043
 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre
pl("PR#", Text),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047
 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri
x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055
 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st
andardize a bit more[] 
[1973] [1974]
Underfull \hbox (badness 1917) in paragraph at lines 8134--8136
[]\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 ,
[1975] [1976] [1977] [1978]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406
 []            \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica
tion", "Built"),[] 

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 []            \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 8408--8408
 []            \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f
ields=date.fields))[] 

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[]\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
[1979]
Underfull \hbox (badness 10000) in paragraph at lines 8450--8452
[]\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 8458--8463
[]\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,

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 []          \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 8505--8505
 []                                   \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[] 
[1980] [1981]
Underfull \hbox (badness 10000) in paragraph at lines 8634--8639
[]\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 8634--8639
[][]\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 8634--8639
\T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest 
ver-sion

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\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
[1982] [1983]
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 []       \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme
nt"),[] 

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 []       \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", 
">"),[] 
[1984] [1985]
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 []         \T1/pcr/m/n/9 "S original, <http://statwww.epfl.ch/davison/BMA/libr
ary.html>"),[] 
[1986] [1987]
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[]\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
[1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995]
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[]\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
[1996] [1997] [1998]
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\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
[1999]
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 []         \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "
no.loss"),[] 
[2000] [2001]
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 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr
anspose = TRUE)[] 
[2002] [2003]
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 []\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[] 
[2004] [2005]
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 []           \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss",
 "no.loss"),[] 

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 []           \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines.
skip,[] 

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 []           \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski
pNul = FALSE)[] 
[2006]
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[]\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
[2007] [2008] [2009]
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 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", 
"HPD"), 

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 []             \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64-
bit"))[] 
[2010]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are

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\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 .

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\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
[2011] [2012] [2013]
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 []        \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c
(1, 0))) 
[2014] [2015] [2016] [2017]
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\T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral
s & oldid = 78252134$[][]\T1/ptm/m/n/10 .
[2018]
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 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni
ng for "IIIIII"[] 

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 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in  
{1,2,..,3899} :[] 
[2019] [2020]
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 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold
 = 0) 
[2021] [2022]
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[]\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-


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\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
[2023]
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 []\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 '[] 
[2024]
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[]\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

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\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,

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\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-

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\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,

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\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
[2025] [2026]
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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p
tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software /
[2027]
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 []             \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F
ALSE, ...)[] 
[2028] [2029] [2030]
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[]\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

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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2031] [2032]
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 []                 \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa
rent")[] 

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[]\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
[2033]
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[]\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

[2034]
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[]\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
[2035] [2036] [2037] [2038]
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[]\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

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[]\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in
g
[2039]
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 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at 
end of report[] 

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[]\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
[2040]
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[2041] [2042]
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[]\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
[2043] [2044]
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[]\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-
[2045] [2046] [2047]
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 []                       \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing =
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[]\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 = <S>) \T1/ptm/m/n/10 will not have

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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive

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[][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on
ly a weak ef-fect, un-less
[2048]
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 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification
 of binary numbers[] 
[2049]
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 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo
ng" non-ASCII:[] 

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 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of  2  in order to se
e  1  (in UTF-8!):[] 

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[2050] [2051]
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[]\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
[2052] [2053] [2054]
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[]\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

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\T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/
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\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
[2055] [2056]
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\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),

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\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
[2057] [2058]
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[]\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

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[][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ f
ormat)$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 http : / / pubs .

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\T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht
ml # tag _ 20 _
[2059] [2060] [2061]
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 []             \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss
"), ...)[] 
[2062] [2063] [2064] [2065] [2066] [2067]
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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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 []             \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc,
 ...),[] 

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[]\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

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\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

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[]\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta
lled.packages[][][](lib.loc =

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[]\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

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\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 ,

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\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[][][]

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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See
[2068]
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\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 =

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\T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault
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[]\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

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[][][]\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 ,
[2069]
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 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c
sb/ch3a.txt") 
[2070] [2071] [2072]
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[][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi-
gnette browser;

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[][]\T1/pcr/m/n/10 RShowDoc[][][](<basename>,package = "<pkg>") \T1/ptm/m/n/10 
dis-plays a ``ren-dered'' vi-gnette (pdf or
[2073]
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 []\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:[]
 
[2074]
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ata = DAT)))[] 

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 []                 \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal),
 data = DD)))[] 
[2075] [2076]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i
s se-lected, or
[2077]
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[]\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.
[2078] [2079]
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[2080]
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[]\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

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[]\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 =
[2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex
Chapter 15.
[2087]
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 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat
e = TRUE) 
[2088] [2089] [2090] [2091] [2092]
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 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun
 = 0.05, 
[2093] [2094] [2095] [2096]) (./MASS-pkg.tex
Chapter 16.
[2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107]
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 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b
eav2$hours/24))[] 
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[2130]
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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 

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 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", 
"F"),[] 
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[]\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
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\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 ,

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\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 ,
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[]\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
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 []            \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL
SE, ...)[] 
[2143]
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 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist =
 "exponential")[] 
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[2155]
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[]\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
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 []        \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n",
 ...)[] 
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 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model 
= FALSE, 
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[2177] [2178] [2179]
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 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP
ACK = FALSE) 
[2180]
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 []\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") 
[2181] [2182]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...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
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2183]
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[]\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
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 []     \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb
ose = TRUE)))[] 
[2189]
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 []     \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr
ellis"))[] 
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 []\T1/pcr/m/n/9 nlmod <- nls(y ~  Const + A * exp(B * x), start=list(Const=100
, A=10, B=1))[] 

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 []     \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c
auchit"))[] 
[2196]
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[]\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat

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[]\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 ) =
[2197]
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 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da
ta = housing)[] 
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\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
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 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam
p = "exact")[] 
[2202]
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 []        \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC
V"), ...)[] 
[2203] [2204] [2205] [2206] [2207] [2208]
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[]\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
[2209] [2210]
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 []    \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control =
 NULL)[] 

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[]\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
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 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS
E, ...)[] 
[2231]
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[]\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 ,

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[]\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),
[2232]
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 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub
le.eps^0.25) 

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 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double
.eps^0.25,[] 

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 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub
le.eps^0.25)[] 
[2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243]
[2244] [2245]) (./Matrix-pkg.tex [2246]
Chapter 17.

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[]\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

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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2247]
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[]\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
[2248]
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[]\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

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\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
[2249]
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[]\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing

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[]\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
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 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp
arse = TRUE) 

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[]\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal 
mean-ing as in
[2252]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a

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 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k =  c(0:2, 6), diag = c(diags, diags[2])
, symm=TRUE)[] 

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 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c(
1:3,2:3,3:2)],[] 
[2253] [2254]
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 []\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:[] 

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 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(<mat1>, <mat
2>, ....., <mat_N>)  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 '[] 

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 []\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}"}.[] 

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 []        \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?[] 

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 []        \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len(
N), each=k)]),[] 

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 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim
plify=FALSE)[] 
[2255]
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[]\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t
ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib .
[2256] [2257] [2258]
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 []\T1/pcr/m/n/10 ##   solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D
","P","Pt"), ...)[] 
[2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- '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
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                   [2261pdfTeX 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.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 pdfTeX warning (ext4): destina
tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been 
already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1163 ## S4 method for signature 'dsparseMatrix'
                                                 ]
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[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2262]
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 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur
e & factorization[] 
[2263]
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 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult =
 0, ...) 

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[]\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
[2264]
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[]\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
[2265]
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 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so
me GOTOblas:[] 

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 []\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(<UTF-8>) gives bad plots[] 

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 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE)
, super = c(FALSE,TRUE)))[] 
[2266]
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[]\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

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\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

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[]\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

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\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
[2267]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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icate ignored
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                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
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                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
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ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
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                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2268]
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[]\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

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\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

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[][][]\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
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[]\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
[2271] [2272] [2273] [2274] [2275]
Underfull \hbox (badness 1484) in paragraph at lines 2234--2236
[]\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix"
,where = "package:Matrix") \T1/ptm/m/n/10 for an
[2276]
Underfull \hbox (badness 7379) in paragraph at lines 2330--2332
[]\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
[2277] [2278] [2279]
Underfull \hbox (badness 4846) in paragraph at lines 2605--2609
[]\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 2368) in paragraph at lines 2610--2614
[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble

Underfull \hbox (badness 10000) in paragraph at lines 2617--2620
[]\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 ;
[2280]
Underfull \hbox (badness 2689) in paragraph at lines 2673--2675
[]\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 2677--2682
[]\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 2677--2682
[][]\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
[2281]
Underfull \hbox (badness 1097) in paragraph at lines 2700--2703
[]\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 2713--2718
[][]\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
[2282]
Underfull \hbox (badness 3646) in paragraph at lines 2951--2954
[]\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 2983--2985
[]\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 2986--2990
[]\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 2995--3001
[]\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t
he re-sult is from class
[2283]
Underfull \hbox (badness 10000) in paragraph at lines 3002--3006
[]\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 3012--3016
[][][]\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
[2284] [2285]
Underfull \hbox (badness 10000) in paragraph at lines 3196--3198
[]\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 3243--3245
[][][]\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)
[2286]
Underfull \hbox (badness 2469) in paragraph at lines 3363--3366
[]\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
[2287] [2288]
Underfull \hbox (badness 10000) in paragraph at lines 3528--3532
[]\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 3528--3532
\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 ,
[2289]
Underfull \hbox (badness 2285) in paragraph at lines 3578--3581
[]\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R
e-turns (and stores) the
[2290] [2291]
Underfull \hbox (badness 10000) in paragraph at lines 3725--3730
[]\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 3725--3730
\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 3737--3740
[]\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : 
if \T1/pcr/m/n/10 uplo ==
[2292]
Underfull \hbox (badness 10000) in paragraph at lines 3813--3815
[]\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
[2293] [2294] [2295]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023
 []\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 4091--4095
[]\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
[2296]
Underfull \hbox (badness 10000) in paragraph at lines 4100--4103
[]\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 4100--4103
\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 4105--4109
[]\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10
 : the
[2297] [2298]
Underfull \hbox (badness 3158) in paragraph at lines 4288--4292
[]\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente
ly use a ``for-ward-solve'' or
[2299] [2300] [2301] [2302]
Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527
 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530
 [] \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 4534--4534
 []\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 4537--4537
 []\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 4547--4547
 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume
nts to sparseMatrix():[] 
[2303] [2304] [2305] [2306]
Underfull \hbox (badness 10000) in paragraph at lines 4849--4854
[]\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 ,
[2307]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930
 []\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 4932--4932
 []  \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 4936--4936
 []  \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE,
 dimnames=dns))[] 
[2308]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943
 []  \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 '[] 
[2309] [2310]
Underfull \hbox (badness 4120) in paragraph at lines 5087--5090
[]\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 5124--5124
 []\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 5130--5130
 [] \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 5131--5131
 [] \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 5134--5134
 []\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 5136--5136
 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH
ECK_EXTRA")) ||[] 
[2311]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143
 []\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 5146--5146
 []   \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi
ly zoom in and out[] 
[2312]
Underfull \hbox (badness 1817) in paragraph at lines 5235--5244
[]\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 5277--5279
[]\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 5279--5282
[]\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 5292--5295
[]\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co
-er-cion to a tra-di-tional
[2313]
Underfull \hbox (badness 4765) in paragraph at lines 5310--5313
[]\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re-
turn the kro-necker
[2314]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370
 []          \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1
, I2)) else TRUE,[] 
[2315] [2316] [2317]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628
 []\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[] 
[2318]
Underfull \hbox (badness 10000) in paragraph at lines 5709--5712
[][][]\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 5720--5720
 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n
ot "formally"[] 
[2319]
Underfull \hbox (badness 1622) in paragraph at lines 5757--5762
[]\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 5757--5762
\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
[2320]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818
 []\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 5819--5819
 []          \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 5826--5826
 []  \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di
mnames(Kmd)))[] 
[2321]
Underfull \hbox (badness 1062) in paragraph at lines 5955--5958
[]\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
[2322]
Underfull \hbox (badness 6063) in paragraph at lines 5984--5987
[]\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
[2323]
Underfull \hbox (badness 2635) in paragraph at lines 6096--6101
[]\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 6096--6101
\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 6104--6107
[]\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.,
[2324]
Underfull \hbox (badness 10000) in paragraph at lines 6214--6224
\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 6214--6224
[][]\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
[2325]
Underfull \hbox (badness 3179) in paragraph at lines 6296--6299
[]\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
[2326]
Underfull \hbox (badness 10000) in paragraph at lines 6394--6397
[]\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.,
[2327]
Underfull \hbox (badness 10000) in paragraph at lines 6469--6472
[]\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 6485--6485
 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 
[2328]
Underfull \hbox (badness 2443) in paragraph at lines 6524--6530
[]\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 6524--6530
[][]\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 6545--6548
[]\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
[2329]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615
 []                                \T1/pcr/m/n/9 # q is a 0-based permutation o
f the columns[] 
[2330] [2331]
Underfull \hbox (badness 6268) in paragraph at lines 6751--6754
[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),

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[]\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,

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\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
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[]\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re-
lies on a cor-rect
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l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7152 ...A{crossprod}{matrix-products}{crossprod}
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l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
                                                  
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\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
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\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.7412 \end{Details}
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l.7412 \end{Details}
                    ]
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[]\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma-
trix mul-ti-pli-ca-tion;

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\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 =

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er sig-na-tures (use

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\T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu
l-ti-pli-ca-tion. Mul-ti-pli-

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to for sev-eral other

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\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

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er sig-na-
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[]\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

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[]\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
[2339]
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[]\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
[2340]
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[]\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
[2341] [2342]
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 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a
ll in this example[] 

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[]\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 .

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\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

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[]\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.,
[2344]
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[]\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note
 that these co-er-cions
[2345]
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[]\T1/ptm/m/n/10 fast sim-
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l.8154 \HeaderA{norm}{Matrix Norms}{norm}
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h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
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l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2347]
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 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x)                      ##  8 x 10
 "dgCMatrix"[] 

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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 

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 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10
 "dtCMatrix"[] 

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[]\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 ,
[2348]
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[]\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
[2349]
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[]\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.,
[2350]
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[]\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.,
[2351]
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 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = (
4+1)*4/2 entries[] 

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[2352]
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[]\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other
 sig-na-tures (use

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[]\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi
s is en-ables typ-i-cal

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[]\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e
r-cion to a tra-di-tional
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 []               \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD
iag = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m
ax.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption("
max.print")),[] 

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 []              \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln
ames = TRUE,[] 

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[]\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

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m
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                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
                                   [2357]
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 []\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![] 

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 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n
ot supported[] 

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 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK
_EXTRA")) ||[] 

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 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case ---------------------
---------------[] 

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 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor
rect colnames[] 

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[]\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of

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[]\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
[2359]
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 []\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"[] 
[2360]
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 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L)))                # war
ning+ ~1.5 sec (2013)[] 

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 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con
siderably faster![] 
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                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2361] [2362]
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 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not
 have full rank[] 
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[]\T1/ptm/m/n/10 optionally fur-ther ar-gu-ments passed to [][]\T1/pcr/m/n/10 s
parseMatrix[][][]()\T1/ptm/m/n/10 , no-tably

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[]\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

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\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
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[]\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
[2367]
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 []                           \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]})
, tolerance = 1e-13),[] 

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 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi
onal matrices:[] 
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l.9829 \aliasA{solve}{solve-methods}{solve}
                                           
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 []      \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P
", "Pt"), ...)[] 

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 []  \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa
ys preferred to[] 
[2369]
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[]\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a

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\T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks
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[2370]
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[]\T1/ptm/m/n/10 All these meth-ods first try Cholmod's

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[]\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines

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[]\T1/ptm/m/n/10 works via

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[]\T1/ptm/m/n/10 these meth-ods typ-i-cally use

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[]\T1/ptm/m/n/10 all work via

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[][][]\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

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 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i
s singular!][] 

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 []  \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on
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[2371]
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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame

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[]\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,

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rasts to be ap-plied to the

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for


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\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
[2372]
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[]\T1/ptm/m/n/10 (for \T1/pcr/m/n/10 fac2sparse()\T1/ptm/m/n/10 :) log-i-cal in
-di-cat-ing if the re-sult must be a

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[]\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-
[2373]
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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0, 0),[] 

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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M)
 == c(3, 0),[] 

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 []  \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M)
 == c(0,12),[] 
[2374] [2375]
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 []             \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = 
TRUE,[] 

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 []             \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = 
FALSE)[] 
[2376]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m
/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a
[2377]
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 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x))                    ##  8 x 10
 "dgCMatrix"[] 

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 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10
 "dsCMatrix"[] 

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 []\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 10583--10583
 []\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 10586--10586
 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar
e consistent[] 
[2378]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609
 []\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 10610--10610
 []\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 10636--10636
 []\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 10638--10638
 []   \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 10640--10640
 []  \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims =
 X@dimension)[] 
[2379]
Underfull \hbox (badness 10000) in paragraph at lines 10733--10741
[]\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject 
of S3 class
[2380]
Underfull \hbox (badness 10000) in paragraph at lines 10784--10788
[][][]\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
<to be read again> 
                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2381] [2382]
Underfull \hbox (badness 10000) in paragraph at lines 10954--10956
[]\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 10982--10982
 [] \T1/pcr/m/n/9 qc  <- qr.coef  (qrm, y); qc. <- qr.coef  (qrm, y.) # 2nd fai
led in Matrix <= 1.1-0[] 

Underfull \hbox (badness 5036) in paragraph at lines 11010--11012
[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2383]
Underfull \hbox (badness 2970) in paragraph at lines 11143--11149
[]\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 11143--11149
\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 ,
[2384]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\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
[2385]
Underfull \hbox (badness 10000) in paragraph at lines 11234--11239
[]\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 11249--11251
[][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc
-tion of sparse vec-tors (apart from
[2386] [2387]
Underfull \hbox (badness 2698) in paragraph at lines 11374--11380
[][][]\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,
[2388]
Underfull \hbox (badness 10000) in paragraph at lines 11467--11469
[]\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 11485--11490
[]\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 11485--11490
\T1/pcr/m/n/10 list(NULL,<character>)\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

Underfull \hbox (badness 2591) in paragraph at lines 11493--11498
\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
[2389]
Underfull \hbox (badness 2057) in paragraph at lines 11565--11567
[]\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.,
[2390] [2391]
Underfull \hbox (badness 6641) in paragraph at lines 11651--11654
[]\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 11691--11695
[]\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 11691--11695
\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
[2392]
Underfull \hbox (badness 7649) in paragraph at lines 11798--11800
[]\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f
rom class
[2393] [2394] [2395]
Underfull \hbox (badness 7362) in paragraph at lines 11999--12001
[]\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
[2396]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037
 []\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 12038--12038
 []\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)[] 
[2397] [2398]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2399] [2400] [2401]) (./boot-pkg.tex [2402]
Chapter 18.
[2403] [2404] [2405] [2406] [2407] [2408] [2409]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530
 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f"
, "w"), 
[2410]
Underfull \hbox (badness 1325) in paragraph at lines 568--575
[]\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 583--588
[]\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-
[2411] [2412] [2413]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\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 851--855
[][][]\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 ,
[2414]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885
 []\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 [2415]
[2416]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\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 1066--1070
\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 1066--1070
\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"
[2417]
Underfull \hbox (badness 1496) in paragraph at lines 1082--1091
[]\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 1082--1091
\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 1082--1091
\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 1103--1109
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2418] [2419] [2420] [2421]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\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-
[2422] [2423] [2424] [2425] [2426]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735
 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix(
1,n,2), 
[2427] [2428] [2429]
Underfull \vbox (badness 10000) has occurred while \output is active [2430]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010
 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4)
 + strata(ulcer),[] 
[2431]
Underfull \hbox (badness 6268) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2432] [2433] [2434]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\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
[2435]
Underfull \hbox (badness 4595) in paragraph at lines 2360--2365
\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 2429--2431
[]\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 2437--2438
[][][]\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 ,
[2436] [2437]
Underfull \hbox (badness 1077) in paragraph at lines 2533--2537
[]\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 2533--2537
\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
[2438] [2439] [2440] [2441] [2442]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892
 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t 
= 25, 

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 []\T1/pcr/m/n/10 EL.profile(y, tmin  =  min(y) + 0.1, tmax = max(y) - 0.1, n.t
  =  25,[] 
[2443] [2444] [2445]
Underfull \hbox (badness 3861) in paragraph at lines 3102--3105
[][][]\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 ,
[2446]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155
 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1
:ncol(mat)) 
[2447] [2448] [2449]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375
 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t
he resampling 
[2450] [2451] [2452] [2453] [2454] [2455] [2456]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835
 []             \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q
 = NULL)[] 
[2457] [2458]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974
 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 =
 grav.z0[3])[] 
[2459] [2460] [2461]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2462]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256
 []\T1/pcr/m/n/9 #  To draw the jackknife-after-bootstrap plot for the head siz
e data as in 
[2463] [2464]
Underfull \hbox (badness 10000) in paragraph at lines 4359--4361
[]\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o
f

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\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
[2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473]
Underfull \hbox (badness 3000) in paragraph at lines 4956--4959
[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2474] [2475] [2476] [2477]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\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 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2478]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314
 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat
a = grav1[, 2])[] 
[2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863
 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c
ity.sp1$spa[1][] 
[2487]
Underfull \hbox (badness 1127) in paragraph at lines 5985--6003
\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
[2488]
Underfull \hbox (badness 2837) in paragraph at lines 6018--6021
[]\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
[2489] [2490] [2491] [2492]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303
 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and 
Wright (1991). 
[2493] [2494]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492
 []\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 6494--6494
 []\T1/pcr/m/n/9 # value of the test statistic 1.84.  In the book exponential t
ilting was used[] 
[2495] [2496] [2497]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\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
[2498] [2499]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899
 []                        \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha =
 c(0.05, 0.95),[] 
[2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex
[2508]
Chapter 19.
[2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519]
[2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex
Chapter 20.
[2525]
Underfull \hbox (badness 1655) in paragraph at lines 133--142
[]\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

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\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 133--142
\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

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\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
[2526] [2527]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252
 []  \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 253--253
 []  \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 254--254
 []  \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method=
 c(.5,.5,0, +.5))[iC]))[] 
[2528] [2529]
Underfull \vbox (badness 10000) has occurred while \output is active [2530]
[2531]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518
 []           \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 522--522
 []           \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5,
 ...)[] 
[2532] [2533]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637
 []      \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c
orrect.d = TRUE)[] 
[2534]
Underfull \hbox (badness 3078) in paragraph at lines 688--691
[]\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
[2535] [2536]
Underfull \hbox (badness 2941) in paragraph at lines 779--782
[][][]\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 
,

Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817
 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo
r this seed):[] 
[2537]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2538]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929
 []     \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code
=3), ...)[] 
[2539]
Underfull \hbox (badness 4872) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is

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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2540]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103
 []        \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE.
factor = SEf)))[] 
[2541]
Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120
 []\T1/pcr/m/n/9 ## You can manually set it before running this :    doExtras <
- TRUE  # or  FALSE[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158
 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap(<iid_rnorm_p=3>)  ==> k = 1  clust
er is optimal")[] 
[2542]
Underfull \hbox (badness 4144) in paragraph at lines 1190--1194
[]\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
[2543]
Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266
 []          \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 1272--1272
 []             \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin
t variability."),[] 
[2544] [2545]
Underfull \hbox (badness 10000) in paragraph at lines 1411--1416
[]\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

Underfull \hbox (badness 10000) in paragraph at lines 1459--1462

[2546]
Underfull \hbox (badness 10000) in paragraph at lines 1476--1480
[][][]\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 1500--1500
 []\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 1510--1510
 []  \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i
dent. only points[] 
[2547]
Underfull \hbox (badness 5741) in paragraph at lines 1550--1553
[]\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
[2548]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616
 []      \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa
rnType,[] 
[2549]
Underfull \hbox (badness 1540) in paragraph at lines 1733--1741
\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 =
[2550] [2551]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824
 []\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 1843--1843
 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st
and = FALSE, 
[2552] [2553] [2554] [2555]
Underfull \hbox (badness 10000) in paragraph at lines 2162--2165

[2556]
Underfull \hbox (badness 3179) in paragraph at lines 2176--2182
[][][]\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.
[2557] [2558]
Underfull \hbox (badness 10000) in paragraph at lines 2334--2337
[][][]\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 ,
[2559]
Underfull \hbox (badness 1292) in paragraph at lines 2402--2405
[]\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

Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\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 2434--2437
[][][]\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 ,
[2560] [2561] [2562] [2563]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650
 []\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 ):[] 
[2564] [2565] [2566]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919
 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro
und (1, 16):[] 
[2567] [2568]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022
 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co
l.axis = "red")[] 
[2569] [2570] [2571]
Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218
 []           \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x
$ac, digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2572]
Underfull \hbox (badness 10000) in paragraph at lines 3286--3289
[]\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
[2573]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336
 []           \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc,
 digits = 2)),[] 

Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337
 []           \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty
 = TRUE, ...)[] 
[2574] [2575] [2576]
Underfull \hbox (badness 10000) in paragraph at lines 3522--3525
[]\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
[2577]
Underfull \hbox (badness 10000) in paragraph at lines 3585--3590
[][][]\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 ,
[2578]
Underfull \hbox (badness 3884) in paragraph at lines 3647--3652
\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 3659--3662
[][][]\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 ,
[2579] [2580] [2581]
Underfull \hbox (badness 10000) in paragraph at lines 3844--3847
[][][]\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 3875--3878
[][][]\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 ,
[2582]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928
 []      \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right =
 TRUE, ...)[] 

Underfull \hbox (badness 2035) in paragraph at lines 3939--3941
[]\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
[2583] [2584] [2585] [2586]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132
 []     \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 4134--4134
 []     \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat
 = TRUE, ...)[] 
[2587] [2588]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272
 []\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 4281--4281
 []   \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 4283--4283
 []      \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma
in")); frame()[] 

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 []\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 4288--4288
 []   \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 4295--4295
 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro
wnames == indices[] 
[2589] [2590] [2591] [2592] [2593] [2594]
Underfull \hbox (badness 10000) in paragraph at lines 4668--4674
[]\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 4684--4686
[]\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
[2595]
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 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10
01:2000}, {2001:3000} 

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 []\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[] 

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 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7  clear "outlier"s  or "wrong group" o
bservations:[] 

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 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? -
- Robust range:[] 
[2596]) (./codetools-pkg.tex
Chapter 21.

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 []           \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch
 = FALSE,[] 

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 []           \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = 
!all,[] 

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 []           \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress
Undefined,[] 
[2597]
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[]\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
[2598]
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 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e
nterInternal,[] 
[2599] [2600] [2601]) (./foreign-pkg.tex [2602]
Chapter 22.
[2603]
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[]\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr
om, or a

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2604] [2605]
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[]\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 ,
[2606]
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 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates =
 FALSE, 
[2607] [2608] [2609]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462
 []          \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t
o.data.frame,[] 
[2610]
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 []          \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen
d", "no"),[] 

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[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

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\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

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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to

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\T1/pcr/m/n/10 paste0(label,duplicated.value.labels.infix,level)\T1/ptm/m/n/10 
,

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[]\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with
 du-

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\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
[2611]
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[]\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en
-[]us / library / ms776446(VS . 85 ) .aspx$[][]

Underfull \hbox (badness 7613) in paragraph at lines 569--575
[]\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
[2612]
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 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg
ument settings.[] 

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 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2613]
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 []\T1/pcr/m/n/9 ## Long Strings (>255 chars) are imported in consecutive separ
ate variables[] 

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 []\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 669--669
 []\T1/pcr/m/n/9 long.string <- apply(x[,c("string_500", "STRIN0")], 1, paste, 
collapse="")[] 
[2614] [2615]
Underfull \hbox (badness 10000) in paragraph at lines 813--814


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 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f
oreign")[1])[] 
[2616] [2617]
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 []  \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G
lobalEnv) 
[2618]
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 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute
(x))) 

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[]\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / /
 www . cs . waikato . ac . nz / ~ml / weka / arff .
[2619] [2620]
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[][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase /
 format / data _ types .

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 []          \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", 
"codes"))[] 
[2621] [2622]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\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 ,
[2623]
Underfull \hbox (badness 2088) in paragraph at lines 1293--1296
[]\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
[2624]) (./lattice-pkg.tex
Chapter 23.
[2625] [2626] [2627]
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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.xyplot"),[] 
[2628]
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 []        \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"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.stripplot"),[] 

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 []       \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le
vels"),[] 

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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.bwplot"),[] 
[2629] [2630] [2631] [2632]
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
[2633] [2634] [2635] [2636]
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[]\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

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\T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a 
use-ful lay-out.
[2637]
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
[2638] [2639]
Underfull \hbox (badness 1097) in paragraph at lines 1225--1227
[]\T1/ptm/m/n/10 Logical flag, whether leg-end should have a

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[]\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to
[2640] [2641] [2642]
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 ,
[2643]
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 ,
[2644]
Underfull \vbox (badness 10000) has occurred while \output is active [2645]
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
[2646]
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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to

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[]\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
[2647] [2648] [2649] [2650]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071
 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl
ot"),[] 
[2651]
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
[2652] [2653] [2654]
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"),[] 

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 []       \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default
.qqmath"),[] 
[2655] [2656] [2657] [2658] [2659]
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")[] 

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 []                \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl
ot"),[] 
[2660] [2661]
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

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[]\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be


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\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 2883--2885
[]\T1/ptm/m/n/10 Logical flag, passed to [][]\T1/pcr/m/n/10 rasterGrob[][][] \T
1/ptm/m/n/10 when
[2662]
Underfull \hbox (badness 1609) in paragraph at lines 2935--2941
[]\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 2935--2941
\T1/ptm/m/n/10 both for the false color im-age and the color key (if present). 
Ef-

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\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 2959--2963
[]\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
[2663] [2664]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060
 []      \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite
 = TRUE),[] 

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 []      \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite
 = TRUE),[] 

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 []      \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite
 = TRUE),[] 

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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
cloud"),[] 

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 []          \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa
ult.wireframe"),[] 
[2665]
Underfull \hbox (badness 2913) in paragraph at lines 3143--3150
[]\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 3143--3150
\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
[2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.parallel}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                
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 []      \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default.
splom"),[] 
[2670]
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 []         \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau
lt.parallel"),[] 
[2671] [2672] [2673] [2674] [2675]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832
 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt(
var(x))) 
[2676]
Underfull \hbox (badness 2277) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings by

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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2677] [2678]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052
 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict 
= FALSE) 

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[]\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

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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when

Underfull \hbox (badness 1728) in paragraph at lines 4105--4109
\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
[2679]
Underfull \hbox (badness 5161) in paragraph at lines 4170--4174
[]\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 4170--4174
\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
[2680] [2681]
Underfull \hbox (badness 1067) in paragraph at lines 4284--4294
[]\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 ,

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\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 ,

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\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

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\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

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\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

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[]\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 ,

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[]\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
[2682] [2683] [2684] [2685] [2686] [2687]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716
 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab
 = "Height")[] 
[2688] [2689]
Underfull \hbox (badness 10000) in paragraph at lines 4903--4906
[]\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 .
[2690] [2691]
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[]\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
[2692] [2693] [2694] [2695] [2696] [2697]
Underfull \hbox (badness 3646) in paragraph at lines 5367--5370
[][][]\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

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 []              \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh
ich.given],[] 

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 []              \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which
.given],[] 
[2698]
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

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\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
[2699]
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[]\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
[2700]
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 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la
bels,[] 
[2701]
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 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose
"), ...)[] 

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 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos
e"), ...)[] 

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 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location"
, "toplevel",[] 

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 []                        \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig
ht", "page"),[] 

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 []               \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in
side"),[] 

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 []                 \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi
ch.given",[] 

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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 which.panel = lattice.getStatus("current.whi
ch.panel",[] 

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 []                                                 \T1/pcr/m/n/10 prefix = pre
fix),[] 

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 []                 \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co
lumn",[] 

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[]\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of


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[]\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point.
 De-faults to
[2702] [2703]
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\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

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[]\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

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\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
[2704] [2705]
Underfull \hbox (badness 10000) in paragraph at lines 6010--6014
[][][]\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 ,
[2706] [2707]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-
[2708] [2709]
Underfull \hbox (badness 3601) in paragraph at lines 6273--6278
[]\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

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\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
[2710]
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 []             \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co
lors")$palette,[] 
[2711] [2712]
Underfull \hbox (badness 1888) in paragraph at lines 6492--6499
\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
[2713]
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[]\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The

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\T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v
alid color. The
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[]\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-

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\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
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[2721]
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[]\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments
 to

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\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
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\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
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
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 []                  \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta
ils.n = 50))[] 
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\T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on 
to

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[]\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
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 []       \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y
 = c(1/6, 4/6)),[] 

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 []       \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d
raw = FALSE),[] 
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e.type)[] 

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ifier, name.type)[] 
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 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden
tifier = "grid")[] 
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[]\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
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo
se

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\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
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 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st
ack, ...)[] 

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t, ...)[] 

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 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr
ipts, ...)[] 
[2744]
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[]\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
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in
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 []                \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b
ottom$labels$labels)[] 
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 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su
nspot.year)),[] 
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[]\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

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\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
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[]\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 ,

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\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 ,
[2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2762] [2763] [2764]
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\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

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 []        \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list(
columns = 2),[] 
[2765] [2766]) (./mgcv-pkg.tex
Chapter 24.
[2767] [2768]
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 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL, 

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e=FALSE,[] 
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 []    \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in
tercept=NULL,...)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2770] [2771] [2772] [2773]
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[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
[2774]
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 []\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)+[] 
[2775] [2776] [2777]
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[]\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
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[]\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
[2781]
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[]\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).
[2782]
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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$
q^.5),col=2)[] 

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 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$
q^.5),col=2)[] 
[2788]
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 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor
+rx+obstruct+adhere,[] 

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 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for
 this stratum...[] 

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 []\T1/pcr/m/n/9 if (i==1) plot(bs$family$data$tr[ind],exp(-bs$family$data$h[in
d]),type="l",ylim=c(0,1),[] 

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 []      \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind])
,lwd=2,col=i)[] 

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 []\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)[] 

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[2790]
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 []  \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid),
 initial = 0,[] 

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 []    \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][
nrow(um)] <- 1[] 

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 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter
polate to te[] 

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 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str
ict=FALSE) 
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\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

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 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset
=NULL,[] 

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[]\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

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2807] [2808]
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\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
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[][][]\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 ,

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[][]\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 ,

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[][]\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 ,
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 []         \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco
l(x)),[] 

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 []         \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol
(x)),[] 
[2822] [2823] [2824] [2825] [2826] [2827]
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[]\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
[2828] [2829]
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 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat
,method="ML")[] 

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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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 []  \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)+[] 
[2840] [2841] [2842]
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 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, 
d1b = 0, 
[2843]
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 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR
UE,...)[] 
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[]\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
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[][][]\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 ,

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[][]\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 .
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[]\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

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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2852] [2853] [2854] [2855] [2856] [2857] [2858]
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[]\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
[2859]
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 []  \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d
ata. A simple plotting[] 
[2860]
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 []      \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j]
,lty=lty[j])[] 

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 []  \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo
r comparison[] 

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 []       \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r
norm(100)*.4[] 
[2862] [2863] [2864] [2865] [2866] [2867]
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 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n
a.action, 

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 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona
lize=FALSE)[] 

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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2868] [2869] [2870] [2871] [2872] [2873]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219
 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1
,deriv=2) 

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 []\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) 
[2874] [2875] [2876] [2877]
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[2880] [2881]
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 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want
 to rule the world.",[] 

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 []      \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y),
nthreads=1)[] 
[2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890]
Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2891] [2892]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359
 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt
ion with bam...[] 
[2893] [2894]
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 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate
d covariates[] 

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 []    \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]]
,na.rm=TRUE)[] 

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[2914]
Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
[]\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 8661--8664
\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 ,

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\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 .
[2915]
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[]\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 ,

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\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
[2916] [2917] [2918]
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 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s
cale=-1,[] 

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 []         \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS
E,xlab=NULL,[] 

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 []         \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi
ds=FALSE,[] 
[2919] [2920] [2921]
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\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
[2922] [2923] [2924] [2925]
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 []        \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread
s=1,...)[] 
[2926] [2927]
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 []        \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL
L,...)[] 
[2928] [2929] [2930] [2931]
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 []  \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[] 
[2933]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

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[]\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
[2934]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2935]
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[]\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from

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[][]\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,
[2936] [2937]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\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,
[2938] [2939] [2940] [2941]
Underfull \hbox (badness 1946) in paragraph at lines 10247--10254
[]\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

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\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 10247--10254
\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

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[]\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 10255--10258
\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.
[2942]
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 []\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 \hbox (badness 10000) in paragraph at lines 10350--10353
[]\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 ,
[2943] [2944] [2945] [2946] [2947]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637
 []\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) 
[2948] [2949] [2950] [2951] [2952] [2953]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if

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 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, 
cov = TRUE, 

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[]\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-
[2954]
Underfull \hbox (badness 10000) in paragraph at lines 11038--11042
[]\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-
[2955] [2956] [2957]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179
 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$
vectors[,ind]))[] 

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[]\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
[2958]
Underfull \hbox (badness 1803) in paragraph at lines 11267--11271
\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 11279--11291
\T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with 
shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec

Underfull \hbox (badness 2401) in paragraph at lines 11296--11300
\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 11296--11300
\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 ,
[2959] [2960] [2961]
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Underfull \hbox (badness 6876) in paragraph at lines 11491--11497
[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one 
or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2963] [2964]
Underfull \hbox (badness 10000) in paragraph at lines 11649--11650
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2965] [2966]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703
 []  \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 11715--11715
 []  \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5,
1.5) (black)[] 

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 []  \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions 
and intervals[] 

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 []  \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i
ntervals away[] 
[2967]
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 []  \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w
ild and wide[] 

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 []  \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:[] 
[2968]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a

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\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
[2969] [2970]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2971]
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 []\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 12018--12018
 []\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[] 
[2972] [2973] [2974]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2975] [2976] [2977] [2978]
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 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m
ethod="REML")[] 
[2979]
Underfull \hbox (badness 10000) in paragraph at lines 12468--12470
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2980] [2981]
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Underfull \hbox (badness 10000) in paragraph at lines 12627--12630
[]\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-

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\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 12627--12630
\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"
[2983]
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 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with
 2 variances[] 
[2984]
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[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

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\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-
[2985] [2986] [2987]
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 []\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...[] 


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[][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the 
sphere, via terms like
[2990]
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[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2991] [2992] [2993] [2994]
Underfull \hbox (badness 3396) in paragraph at lines 13358--13361
[][][]\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
[2995]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2996] [2997] [2998] [2999]
Underfull \hbox (badness 10000) in paragraph at lines 13627--13630
[]\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t
en pro-

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\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
[3000]
Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\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 13660--13664
[][]\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 13660--13664
[][]\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 ,
[3001] [3002] [3003] [3004] [3005]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[3006]
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 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0,
centre=FALSE)[] 
[3007] [3008]
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 []                  \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars
"),...)[] 
[3009] [3010]
Underfull \hbox (badness 4846) in paragraph at lines 14294--14297
[]\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
[3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021]
[3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483
 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA
LSE, ...)[] 
[3031] [3032] [3033] [3034] [3035]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777
 []\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 15778--15778
 []\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 15790--15790
 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val
ues, to check we[] 
[3036] [3037] [3038]) (./nlme-pkg.tex
Chapter 25.
[3039]
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
[3040]
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
[3041] [3042] [3043] [3044] [3045]
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,[] 
[3046] [3047]
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 ---------------------------
---------------[] 
[3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055]
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"),[] 
[3056]
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
[3057] [3058] [3059] [3060] [3061] [3062] [3063]
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 ,
[3064]
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
[3065] [3066] [3067] [3068] [3069]
Underfull \hbox (badness 2042) in paragraph at lines 1994--2000
\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 ,
[3070]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056
 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1)  # same as collapse(Pixel, colla
pse = "Dog")[] 
[3071]
Underfull \hbox (badness 1132) in paragraph at lines 2145--2147
[]\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac
ted us-ing the
[3072] [3073]
Underfull \hbox (badness 4168) in paragraph at lines 2256--2262
[][][]\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 ,
[3074]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281
 []  \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres
sure^4))*QB,[] 
[3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 2844--2848
[][][]\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 ,
[3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093]
[3094]
Underfull \hbox (badness 6493) in paragraph at lines 3580--3588
[][][]\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 ,
[3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105]
[3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116]
[3117] [3118]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\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 ,
[3119] [3120] [3121] [3122] [3123] [3124] [3125]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\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 ,
[3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134]
Underfull \hbox (badness 2799) in paragraph at lines 6098--6104
\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
[3135]
Underfull \hbox (badness 7133) in paragraph at lines 6159--6163
[]\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 ,
[3136]
Underfull \hbox (badness 2057) in paragraph at lines 6243--6254
[][][]\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 ,
[3137]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\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 6339--6339
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3138] [3139] [3140] [3141]
Underfull \hbox (badness 7133) in paragraph at lines 6557--6561
[]\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 ,
[3142]
Underfull \hbox (badness 10000) in paragraph at lines 6656--6662
[][][]\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 6683--6683
 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min
Scale = 0.001, 
[3143]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3144]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751
 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3145] [3146] [3147]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\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 ,
[3148]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012
 []                \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla
ry fissure" ),[] 

Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017
 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new )   # fixed and groups formulae extracted
 from object[] 

Underfull \hbox (badness 2875) in paragraph at lines 7039--7041
[]\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
[3149] [3150] [3151]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\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 ,
[3152] [3153] [3154]
Underfull \hbox (badness 10000) in paragraph at lines 7406--7414
[]\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 7406--7414
\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 7406--7414
\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 7429--7432
[][][]\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 ,
[3155] [3156] [3157]
Underfull \hbox (badness 3354) in paragraph at lines 7644--7646
[]\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
[3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165]
Underfull \hbox (badness 10000) in paragraph at lines 8156--8173
[][][]\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 8156--8173
[][]\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 8199--8199
 []    \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data 
= TRUE)[] 

Underfull \hbox (badness 1642) in paragraph at lines 8208--8230
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o
f the form
[3166] [3167] [3168] [3169] [3170]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473
 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni
terEM = 25, 

Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3171]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565
 []\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
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3172] [3173] [3174] [3175] [3176]
[3177] [3178] [3179] [3180] [3181] [3182] [3183]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\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 9335--9335
 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me
thod = "ML") 
[3184]
Underfull \hbox (badness 6300) in paragraph at lines 9417--9420
[]\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
[3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...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
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3189]
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[]\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a
s

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[]\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive
-definite

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\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
[3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197]
Underfull \hbox (badness 7291) in paragraph at lines 10214--10216
[]\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
[3198] [3199] [3200]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights, 
[3201]
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3202] [3203] [3204]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635
 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, 
weights,[] 
[3205] [3206]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786
 []            \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma =
 NULL, ...)[] 

Underfull \hbox (badness 2213) in paragraph at lines 10797--10802
[]\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[][][]
[3207]
Underfull \hbox (badness 8075) in paragraph at lines 10819--10823
[]\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=

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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is

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 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio
ns be printed[] 
[3208] [3209] [3210] [3211]
Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130
 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* 
message instead of one *each*[] 
[3212] [3213] [3214] [3215] [3216] [3217]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3218] [3219] [3220] [3221] [3222] [3223]
Underfull \hbox (badness 6268) in paragraph at lines 11906--11916
[][][]\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 ,
[3224] [3225] [3226] [3227]
Underfull \hbox (badness 10000) in paragraph at lines 12167--12173
[][][]\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 ,
[3228] [3229] [3230] [3231] [3232]
Underfull \hbox (badness 6876) in paragraph at lines 12489--12491
[]\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
[3233] [3234]
Underfull \hbox (badness 2452) in paragraph at lines 12645--12652
[][][]\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 ,
[3235]
Underfull \hbox (badness 10000) in paragraph at lines 12710--12716
[][][]\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 ,
[3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299
 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo
nt)), .. lme(*)) 
[3245] [3246] [3247] [3248] [3249]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664
 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 
0, id = 0.05)[] 
[3250]
Underfull \hbox (badness 10000) in paragraph at lines 13691--13694
[]\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
[3251]
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[]\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 13734--13741
\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

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 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect,
 panel,[] 
[3252]
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[]\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

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\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

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[]\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De
-fault is

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\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
[3253]
Underfull \hbox (badness 10000) in paragraph at lines 13906--13909
[]\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
[3254]
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\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 ,
[3255]
Underfull \hbox (badness 10000) in paragraph at lines 14000--14002
[][][]\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 ,
[3256] [3257] [3258] [3259]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3260] [3261] [3262] [3263]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524
 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female",
"Male","Male"),[] 
[3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e
xt4): destination with the same identifier (name{Rfn.random.effects}) has been 
already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...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
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3273] [3274] [3275]
[3276] [3277] [3278] [3279] [3280] [3281] [3282]
Underfull \hbox (badness 1009) in paragraph at lines 15834--15843
\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
[3283] [3284] [3285]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981
 []          \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi
st = FALSE, ...)[] 
[3286] [3287] [3288] [3289] [3290]
Underfull \hbox (badness 10000) in paragraph at lines 16316--16322
[][][]\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 ,
[3291]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347
 []         \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG
en, ...)[] 
[3292] [3293] [3294] [3295] [3296] [3297] [3298]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3299] [3300] [3301] [3302] [3303]
Underfull \hbox (badness 1867) in paragraph at lines 17171--17180
\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 17171--17180
\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

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\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 17171--17180
\T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for

Underfull \hbox (badness 7397) in paragraph at lines 17171--17180
\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
[3304]
Underfull \hbox (badness 1521) in paragraph at lines 17235--17243
\T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat
ion of variance

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\T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat
ions per stratum" \T1/ptm/m/n/10 for

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\T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar
iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and
[3305] [3306] [3307] [3308]
Underfull \hbox (badness 10000) in paragraph at lines 17482--17489
[][][]\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 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 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 ,
[3309] [3310] [3311] [3312] [3313] [3314] [3315]
Underfull \hbox (badness 10000) in paragraph at lines 18017--18027
[][][]\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 ,

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[][]\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 ,
[3316]
Underfull \hbox (badness 3579) in paragraph at lines 18055--18060
\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
[3317]
Underfull \hbox (badness 3579) in paragraph at lines 18119--18124
\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
[3318]
Underfull \hbox (badness 3579) in paragraph at lines 18182--18187
\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
[3319]
Underfull \hbox (badness 1577) in paragraph at lines 18243--18245
[]\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

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\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
[3320]
Underfull \hbox (badness 3579) in paragraph at lines 18308--18313
\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 18341--18350
[][][]\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 18341--18350
[][]\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 ,
[3321]
Underfull \hbox (badness 3579) in paragraph at lines 18380--18385
\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
[3322] [3323]
Underfull \hbox (badness 1009) in paragraph at lines 18526--18535
\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
[3324] [3325]
Underfull \hbox (badness 1009) in paragraph at lines 18658--18667
\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
[3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex
Chapter 26.
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom}
) has been already used, duplicate ignored
<to be read again> 
                   \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
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                   \relax 
l.47 ...t Multinomial Log-linear Models}{multinom}
                                                   [3335]
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 []         \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored =
 FALSE,[] 
[3336] [3337] [3338]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369
 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3339]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426
 []\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)),[] 

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 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay
=5e-4, maxit=200)[] 
[3340] [3341]
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 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 
2, rang = 0.1,[] 
[3342]) (./rpart-pkg.tex
Chapter 27.
[3343] [3344] [3345] [3346]
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 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse =
 TRUE, ...)[] 
[3347] [3348] [3349] [3350]
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
[3351] [3352]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728
 []     \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep =
 ""),[] 
[3353] [3354]
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 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie
s, probabilities[] 
[3355]
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 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d
igits"), ...)[] 
[3356] [3357] [3358]
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 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m
ethod, 

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 []      \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos
t, ...)[] 
[3359]
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
[3360]
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 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the 
text is clipped[] 

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 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c
p = 0.01, 

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 []              \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate 
= 2, xval = 10,[] 
[3361] [3362] [3363] [3364] [3365] [3366]
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 ',
[3367] [3368]
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,[] 
[3369] [3370] [3371]) (./spatial-pkg.tex [3372]
Chapter 28.
[3373] [3374] [3375] [3376] [3377] [3378]
Underfull \hbox (badness 10000) in paragraph at lines 423--427

[3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389]
[3390] [3391]) (./survival-pkg.tex [3392]
Chapter 29.
[3393] [3394]
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 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data
 = lung, nmin = 1[] 

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 []\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.[] 
[3395] [3396]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.aml}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
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ation with the same identifier (name{Rfn.aml.1}) has been already used, duplica
te ignored
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                   \relax 
l.326 ... Myelogenous Leukemia survival data}{aml}
                                                   [3397] [3398]
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 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da
ta = ovarian) 

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 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d
ata=ovarian)[] 
[3399]
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 []    \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog),
 lung)[] 
[3400] [3401]
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 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c
ohort.size, 

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 []    \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan",
"II.Borgan"),[] 
[3403] [3404]
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 []   \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz
e=stratsizes,[] 
[3405] [3406] [3407]
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.

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 []\T1/pcr/m/n/9 ppois(4, 10.24153)     #chance of seeing 4 or fewer events wit
h large rate[] 
[3408] [3409]
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 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat
um), data=infert) 
[3410]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
on}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                   [3411]
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 []  \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G
2", "I"),[] 
[3412] [3413]
Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425
 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in
fluence =0,[] 
[3414] [3415] [3416] [3417] [3418]
Underfull \hbox (badness 1337) in paragraph at lines 1799--1803
[][][]\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 ,
[3419]
Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854
 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix
=TRUE)[] 
[3420] [3421] [3422] [3423] [3424] [3425] [3426]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324
 [] \T1/pcr/m/n/9 [1] "extreme"     "logistic"    "gaussian"    "weibull"     "
exponential"[] 

Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351
 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, 
etype, 
[3427] [3428] [3429]
Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574
 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t
df = 5,[] 
[3430] [3431] [3432] [3433]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858
 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt
y(id), kidney) 
[3434]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894
 []           \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 2908--2910
[]\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
[3435]
Underfull \hbox (badness 1048) in paragraph at lines 2963--2965
[]\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se
e the note in
[3436]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037
 []                 \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 )))[] 

[3437] [3438]
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 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential
ly the same.[] 
[3441] [3442] [3443] [3444] [3445]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560
 []                    \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 )))[] 
[3446]
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[3448] [3449] [3450] [3451] [3452]
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 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca
le=1,[] 
[3453] [3454]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165
 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), 
collapse,[] 
[3455]
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 []\T1/pcr/m/n/9 mresid <- (lung$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[] 
[3456]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299
 []  \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means
, na.rm=TRUE)[] 
[3457]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385
 []\T1/pcr/m/n/9 pct <- 1:98/100   # The 100th percentile of predicted survival
 is at +infinity[] 
[3458] [3459]
Underfull \hbox (badness 1852) in paragraph at lines 4533--4535
[]\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
[3460] [3461]
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 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me
thod, 

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 []   \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co
mbine, ...)[] 
[3462] [3463] [3464]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833
 []  \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year=
entry.dt),[] 
[3465]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935
 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age 
+ sex,  mgus,[] 

Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956
 []\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 4958--4958
 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5
0,60,70,100)) +[] 
[3466] [3467] [3468] [3469] [3470]
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[3472] [3473]
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 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb
etas",[] 

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\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
[3474] [3475] [3476] [3477] [3478]
Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860
 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the
ta=5), cancer)[] 

Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861
 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog
, theta=1), cancer)[] 
pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) 
has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.5866 ...ata from a soldering experiment}{solder}
                                                   [3479] [3480]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972
 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1,
 col = 1, 
[3481] [3482] [3483] [3484] [3485]
Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333
 []\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 6334--6334
 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli
ne = FALSE,[] 
[3486] [3487] [3488] [3489]
Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626
 []    \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 ),[] 
[3490] [3491] [3492]
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[]\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
[3493] [3494]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form

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\T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample 
test, the
[3495]
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 []                  \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1
, year=accept.dt),[] 
[3496]
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 []        \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv
idual.h",[] 

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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
[3497]
Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249
 []                      \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d
t-entry.dt)),[] 
[3498]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335
 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival 
by 1/2 years[] 
[3499] [3500] [3501]
Underfull \hbox (badness 10000) in paragraph at lines 7560--7565
[][][]\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 ,
[3502]
Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581
 []        \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", 
"arcsin"),[] 
[3503] [3504]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3505] [3506] [3507]
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[]\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-

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\T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a-

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\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-

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\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
[3508]
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 []\T1/pcr/m/n/9 #  There are no interval censored subjects, only left-censored
 (status=3),[] 
[3509] [3510] [3511] [3512]
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 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit,
 survtype, 
[3513]
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
[3514] [3515]
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\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 .

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\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 ,

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\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
[3516]
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 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi
on. The survreg[] 
[3517] [3518] [3519]
Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830
 []                 \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 )[] 
[3520] [3521]
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 []                            \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x
^2*temp -1))[] 

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 []                 \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 )[] 
[3522] [3523] [3524] [3525]
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 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic
al trial plus[] 

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 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data
 set has data[] 
[3526]
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 []               \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day
, alk.phos))[] 

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 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil
i), data=pbc2)[] 
[3527] [3528] [3529] [3530] [3531] [3532] [3533]
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 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l
inear",[] 
[3534] [3535] [3536]) (./fullrefman.ind [3537] [3538] [3539] [3540] [3541]
[3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550] [3551] [3552]
[3553] [3554] [3555] [3556] [3557]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , 
[3558] [3559] [3560] [3561] [3562]
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[]| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , 
[3563]
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[]| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , 

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[]| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 

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Output written on fullrefman.pdf (3744 pages, 10279426 bytes).
Transcript written on fullrefman.log.
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
+ exit 0
Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.20860
+ 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-3.6.1
+ 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-3.6.1'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/m4'
make[1]: Nothing to be done for 'install'.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/m4'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tools'
make[1]: Nothing to be done for 'install'.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tools'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc'
installing doc ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.6
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/man/man1
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/html'
installing doc/html ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.6/html
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make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
installing doc/manual ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.6/manual
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/doc/R-3.6/manual/images
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/etc'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
installing etc ...
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/etc'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/share'
installing share ...
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/R
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/dictionaries
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/encodings
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/java
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/licenses
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/make
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/Rd
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/Rd/macros
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bib
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/bibtex/bst
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/texmf/tex/latex
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/share'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/bin
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/include'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/include/R_ext'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/include/R_ext'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/include'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/blas'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/blas'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tzone'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tzone'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/xdr'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/xdr'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/intl'
make[3]: Nothing to be done for 'install'.
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/intl'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Nothing to be done for 'install'.
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H    -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing  -L/usr/local/lib64 -DR_HOME='"/usr/lib64/R"' \
  -o Rscript ./Rscript.c
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/pkgconfig
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11'
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[1]: Nothing to be done for 'install'.
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
installing R manuals in PDF format ...
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/share/info
/usr/libexec/rpm-build/install -p -m 644 "./dir" "/usr/src/tmp/R-base-buildroot/usr/share/info"
installing R info pages ...
updating '/usr/share/info/dir' ...
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
you need to adjust /usr/share/info/dir manually
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual'
make: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1'
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so
++ relative /usr/lib64/libR.so /usr/lib64/R/lib/libR.so
+ ln -s ../../libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so
+ ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so
++ relative /usr/share/doc/R-3.6 /usr/lib64/R/doc
+ ln -s ../../share/doc/R-3.6 /usr/src/tmp/R-base-buildroot/usr/lib64/R/doc
++ relative /usr/include/R /usr/lib64/R/include
+ ln -s ../../include/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/include
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/R
++ relative /usr/lib64/R/bin/R /usr/bin/R
+ ln -snfv ../lib64/R/bin/R /usr/src/tmp/R-base-buildroot/usr/bin/R
'/usr/src/tmp/R-base-buildroot/usr/bin/R' -> '../lib64/R/bin/R'
+ cmp /usr/src/tmp/R-base-buildroot/usr/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/Rscript
++ relative /usr/lib64/R/bin/Rscript /usr/bin/Rscript
+ ln -snfv ../lib64/R/bin/Rscript /usr/src/tmp/R-base-buildroot/usr/bin/Rscript
'/usr/src/tmp/R-base-buildroot/usr/bin/Rscript' -> '../lib64/R/bin/Rscript'
+ fgrep -r /usr/src/tmp/R-base-buildroot /usr/src/tmp/R-base-buildroot
+ mkdir -p /usr/src/tmp/R-base-buildroot/etc/R
+ mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Makeconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/Renviron /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/javaconf /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/ldpaths /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc/repositories /usr/src/tmp/R-base-buildroot/etc/R/
+ rmdir /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
++ relative /etc/R /usr/lib64/R/etc
+ ln -s ../../../etc/R /usr/src/tmp/R-base-buildroot/usr/lib64/R/etc
+ mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/applications
+ cat
+ '[' -f /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool ']'
++ relative /usr/bin/libtool /usr/lib64/R/bin/libtool
+ ln -snfv ../../../bin/libtool /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool
'/usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool' -> '../../../bin/libtool'
+ rm -fv /usr/src/tmp/R-base-buildroot/usr/share/info/dir
removed '/usr/src/tmp/R-base-buildroot/usr/share/info/dir'
+ /usr/lib/rpm/brp-alt
Cleaning files in /usr/src/tmp/R-base-buildroot (auto)
mode of './usr/lib64/libR.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/survival/libs/survival.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/mgcv/libs/mgcv.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/Matrix/libs/Matrix.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nlme/libs/nlme.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/spatial/libs/spatial.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/nnet/libs/nnet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/KernSmooth/libs/KernSmooth.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/parallel/libs/parallel.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tcltk/libs/tcltk.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/splines/libs/splines.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grid/libs/grid.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/methods/libs/methods.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/stats/libs/stats.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/graphics/libs/graphics.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/cairo.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/grDevices/libs/grDevices.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop,gnuconfig)
/usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -fopenmp  -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -fopenmp -L${rlibdir} -lR'
Checking contents of files in /usr/src/tmp/R-base-buildroot/ (default)
Compressing files in /usr/src/tmp/R-base-buildroot (auto)
Verifying info files in /usr/src/tmp/R-base-buildroot/usr/share/info (normal)
Adjusting library links in /usr/src/tmp/R-base-buildroot
./usr/lib64:
	libR.so -> libR.so
./usr/lib64/R/lib:
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)
Hardlinking identical .pyc and .pyo files
Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.46330
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.6.1
+ export TZ=
+ TZ=
+ make check
make: Entering directory '/usr/src/RPM/BUILD/R-3.6.1'
make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/tests/Examples'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
running strict specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/tests'
running sloppy specific tests
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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' ... 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' ...33c33
< [1] "2040-07-01 12:00:00 GMT"
---
> [1] "2040-07-01 12:00:00 BST"
44c44
< [1] "2040-07-01 12:00:00 EST"
---
> [1] "2040-07-01 12:00:00 EDT"
 OK
running code in 'iec60559.R' ... OK
  comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
checking Sys.timezone ...
make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
running code in 'timezone.R' ...make[4]: *** [Makefile.common:106: timezone.Rout] Error 1
make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
  Sys.timezone() appears unknown
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
running regression tests ...
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/tests'
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
running code in 'reg-tests-3.R' ... OK
  comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ... OK
  comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK
running tests of plotting Latin-1
  expect failure or some differences if not in a Latin-1 or UTF-8 locale
running code in 'reg-plot-latin1.R' ... FAILED
running code in 'reg-S4.R' ... OK
  comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK
make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
running tests of Internet functions
make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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] "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">"
>  [2] "<html>"                                                                                                   
>  [3] "<head>"                                                                                                   
>  [4] "<title>The Comprehensive R Archive Network</title>"                                                       
>  [5] "<META HTTP-EQUIV=\"content-type\" CONTENT=\"text/html; charset=utf-8\">"                                  
>  [6] "<link rel=\"icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                           
>  [7] "<link rel=\"shortcut icon\" href=\"favicon.ico\" type=\"image/x-icon\">"                                  
>  [8] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"                                               
>  [9] "</head>"                                                                                                  
> [10] ""                                                                                                         
> [11] "<FRAMESET cols=\"1*, 4*\" style=\"border: none;\">"                                                       
> [12] "<FRAMESET rows=\"120, 1*\">"                                                                              
> [13] "<FRAME src=\"logo.html\" name=\"logo\" frameborder=0>"                                                    
> [14] "<FRAME src=\"navbar.html\" name=\"contents\" frameborder=0>"                                              
> [15] "</FRAMESET>"                                                                                              
> [16] "<FRAME src=\"banner.shtml\" name=\"banner\" frameborder=0>"                                               
> [17] "<noframes>"                                                                                               
> [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] "</noframes>"                                                                                              
> [23] "</FRAMESET>"                                                                                              
> > 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-3.6.1/tests'
make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests'
make: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1'
+ exit 0
Processing files: R-base-3.6.1-alt1
Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.99798
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ cd R-3.6.1
+ DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ export DOCDIR
+ rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1
+ exit 0
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warning: File listed twice: /usr/lib64/R/library/MASS/html/birthwt.html
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warning: File listed twice: /usr/lib64/R/library/utils/html/PkgUtils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Question.html
warning: File listed twice: /usr/lib64/R/library/utils/html/R.css
warning: File listed twice: /usr/lib64/R/library/utils/html/REMOVE.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RHOME.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RShowDoc.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RSiteSearch.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rconsole.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rprof.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rprofmem.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rscript.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Rtangle.html
warning: File listed twice: /usr/lib64/R/library/utils/html/RweaveLatex.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SHLIB.html
warning: File listed twice: /usr/lib64/R/library/utils/html/Sweave.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SweaveSyntConv.html
warning: File listed twice: /usr/lib64/R/library/utils/html/SweaveUtils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/URLencode.html
warning: File listed twice: /usr/lib64/R/library/utils/html/View.html
warning: File listed twice: /usr/lib64/R/library/utils/html/adist.html
warning: File listed twice: /usr/lib64/R/library/utils/html/alarm.html
warning: File listed twice: /usr/lib64/R/library/utils/html/apropos.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aregexec.html
warning: File listed twice: /usr/lib64/R/library/utils/html/arrangeWindows.html
warning: File listed twice: /usr/lib64/R/library/utils/html/askYesNo.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aspell-utils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/aspell.html
warning: File listed twice: /usr/lib64/R/library/utils/html/available.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/bibentry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseEnv.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseURL.html
warning: File listed twice: /usr/lib64/R/library/utils/html/browseVignettes.html
warning: File listed twice: /usr/lib64/R/library/utils/html/bug.report.html
warning: File listed twice: /usr/lib64/R/library/utils/html/capture.output.html
warning: File listed twice: /usr/lib64/R/library/utils/html/changedFiles.html
warning: File listed twice: /usr/lib64/R/library/utils/html/choose.dir.html
warning: File listed twice: /usr/lib64/R/library/utils/html/choose.files.html
warning: File listed twice: /usr/lib64/R/library/utils/html/chooseBioCmirror.html
warning: File listed twice: /usr/lib64/R/library/utils/html/chooseCRANmirror.html
warning: File listed twice: /usr/lib64/R/library/utils/html/citEntry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/citation.html
warning: File listed twice: /usr/lib64/R/library/utils/html/cite.html
warning: File listed twice: /usr/lib64/R/library/utils/html/clipboard.html
warning: File listed twice: /usr/lib64/R/library/utils/html/close.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/combn.html
warning: File listed twice: /usr/lib64/R/library/utils/html/compareVersion.html
warning: File listed twice: /usr/lib64/R/library/utils/html/contrib.url.html
warning: File listed twice: /usr/lib64/R/library/utils/html/count.fields.html
warning: File listed twice: /usr/lib64/R/library/utils/html/create.post.html
warning: File listed twice: /usr/lib64/R/library/utils/html/data.html
warning: File listed twice: /usr/lib64/R/library/utils/html/dataentry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/debugcall.html
warning: File listed twice: /usr/lib64/R/library/utils/html/debugger.html
warning: File listed twice: /usr/lib64/R/library/utils/html/demo.html
warning: File listed twice: /usr/lib64/R/library/utils/html/download.file.html
warning: File listed twice: /usr/lib64/R/library/utils/html/download.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/edit.data.frame.html
warning: File listed twice: /usr/lib64/R/library/utils/html/edit.html
warning: File listed twice: /usr/lib64/R/library/utils/html/example.html
warning: File listed twice: /usr/lib64/R/library/utils/html/file.edit.html
warning: File listed twice: /usr/lib64/R/library/utils/html/filetest.html
warning: File listed twice: /usr/lib64/R/library/utils/html/findLineNum.html
warning: File listed twice: /usr/lib64/R/library/utils/html/fix.html
warning: File listed twice: /usr/lib64/R/library/utils/html/flush.console.html
warning: File listed twice: /usr/lib64/R/library/utils/html/format.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getAnywhere.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getFromNamespace.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getParseData.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getS3method.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getWindowsHandle.html
warning: File listed twice: /usr/lib64/R/library/utils/html/getWindowsHandles.html
warning: File listed twice: /usr/lib64/R/library/utils/html/glob2rx.html
warning: File listed twice: /usr/lib64/R/library/utils/html/globalVariables.html
warning: File listed twice: /usr/lib64/R/library/utils/html/hasName.html
warning: File listed twice: /usr/lib64/R/library/utils/html/head.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.request.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.search.html
warning: File listed twice: /usr/lib64/R/library/utils/html/help.start.html
warning: File listed twice: /usr/lib64/R/library/utils/html/hsearch-utils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/install.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/installed.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/isS3method.html
warning: File listed twice: /usr/lib64/R/library/utils/html/isS3stdGen.html
warning: File listed twice: /usr/lib64/R/library/utils/html/localeToCharset.html
warning: File listed twice: /usr/lib64/R/library/utils/html/ls_str.html
warning: File listed twice: /usr/lib64/R/library/utils/html/maintainer.html
warning: File listed twice: /usr/lib64/R/library/utils/html/make.packages.html.html
warning: File listed twice: /usr/lib64/R/library/utils/html/make.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/memory.size.html
warning: File listed twice: /usr/lib64/R/library/utils/html/menu.html
warning: File listed twice: /usr/lib64/R/library/utils/html/methods.html
warning: File listed twice: /usr/lib64/R/library/utils/html/mirrorAdmin.html
warning: File listed twice: /usr/lib64/R/library/utils/html/modifyList.html
warning: File listed twice: /usr/lib64/R/library/utils/html/news.html
warning: File listed twice: /usr/lib64/R/library/utils/html/nsl.html
warning: File listed twice: /usr/lib64/R/library/utils/html/object.size.html
warning: File listed twice: /usr/lib64/R/library/utils/html/package.skeleton.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageDescription.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageName.html
warning: File listed twice: /usr/lib64/R/library/utils/html/packageStatus.html
warning: File listed twice: /usr/lib64/R/library/utils/html/page.html
warning: File listed twice: /usr/lib64/R/library/utils/html/person.html
warning: File listed twice: /usr/lib64/R/library/utils/html/process.events.html
warning: File listed twice: /usr/lib64/R/library/utils/html/prompt.html
warning: File listed twice: /usr/lib64/R/library/utils/html/promptData.html
warning: File listed twice: /usr/lib64/R/library/utils/html/promptPackage.html
warning: File listed twice: /usr/lib64/R/library/utils/html/rcompgen.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.DIF.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.fortran.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.fwf.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.socket.html
warning: File listed twice: /usr/lib64/R/library/utils/html/read.table.html
warning: File listed twice: /usr/lib64/R/library/utils/html/readRegistry.html
warning: File listed twice: /usr/lib64/R/library/utils/html/recover.html
warning: File listed twice: /usr/lib64/R/library/utils/html/relist.html
warning: File listed twice: /usr/lib64/R/library/utils/html/remove.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/removeSource.html
warning: File listed twice: /usr/lib64/R/library/utils/html/roman.html
warning: File listed twice: /usr/lib64/R/library/utils/html/rtags.html
warning: File listed twice: /usr/lib64/R/library/utils/html/savehistory.html
warning: File listed twice: /usr/lib64/R/library/utils/html/select.list.html
warning: File listed twice: /usr/lib64/R/library/utils/html/sessionInfo.html
warning: File listed twice: /usr/lib64/R/library/utils/html/setRepositories.html
warning: File listed twice: /usr/lib64/R/library/utils/html/setWindowTitle.html
warning: File listed twice: /usr/lib64/R/library/utils/html/shortPathName.html
warning: File listed twice: /usr/lib64/R/library/utils/html/sourceutils.html
warning: File listed twice: /usr/lib64/R/library/utils/html/stack.html
warning: File listed twice: /usr/lib64/R/library/utils/html/str.html
warning: File listed twice: /usr/lib64/R/library/utils/html/strcapture.html
warning: File listed twice: /usr/lib64/R/library/utils/html/summaryRprof.html
warning: File listed twice: /usr/lib64/R/library/utils/html/tar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/toLatex.html
warning: File listed twice: /usr/lib64/R/library/utils/html/txtProgressBar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/type.convert.html
warning: File listed twice: /usr/lib64/R/library/utils/html/untar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/unzip.html
warning: File listed twice: /usr/lib64/R/library/utils/html/update.packages.html
warning: File listed twice: /usr/lib64/R/library/utils/html/url.show.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-defunct.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-deprecated.html
warning: File listed twice: /usr/lib64/R/library/utils/html/utils-package.html
warning: File listed twice: /usr/lib64/R/library/utils/html/vignette.html
warning: File listed twice: /usr/lib64/R/library/utils/html/warnErrList.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winDialog.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winMenus.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winProgressBar.html
warning: File listed twice: /usr/lib64/R/library/utils/html/winextras.html
warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html
warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.wuM9WY
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/lib64/libR.so: 1234 symbols, 21 bpp
++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}'
--- find-provides-deps	2022-01-31 04:29:57.533720240 +0000
+++ filter-provides-deps	2022-01-31 04:29:57.535720267 +0000
@@ -1 +1,2 @@
 libR.so()(64bit) = set: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
+libR-2.11.so()(64bit) = set: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
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.cazQiY
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/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5
lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules/lapack.so: underlinked libraries: /lib64/libdl.so.2
shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable
find-requires: FINDPACKAGE-COMMANDS: cat grep sh
Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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
Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.27)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFsTG1phW01upHNOW8SpbeVohC5Pwchq6KplkgZIPAQh02Zr5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libgomp.so.1()(64bit) >= set:mis5Xj4o6xrqO4ZGM8MScp68PsbwUdLBn0, libgomp.so.1(GOMP_1.0)(64bit), libgomp.so.1(GOMP_4.0)(64bit), libgomp.so.1(OMP_1.0)(64bit), libicui18n.so.65()(64bit) >= set:rolIY5WucOij1kVmNEZ6KImTd0, libicuuc.so.65()(64bit) >= set:pmfKgUVR3uSC2LbF2, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITkXeYooZo0Vt8WFt6QYIOIZmWow6fzRMDwp9MGO0ZhldKUzW8W1RsJZtAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, liblzma.so.5()(64bit) >= set:kgIy0DJdgZuHF5yXYppdmYIDYAa1, liblzma.so.5(XZ_5.0)(64bit), libm.so.6(GLIBC_2.2.5)(64bit), libm.so.6(GLIBC_2.23)(64bit), libopenblas.so.0()(64bit) >= set:qlsiqIe00icRW574Ku0AAyAyab7fG6SOSAPoPNmLYbhPezMnFyfKftDkkVQaeAYUqnr3WgpZJxDHDDHYiTG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:ieELhsZ4oFM1uTpGS8bAqz69j4, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libpthread.so.0(GLIBC_2.2.5)(64bit), libreadline.so.7()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPltLOR05Zx8IO0, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1()(64bit) >= set:kgb6dgb5xDnazO8BhqfiJqdZd6eIL9, rtld(GNU_HASH), sh
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.UW0nF1
Creating R-base-debuginfo package
Processing files: R-full-3.6.1-alt1
Requires: R-devel = 3.6.1-alt1, R-tcltk = 3.6.1-alt1, R-doc-html = 3.6.1-alt1, gcc-c++, gcc-fortran, liblapack-devel, make
Processing files: R-devel-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.AMYpA9
find-provides: broken symbolic link /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/libtool -> ../../../bin/libtool is not going to provide anything
find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,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.IYF2il
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
 #  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
 #  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) = 3.6.1
Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils
Requires(pre): R-base = 3.6.1-alt1
Requires(postun): R-base = 3.6.1-alt1
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.kML87J
Processing files: R-tcltk-3.6.1-alt1
warning: File listed twice: /usr/lib64/R/library/tcltk/html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html
warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.qBw9Bc
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.YsJRAI
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) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0
Requires: R-base = 3.6.1-alt1, libR.so()(64bit) >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE12warZ61UkMZtzOOW0cQ6tLN8BjJrkKZnL1TEzhiItObZCaSl9pqVwPzwTv35ZmWMAXnz5WOpBZwwMBble1hwYqhmdgOF2MNqAeQO4ABz2QjcXaAt0mBDLIbcof, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk)
Requires(rpmlib): rpmlib(SetVersions)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.kULx3h
Creating R-tcltk-debuginfo package
Processing files: R-doc-html-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.oMKt3U
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.KFolyB
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 = 3.6.1-alt1
Processing files: R-doc-pdf-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.uHaZDl
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.Qezpe9
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 > 3.6.1, R-base < 3.6.1
Processing files: R-doc-info-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.yjgFi0
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.4ZKERU
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 > 3.6.1, R-base < 3.6.1
Processing files: R-base-debuginfo-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.m3ryaT
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.mvNZXU
find-requires: running scripts (debuginfo)
Provides: debug64(libR.so)
Requires: R-base = 3.6.1-alt1, /usr/lib/debug/lib64/ld-linux-x86-64.so.2.debug, debug64(ld-linux-x86-64.so.2), debug64(libX11.so.6), debug64(libXmu.so.6), debug64(libXt.so.6), debug64(libbz2.so.1), debug64(libc.so.6), debug64(libcairo.so.2), debug64(libcurl.so.4), debug64(libdl.so.2), debug64(libgobject-2.0.so.0), debug64(libgomp.so.1), debug64(libicui18n.so.65), debug64(libicuuc.so.65), debug64(libjpeg.so.62), debug64(liblapack.so.4), debug64(liblzma.so.5), debug64(libm.so.6), debug64(libopenblas.so.0), debug64(libpango-1.0.so.0), debug64(libpangocairo-1.0.so.0), debug64(libpcre.so.3), debug64(libpng16.so.16), debug64(libpthread.so.0), debug64(libreadline.so.7), debug64(librt.so.1), debug64(libtiff.so.5), debug64(libz.so.1)
Processing files: R-tcltk-debuginfo-3.6.1-alt1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.KrdCo6
find-provides: running scripts (debuginfo)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.QSHzkl
find-requires: running scripts (debuginfo)
Requires: R-tcltk = 3.6.1-alt1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so)
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk a strict dependency on R-base
Adding to R-doc-html a strict dependency on R-base
Adding to R-base-debuginfo a strict dependency on R-base
Adding to R-full a strict dependency on R-devel
Adding to R-full a strict dependency on R-tcltk
Adding to R-full a strict dependency on R-doc-html
Adding to R-tcltk-debuginfo a strict dependency on R-tcltk
Adding to R-devel a strict dependency on R-base
Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo
Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo
also prunning dir /usr/src/debug/R-3.6.1/include/R_ext
also prunning dir /usr/src/debug/R-3.6.1/src/include
also prunning dir /usr/src/debug/R-3.6.1/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 5 extra deps from R-tcltk due to repentancy on R-base
Removing 1 extra deps from R-tcltk-debuginfo due to repentancy on R-base-debuginfo
warning: Installed (but unpackaged) file(s) found:
    /usr/lib64/R/COPYING
    /usr/lib64/R/SVN-REVISION
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-3.6.1-alt1.x86_64.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/noarch/R-full-3.6.1-alt1.noarch.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-3.6.1-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-3.6.1-alt1.x86_64.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-3.6.1-alt1.noarch.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-3.6.1-alt1.noarch.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-3.6.1-alt1.noarch.rpm (w2.lzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-3.6.1-alt1.x86_64.rpm (w2T16.xzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-3.6.1-alt1.x86_64.rpm (w2.lzdio)
790.70user 145.97system 9:33.60elapsed 163%CPU (0avgtext+0avgdata 941948maxresident)k
0inputs+0outputs (0major+24513157minor)pagefaults 0swaps
902.80user 170.17system 12:05.55elapsed 147%CPU (0avgtext+0avgdata 941948maxresident)k
240inputs+0outputs (34409major+26171875minor)pagefaults 0swaps
--- R-base-3.6.1-alt1.x86_64.rpm.repo	2021-06-21 20:06:08.000000000 +0000
+++ R-base-3.6.1-alt1.x86_64.rpm.hasher	2022-01-31 04:30:53.247486074 +0000
@@ -4435,3 +4435,3 @@
 File: /usr/lib64/R/bin/Rprof	100755	root:root	8b1dc2b3c9cdfdf00b76f9bab559f740	
-File: /usr/lib64/R/bin/Rscript	100755	root:root	699d3f76b6d07c4faebd9335f8965445	
+File: /usr/lib64/R/bin/Rscript	100755	root:root	d935289d7833788c6c5e65ab2c747430	
 File: /usr/lib64/R/bin/Stangle	100755	root:root	5f3ec1749e89b212df274d861d5dd1f6	
@@ -4439,3 +4439,3 @@
 File: /usr/lib64/R/bin/exec	40755	root:root		
-File: /usr/lib64/R/bin/exec/R	100755	root:root	fdc3ffa02a44c62ae0333e98e2e640a8	
+File: /usr/lib64/R/bin/exec/R	100755	root:root	c0f31c896b493badf305066072ef758b	
 File: /usr/lib64/R/bin/javareconf	100755	root:root	f1c35ee536a466fbe7d3218f56082d17	
@@ -4449,3 +4449,3 @@
 File: /usr/lib64/R/library/KernSmooth	40755	root:root		
-File: /usr/lib64/R/library/KernSmooth/DESCRIPTION	100644	root:root	a7c04ebce33bf44668d3bfc5283a029e	
+File: /usr/lib64/R/library/KernSmooth/DESCRIPTION	100644	root:root	7397c1f3ce2749e494ce300bbe3b3d27	
 File: /usr/lib64/R/library/KernSmooth/INDEX	100644	root:root	56080cdf3d21fa33a8cae73825b9ef9f	
@@ -4457,3 +4457,3 @@
 File: /usr/lib64/R/library/KernSmooth/Meta/nsInfo.rds	100644	root:root	14105c52aa0a87f929490a96c046eb9b	
-File: /usr/lib64/R/library/KernSmooth/Meta/package.rds	100644	root:root	4e49a83076276b0fb5f0e8f188c20a04	
+File: /usr/lib64/R/library/KernSmooth/Meta/package.rds	100644	root:root	f5787a562d26a1832eee92f8c0e090e0	
 File: /usr/lib64/R/library/KernSmooth/NAMESPACE	100644	root:root	a93c919c53d25488f67acbe057fff7ed	
@@ -4465,6 +4465,6 @@
 File: /usr/lib64/R/library/KernSmooth/help/AnIndex	100644	root:root	000e790525eb6d551fc2a2f3edd1f6d1	
-File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb	100644	root:root	7118c7c4024fbe27b20c90560229616c	
-File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx	100644	root:root	b3fd52cfdfdb1f85de309508d98e8567	
+File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb	100644	root:root	bc065e0e86ded1e1e1f4fd3ede802a39	
+File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx	100644	root:root	73dfb2c7e0715ce70bd025aa03dea5ea	
 File: /usr/lib64/R/library/KernSmooth/help/aliases.rds	100644	root:root	f7a179acd24bb9df14b155c528b37ad7	
-File: /usr/lib64/R/library/KernSmooth/help/paths.rds	100644	root:root	cce41ed35c6a3b358aaab0ca8f4f3f52	
+File: /usr/lib64/R/library/KernSmooth/help/paths.rds	100644	root:root	3ecaa8fa84bdceb09366e5c429be6923	
 File: /usr/lib64/R/library/KernSmooth/html	40755	root:root		
@@ -4480,3 +4480,3 @@
 File: /usr/lib64/R/library/KernSmooth/libs	40755	root:root		
-File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so	100644	root:root	2562202da933257bfd8915b48434d738	
+File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so	100644	root:root	ccbdd4c73f50e3f25be6313fbe7ea9de	
 File: /usr/lib64/R/library/KernSmooth/po	40755	root:root		
@@ -4499,3 +4499,3 @@
 File: /usr/lib64/R/library/MASS/CITATION	100644	root:root	7bf40cbb20005f08d1f9163582f0d815	
-File: /usr/lib64/R/library/MASS/DESCRIPTION	100644	root:root	4973c6c660d2e098b6ff7778922be0e3	
+File: /usr/lib64/R/library/MASS/DESCRIPTION	100644	root:root	1a2dff13defe45f8b1ac6d4e6ba83a49	
 File: /usr/lib64/R/library/MASS/INDEX	100644	root:root	35aff05a505ecf7e81e0473767794ca9	
@@ -4508,3 +4508,3 @@
 File: /usr/lib64/R/library/MASS/Meta/nsInfo.rds	100644	root:root	4ffb7e3e1f443b3678a805bfb7919c4b	
-File: /usr/lib64/R/library/MASS/Meta/package.rds	100644	root:root	42dfe7f3f8de8d9cfb364f5e1552f43f	
+File: /usr/lib64/R/library/MASS/Meta/package.rds	100644	root:root	bc2ead63c03ba722c958c1db77c03fe9	
 File: /usr/lib64/R/library/MASS/NAMESPACE	100644	root:root	0ac7b30ad35a4c19ea69d76a6a366b02	
@@ -4521,6 +4521,6 @@
 File: /usr/lib64/R/library/MASS/help/AnIndex	100644	root:root	1b15ad7a8d55d0d6c0752ef74dd744f9	
-File: /usr/lib64/R/library/MASS/help/MASS.rdb	100644	root:root	15d4306c12f243fcf7ed8a83dc20a7c2	
-File: /usr/lib64/R/library/MASS/help/MASS.rdx	100644	root:root	2c517d92562379b17d4a6c2134576fb8	
+File: /usr/lib64/R/library/MASS/help/MASS.rdb	100644	root:root	a0694e9974794084b8ffbf1175961af5	
+File: /usr/lib64/R/library/MASS/help/MASS.rdx	100644	root:root	a622cb2cd7b8468e8be6af442a165915	
 File: /usr/lib64/R/library/MASS/help/aliases.rds	100644	root:root	9d27d9e179b3ccb72e96f84ffe3d0e55	
-File: /usr/lib64/R/library/MASS/help/paths.rds	100644	root:root	b1fd5b8e0c31f2f5a350ea3451ff3bc1	
+File: /usr/lib64/R/library/MASS/help/paths.rds	100644	root:root	8fc380fd9d0d7e7df0dc89708096a68e	
 File: /usr/lib64/R/library/MASS/html	40755	root:root		
@@ -4685,3 +4685,3 @@
 File: /usr/lib64/R/library/MASS/libs	40755	root:root		
-File: /usr/lib64/R/library/MASS/libs/MASS.so	100644	root:root	4445eb539750ecf4f1ab4598cef459b1	
+File: /usr/lib64/R/library/MASS/libs/MASS.so	100644	root:root	810d17ae6d83cf628282bc135e50b232	
 File: /usr/lib64/R/library/MASS/po	40755	root:root		
@@ -4721,3 +4721,3 @@
 File: /usr/lib64/R/library/Matrix/Copyrights	100644	root:root	8734f0b040c6292983d273d4251d250a	
-File: /usr/lib64/R/library/Matrix/DESCRIPTION	100644	root:root	5d096d94375afd5f6940d0be245bb29c	
+File: /usr/lib64/R/library/Matrix/DESCRIPTION	100644	root:root	43048582f7f8ee6e87dee4d9c14144db	
 File: /usr/lib64/R/library/Matrix/Doxyfile	100644	root:root	ac3697580885d17a062ce39df01338ad	
@@ -4732,3 +4732,3 @@
 File: /usr/lib64/R/library/Matrix/Meta/nsInfo.rds	100644	root:root	90fd1396706ec9b7a585404a83b7da82	
-File: /usr/lib64/R/library/Matrix/Meta/package.rds	100644	root:root	b9ab4e6293b403fb1dd94163e25ec6e7	
+File: /usr/lib64/R/library/Matrix/Meta/package.rds	100644	root:root	163526b962fde6b92298641cf49926a9	
 File: /usr/lib64/R/library/Matrix/Meta/vignette.rds	100644	root:root	f6a48395281382c8210c31d00fb9d7a7	
@@ -4783,6 +4783,6 @@
 File: /usr/lib64/R/library/Matrix/help/AnIndex	100644	root:root	4e35b3b25bd4de84042b1822f305eebb	
-File: /usr/lib64/R/library/Matrix/help/Matrix.rdb	100644	root:root	8cff1c65d784e1e85ef2be05a7618764	
-File: /usr/lib64/R/library/Matrix/help/Matrix.rdx	100644	root:root	0826d3238bb1d15a94b5398256b537a6	
+File: /usr/lib64/R/library/Matrix/help/Matrix.rdb	100644	root:root	1858f4f0646ab5ec6017b36f3f59b9fe	
+File: /usr/lib64/R/library/Matrix/help/Matrix.rdx	100644	root:root	cdfc039d063d24dd32d040c0ee9083b3	
 File: /usr/lib64/R/library/Matrix/help/aliases.rds	100644	root:root	8417c0b779341210d44eb23b5c1d0b7a	
-File: /usr/lib64/R/library/Matrix/help/paths.rds	100644	root:root	8a516eeb405145334687bba23f6a60ea	
+File: /usr/lib64/R/library/Matrix/help/paths.rds	100644	root:root	119d8167a367fb8b2b9703c4772ff5c4	
 File: /usr/lib64/R/library/Matrix/html	40755	root:root		
@@ -4913,3 +4913,3 @@
 File: /usr/lib64/R/library/Matrix/libs	40755	root:root		
-File: /usr/lib64/R/library/Matrix/libs/Matrix.so	100644	root:root	c574c7543ea9e6a36330dccfccc5f83b	
+File: /usr/lib64/R/library/Matrix/libs/Matrix.so	100644	root:root	639b8c9b5cc77ef854ede9ff0bcb2965	
 File: /usr/lib64/R/library/Matrix/po	40755	root:root		
@@ -4939,3 +4939,3 @@
 File: /usr/lib64/R/library/base/CITATION	100644	root:root	16a31abf39268631f20e1478bf64d659	
-File: /usr/lib64/R/library/base/DESCRIPTION	100644	root:root	1a4520f229b709d934c30ff56aac4b76	
+File: /usr/lib64/R/library/base/DESCRIPTION	100644	root:root	235e10de343998f372e1745759ab505f	
 File: /usr/lib64/R/library/base/INDEX	100644	root:root	1cdac3b4cd5dd2cdedd81985ebea7f81	
@@ -4947,3 +4947,3 @@
 File: /usr/lib64/R/library/base/Meta/links.rds	100644	root:root	d1810ad1e508b718e3e2c4a32ff3de1c	
-File: /usr/lib64/R/library/base/Meta/package.rds	100644	root:root	986c94f099b12e80f450dd49b6e4e171	
+File: /usr/lib64/R/library/base/Meta/package.rds	100644	root:root	19e2896dfcb8a84b3b6994d496c1466d	
 File: /usr/lib64/R/library/base/R	40755	root:root		
@@ -5401,3 +5401,3 @@
 File: /usr/lib64/R/library/boot/CITATION	100644	root:root	5dc2147b194c15507379de49828222c1	
-File: /usr/lib64/R/library/boot/DESCRIPTION	100644	root:root	7b80e5e2f6a1dff41b797d0db69ba0b5	
+File: /usr/lib64/R/library/boot/DESCRIPTION	100644	root:root	361ca9080a0c526aec31c21e7f302fe4	
 File: /usr/lib64/R/library/boot/INDEX	100644	root:root	e6929f73b03924d15f3af4a4c8549a45	
@@ -5410,3 +5410,3 @@
 File: /usr/lib64/R/library/boot/Meta/nsInfo.rds	100644	root:root	6827d841585420cef9946487500a5dc1	
-File: /usr/lib64/R/library/boot/Meta/package.rds	100644	root:root	f825f83470f2426bdebf968de671c114	
+File: /usr/lib64/R/library/boot/Meta/package.rds	100644	root:root	63be448c47d195ba90e851839812d67a	
 File: /usr/lib64/R/library/boot/NAMESPACE	100644	root:root	52cc784fd6ef9af32d9586726a53bb89	
@@ -5424,5 +5424,5 @@
 File: /usr/lib64/R/library/boot/help/aliases.rds	100644	root:root	3a4a7e8689b33a0e13309487d73b95da	
-File: /usr/lib64/R/library/boot/help/boot.rdb	100644	root:root	f68b781016abe2d16536e9d239a95722	
-File: /usr/lib64/R/library/boot/help/boot.rdx	100644	root:root	40998a4f4d48375dd9d5c5224dda113e	
-File: /usr/lib64/R/library/boot/help/paths.rds	100644	root:root	764b0e63b6a75b6ad39a61bce09149ad	
+File: /usr/lib64/R/library/boot/help/boot.rdb	100644	root:root	27c4ec519a879a428475671c9981d382	
+File: /usr/lib64/R/library/boot/help/boot.rdx	100644	root:root	5c8775122dbfdc398332355ea2072c84	
+File: /usr/lib64/R/library/boot/help/paths.rds	100644	root:root	a948bc7d3b2c8687f097ba6d283977b1	
 File: /usr/lib64/R/library/boot/html	40755	root:root		
@@ -5539,3 +5539,3 @@
 File: /usr/lib64/R/library/class/CITATION	100644	root:root	3bad31311a37fe2f39e9c2ad876ab94c	
-File: /usr/lib64/R/library/class/DESCRIPTION	100644	root:root	ab062363372fe793713bb435ad28d435	
+File: /usr/lib64/R/library/class/DESCRIPTION	100644	root:root	30ea51934a8269930fb385ea0993c53b	
 File: /usr/lib64/R/library/class/INDEX	100644	root:root	4c820896ea79bb489343f312e7918082	
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 File: /usr/lib64/R/library/graphics/INDEX	100644	root:root	6ae3bb3a4abff88a80a2dadee3fe15e5	
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 File: /usr/lib64/R/library/graphics/NAMESPACE	100644	root:root	9192cc76322955655202fbff792a2f5d	
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-File: /usr/lib64/R/library/graphics/libs/graphics.so	100644	root:root	eb8be7894589803c155c98037c1a650f	
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 File: /usr/lib64/R/library/grid	40755	root:root		
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 File: /usr/lib64/R/library/grid/INDEX	100644	root:root	1842ba55d39e887993f28eab2fca7c6f	
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 File: /usr/lib64/R/library/grid/Meta/vignette.rds	100644	root:root	3c7294bbfaa6c2fc41dc5650c2039480	
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 File: /usr/lib64/R/library/lattice	40755	root:root		
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-File: /usr/lib64/R/library/lattice/DESCRIPTION	100644	root:root	2d3fdc83db9b52b9496b068977a911d1	
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 File: /usr/lib64/R/library/lattice/INDEX	100644	root:root	1688883220734cb14dc80bc71da9d12e	
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 File: /usr/lib64/R/library/lattice/NAMESPACE	100644	root:root	23d895116e9dcd18d41dff4f06921d8d	
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 File: /usr/lib64/R/library/lattice/html	40755	root:root		
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 File: /usr/lib64/R/library/lattice/po	40755	root:root		
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 File: /usr/lib64/R/library/methods/INDEX	100644	root:root	dec4541b7fa37a86381188e14fa3594a	
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 File: /usr/lib64/R/library/methods/NAMESPACE	100644	root:root	db383a63e8f9526f94bcadcc52ed454a	
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 File: /usr/lib64/R/library/methods/help	40755	root:root		
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 File: /usr/lib64/R/library/mgcv	40755	root:root		
 File: /usr/lib64/R/library/mgcv/CITATION	100755	root:root	e70536903ca327ade1496529ab817b60	
-File: /usr/lib64/R/library/mgcv/DESCRIPTION	100644	root:root	1aaf34ae2e1daee60ebd5445a6cde9da	
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 File: /usr/lib64/R/library/mgcv/INDEX	100644	root:root	4a0d064f31b69c63944922d9203b08a2	
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 File: /usr/lib64/R/library/mgcv/NAMESPACE	100644	root:root	a7edea9aaf9e16a95b7844f9161515d6	
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 File: /usr/lib64/R/library/mgcv/html	40755	root:root		
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 File: /usr/lib64/R/library/mgcv/libs	40755	root:root		
-File: /usr/lib64/R/library/mgcv/libs/mgcv.so	100644	root:root	5fb53fd2298fbda39b3c150142017d4e	
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 File: /usr/lib64/R/library/mgcv/po	40755	root:root		
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 File: /usr/lib64/R/library/nlme/INDEX	100644	root:root	c843826752e9f806f255d79801354abb	
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 File: /usr/lib64/R/library/nlme/NAMESPACE	100644	root:root	607f47e45ab4c7e76698254e83a98e49	
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 File: /usr/lib64/R/library/nlme/html	40755	root:root		
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-File: /usr/lib64/R/library/nlme/libs/nlme.so	100644	root:root	b12efd544e11851b8dbc11014dbee5b8	
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 File: /usr/lib64/R/library/nlme/mlbook	40755	root:root		
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 File: /usr/lib64/R/library/nnet/INDEX	100644	root:root	205d56021a52b73ba35c2e0f3efe76a2	
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 File: /usr/lib64/R/library/nnet/NAMESPACE	100644	root:root	3108fb45014de53cb6a33bdac2bc71b3	
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 File: /usr/lib64/R/library/nnet/html	40755	root:root		
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 File: /usr/lib64/R/library/nnet/libs	40755	root:root		
-File: /usr/lib64/R/library/nnet/libs/nnet.so	100644	root:root	f26faf7988d9e196be688311c7c8711e	
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 File: /usr/lib64/R/library/nnet/po	40755	root:root		
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-File: /usr/lib64/R/library/parallel/DESCRIPTION	100644	root:root	6d7a50f83d786ddb56578f93291a0cce	
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 File: /usr/lib64/R/library/parallel/INDEX	100644	root:root	7ec8f1d10671ebfa45c535c031323369	
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 File: /usr/lib64/R/library/parallel/Meta/vignette.rds	100644	root:root	414d9cbc64558dd94f2b51d36c36b409	
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 File: /usr/lib64/R/library/rpart	40755	root:root		
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 File: /usr/lib64/R/library/rpart/INDEX	100644	root:root	3070a601c9885212060bee8c303c83c2	
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 File: /usr/lib64/R/library/rpart/Meta/vignette.rds	100644	root:root	94d190c957d0df117a5086fd3e8f134f	
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 File: /usr/lib64/R/library/rpart/html	40755	root:root		
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 File: /usr/lib64/R/library/rpart/po	40755	root:root		
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 File: /usr/lib64/R/library/spatial/INDEX	100644	root:root	449f654cbadcc88e46e433cf4251aebd	
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 File: /usr/lib64/R/library/spatial/NAMESPACE	100644	root:root	9669a5ba859da001694e764789a4ce73	
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 File: /usr/lib/debug/usr/lib64/R/library/MASS	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/MASS/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/MASS/libs/MASS.so.debug	100644	root:root	d2df4abcfd1cb20669db8d61de4a06a9	
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 File: /usr/lib/debug/usr/lib64/R/library/Matrix	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/Matrix/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/Matrix/libs/Matrix.so.debug	100644	root:root	f7115c9c4423c0740604176573092712	
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 File: /usr/lib/debug/usr/lib64/R/library/class	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/class/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/class/libs/class.so.debug	100644	root:root	33392ab8f1ea02101d81246c821f4421	
+File: /usr/lib/debug/usr/lib64/R/library/class/libs/class.so.debug	100644	root:root	bc63c77a547bdedd5a028408b42e748b	
 File: /usr/lib/debug/usr/lib64/R/library/cluster	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/cluster/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/cluster/libs/cluster.so.debug	100644	root:root	a77eaf1931bab43c9f741cb4ac88c113	
+File: /usr/lib/debug/usr/lib64/R/library/cluster/libs/cluster.so.debug	100644	root:root	707781bc347998920c63de9b305f0e14	
 File: /usr/lib/debug/usr/lib64/R/library/foreign	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/foreign/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/foreign/libs/foreign.so.debug	100644	root:root	fa13f36665f2a0610623ab9ebe859950	
+File: /usr/lib/debug/usr/lib64/R/library/foreign/libs/foreign.so.debug	100644	root:root	f9bfab4875f8b46fe01eaf88407accbb	
 File: /usr/lib/debug/usr/lib64/R/library/grDevices	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/grDevices/libs	40755	root:root		
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-File: /usr/lib/debug/usr/lib64/R/library/grDevices/libs/grDevices.so.debug	100644	root:root	37488ac9cd903c461a3907be217c76c8	
+File: /usr/lib/debug/usr/lib64/R/library/grDevices/libs/cairo.so.debug	100644	root:root	b87a0596f127b15bf8ecd928b42f91eb	
+File: /usr/lib/debug/usr/lib64/R/library/grDevices/libs/grDevices.so.debug	100644	root:root	6a62482569fdef1d5a55d83bb8b864c6	
 File: /usr/lib/debug/usr/lib64/R/library/graphics	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/graphics/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/graphics/libs/graphics.so.debug	100644	root:root	abe787ed60f028c4bca01ed738aab647	
+File: /usr/lib/debug/usr/lib64/R/library/graphics/libs/graphics.so.debug	100644	root:root	8fa2b0cddbfe848f1af77a92e24be425	
 File: /usr/lib/debug/usr/lib64/R/library/grid	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/grid/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/grid/libs/grid.so.debug	100644	root:root	fb3fa4f8e60f1ce6a539caa6226ff090	
+File: /usr/lib/debug/usr/lib64/R/library/grid/libs/grid.so.debug	100644	root:root	a61df1a3b277c9b7f5954bce86ef3a16	
 File: /usr/lib/debug/usr/lib64/R/library/lattice	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/lattice/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/lattice/libs/lattice.so.debug	100644	root:root	71ff0971d45ea5b1223cb4fb18597c17	
+File: /usr/lib/debug/usr/lib64/R/library/lattice/libs/lattice.so.debug	100644	root:root	330d0cd46838bbda7bbee514e04cccaa	
 File: /usr/lib/debug/usr/lib64/R/library/methods	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/methods/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/methods/libs/methods.so.debug	100644	root:root	11a66fc6817ee4e9c933ae8ace2f76fb	
+File: /usr/lib/debug/usr/lib64/R/library/methods/libs/methods.so.debug	100644	root:root	6ddd3f9626fff033fefacbfbb5eb8653	
 File: /usr/lib/debug/usr/lib64/R/library/mgcv	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/mgcv/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/mgcv/libs/mgcv.so.debug	100644	root:root	d983f721351c43f93d3aff0c14946b3f	
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 File: /usr/lib/debug/usr/lib64/R/library/nlme	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/nlme/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/nlme/libs/nlme.so.debug	100644	root:root	0f6128d8935d5fe79353ce04263f3115	
+File: /usr/lib/debug/usr/lib64/R/library/nlme/libs/nlme.so.debug	100644	root:root	70dd3e1c71f18fb3eca723d86eb8c67d	
 File: /usr/lib/debug/usr/lib64/R/library/nnet	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/nnet/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/nnet/libs/nnet.so.debug	100644	root:root	0763213d7049c617e4417e93e1710d97	
+File: /usr/lib/debug/usr/lib64/R/library/nnet/libs/nnet.so.debug	100644	root:root	4ee9203dcde99721b8523ff08ba3856d	
 File: /usr/lib/debug/usr/lib64/R/library/parallel	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/parallel/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/parallel/libs/parallel.so.debug	100644	root:root	c5fedeeca660fc06629a1d2ddb202c43	
+File: /usr/lib/debug/usr/lib64/R/library/parallel/libs/parallel.so.debug	100644	root:root	678762c977fd13ae02d0dd6f16b939f3	
 File: /usr/lib/debug/usr/lib64/R/library/rpart	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/rpart/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/rpart/libs/rpart.so.debug	100644	root:root	809821824f21b2fbbf21f514785ad79f	
+File: /usr/lib/debug/usr/lib64/R/library/rpart/libs/rpart.so.debug	100644	root:root	327e7531bc915d30bd0baf07a91fdc6f	
 File: /usr/lib/debug/usr/lib64/R/library/spatial	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/spatial/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/spatial/libs/spatial.so.debug	100644	root:root	ddcda654086a31b03b5143625a9b3ffd	
+File: /usr/lib/debug/usr/lib64/R/library/spatial/libs/spatial.so.debug	100644	root:root	84772c910fb08cb6ff6b621ede098af5	
 File: /usr/lib/debug/usr/lib64/R/library/splines	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/splines/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/splines/libs/splines.so.debug	100644	root:root	029a10750e1143886c58c642c860ab64	
+File: /usr/lib/debug/usr/lib64/R/library/splines/libs/splines.so.debug	100644	root:root	176cbe57be783f4d3eb0813a4837c3db	
 File: /usr/lib/debug/usr/lib64/R/library/stats	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/stats/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/stats/libs/stats.so.debug	100644	root:root	5c9dbfc22e09e446a177f0e7cb492c0b	
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 File: /usr/lib/debug/usr/lib64/R/library/survival	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/survival/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/survival/libs/survival.so.debug	100644	root:root	9868fd27ef69c2621d66f1bf64bc0199	
+File: /usr/lib/debug/usr/lib64/R/library/survival/libs/survival.so.debug	100644	root:root	f12762ff5e88a463af41d4943bfe2ff5	
 File: /usr/lib/debug/usr/lib64/R/library/tools	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/tools/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/tools/libs/tools.so.debug	100644	root:root	b79bb789ab3750bae14e5b73da1e1e42	
+File: /usr/lib/debug/usr/lib64/R/library/tools/libs/tools.so.debug	100644	root:root	88421462117230167afd93090f55b14c	
 File: /usr/lib/debug/usr/lib64/R/library/utils	40755	root:root		
 File: /usr/lib/debug/usr/lib64/R/library/utils/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/utils/libs/utils.so.debug	100644	root:root	0e939b30590e39546e577d5f77ba4410	
+File: /usr/lib/debug/usr/lib64/R/library/utils/libs/utils.so.debug	100644	root:root	936afe734bac509824e0230e0d993637	
 File: /usr/lib/debug/usr/lib64/R/modules	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/modules/R_X11.so.debug	100644	root:root	b480b9efdddf191c48246e680d661bc9	
-File: /usr/lib/debug/usr/lib64/R/modules/R_de.so.debug	100644	root:root	1666329b551d6da698632f7f701c6bf6	
-File: /usr/lib/debug/usr/lib64/R/modules/internet.so.debug	100644	root:root	69d5dd8ddf0fe1b3da8093d09289d50e	
-File: /usr/lib/debug/usr/lib64/R/modules/lapack.so.debug	100644	root:root	0853afb91e4879fbbfbddd123dd78f9a	
+File: /usr/lib/debug/usr/lib64/R/modules/R_X11.so.debug	100644	root:root	238f549c414d85ad81a5eff885ae331d	
+File: /usr/lib/debug/usr/lib64/R/modules/R_de.so.debug	100644	root:root	fe7d3925b60de466323637ca3d09a221	
+File: /usr/lib/debug/usr/lib64/R/modules/internet.so.debug	100644	root:root	317b8fa26903ec3160f43e10bda3d705	
+File: /usr/lib/debug/usr/lib64/R/modules/lapack.so.debug	100644	root:root	9081b4e8e1320bd3bbcdb49097a62832	
 File: /usr/lib/debug/usr/lib64/libR-2.11.so.debug	120777	root:root		libR.so.debug
-File: /usr/lib/debug/usr/lib64/libR.so.debug	100644	root:root	773c79c4e7d2e873071d1ab3b67cc7cc	
+File: /usr/lib/debug/usr/lib64/libR.so.debug	100644	root:root	ad722f6e988f3cc0e3560b6599740d6b	
 File: /usr/src/debug/R-3.6.1	40755	root:root		
@@ -1468,2 +1464,2 @@
 File: /usr/src/debug/R-3.6.1/src/unix/system.c	100644	root:root	bd517080e8ef1fe61209d61f9e607227	
-RPMIdentity: a3ada42b8482524a93e51f6e6559d3011cebf5de63b0e2b64086fb4c14bc30cc9ac423686c964408e20d226c7a7bbed8b7fe6c915277ca16acd1037e25d3d37c
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--- R-doc-pdf-3.6.1-alt1.noarch.rpm.repo	2021-06-21 20:06:09.000000000 +0000
+++ R-doc-pdf-3.6.1-alt1.noarch.rpm.hasher	2022-01-31 04:30:53.608491037 +0000
@@ -23,3 +23,3 @@
 File: /usr/share/doc/R-3.6/manual/R-lang.pdf	100644	root:root	c2a86388b8d24dd1a62b8cb312b519a9	
-File: /usr/share/doc/R-3.6/manual/fullrefman.pdf	100644	root:root	5059b5986245e231d443aa4bd178c0c9	
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+File: /usr/share/doc/R-3.6/manual/fullrefman.pdf	100644	root:root	0677cdb6ceb8911d6adbb02975b7db2f	
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--- R-tcltk-3.6.1-alt1.x86_64.rpm.repo	2021-06-21 20:06:08.000000000 +0000
+++ R-tcltk-3.6.1-alt1.x86_64.rpm.hasher	2022-01-31 04:30:53.750492989 +0000
@@ -77,3 +77,3 @@
 File: /usr/lib64/R/library/tcltk	40755	root:root		
-File: /usr/lib64/R/library/tcltk/DESCRIPTION	100644	root:root	b61fc047c91f3c487335a20a903c023e	
+File: /usr/lib64/R/library/tcltk/DESCRIPTION	100644	root:root	bd0a5ca37948e799aa970b91fed9b7f2	
 File: /usr/lib64/R/library/tcltk/INDEX	100644	root:root	3f025b52e186e954ea71bfbb6ced3854	
@@ -86,3 +86,3 @@
 File: /usr/lib64/R/library/tcltk/Meta/nsInfo.rds	100644	root:root	730c9124cb8fa53f6d091bdb26981a34	
-File: /usr/lib64/R/library/tcltk/Meta/package.rds	100644	root:root	fe8939c6345a6d2aa38cc0b9c52252b5	
+File: /usr/lib64/R/library/tcltk/Meta/package.rds	100644	root:root	1832445679c309892a0cab707acaea09	
 File: /usr/lib64/R/library/tcltk/NAMESPACE	100644	root:root	a2f3d22e5fd7d735a120b528c265c7bd	
@@ -134,3 +134,3 @@
 File: /usr/lib64/R/library/tcltk/libs	40755	root:root		
-File: /usr/lib64/R/library/tcltk/libs/tcltk.so	100644	root:root	d759b4d39ecb539ef11e1652dd1482c7	
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+File: /usr/lib64/R/library/tcltk/libs/tcltk.so	100644	root:root	de567cf2b06ab8863625fd15d5ea6d06	
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--- R-tcltk-debuginfo-3.6.1-alt1.x86_64.rpm.repo	2021-06-21 20:06:08.000000000 +0000
+++ R-tcltk-debuginfo-3.6.1-alt1.x86_64.rpm.hasher	2022-01-31 04:30:53.815493882 +0000
@@ -1,4 +1,4 @@
-/usr/lib/debug/.build-id/6a	40755	root:root	
-/usr/lib/debug/.build-id/6a/3286bf9e18963cc5387039236a2c596a00c6aa	120777	root:root	../../../../lib64/R/library/tcltk/libs/tcltk.so
-/usr/lib/debug/.build-id/6a/3286bf9e18963cc5387039236a2c596a00c6aa.debug	120777	root:root	../../usr/lib64/R/library/tcltk/libs/tcltk.so.debug
+/usr/lib/debug/.build-id/c3	40755	root:root	
+/usr/lib/debug/.build-id/c3/c0caa901a3929d40c62b331acd49c724943f5f	120777	root:root	../../../../lib64/R/library/tcltk/libs/tcltk.so
+/usr/lib/debug/.build-id/c3/c0caa901a3929d40c62b331acd49c724943f5f.debug	120777	root:root	../../usr/lib64/R/library/tcltk/libs/tcltk.so.debug
 /usr/lib/debug/usr/lib64/R	40755	root:root	
@@ -23,5 +23,5 @@
 Provides: R-tcltk-debuginfo = 3.6.1-alt1:p9+274919.100.2.1
-File: /usr/lib/debug/.build-id/6a	40755	root:root		
-File: /usr/lib/debug/.build-id/6a/3286bf9e18963cc5387039236a2c596a00c6aa	120777	root:root		../../../../lib64/R/library/tcltk/libs/tcltk.so
-File: /usr/lib/debug/.build-id/6a/3286bf9e18963cc5387039236a2c596a00c6aa.debug	120777	root:root		../../usr/lib64/R/library/tcltk/libs/tcltk.so.debug
+File: /usr/lib/debug/.build-id/c3	40755	root:root		
+File: /usr/lib/debug/.build-id/c3/c0caa901a3929d40c62b331acd49c724943f5f	120777	root:root		../../../../lib64/R/library/tcltk/libs/tcltk.so
+File: /usr/lib/debug/.build-id/c3/c0caa901a3929d40c62b331acd49c724943f5f.debug	120777	root:root		../../usr/lib64/R/library/tcltk/libs/tcltk.so.debug
 File: /usr/lib/debug/usr/lib64/R	40755	root:root		
@@ -30,3 +30,3 @@
 File: /usr/lib/debug/usr/lib64/R/library/tcltk/libs	40755	root:root		
-File: /usr/lib/debug/usr/lib64/R/library/tcltk/libs/tcltk.so.debug	100644	root:root	bcb37824bb774ca121ef82f79cb40355	
+File: /usr/lib/debug/usr/lib64/R/library/tcltk/libs/tcltk.so.debug	100644	root:root	7654c471ac5a689ee50e1f8b04c312a7	
 File: /usr/src/debug/R-3.6.1	40755	root:root		
@@ -40,2 +40,2 @@
 File: /usr/src/debug/R-3.6.1/src/library/tcltk/src/tcltk_unix.c	100644	root:root	ee82d33c5878491887e6c2c581413e23	
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