<86>Dec 6 03:03:59 userdel[1704738]: delete user 'rooter' <86>Dec 6 03:03:59 userdel[1704738]: removed group 'rooter' owned by 'rooter' <86>Dec 6 03:03:59 groupadd[1704745]: group added to /etc/group: name=rooter, GID=615 <86>Dec 6 03:03:59 groupadd[1704745]: group added to /etc/gshadow: name=rooter <86>Dec 6 03:03:59 groupadd[1704745]: new group: name=rooter, GID=615 <86>Dec 6 03:03:59 useradd[1704753]: new user: name=rooter, UID=615, GID=615, home=/root, shell=/bin/bash <86>Dec 6 03:03:59 userdel[1704768]: delete user 'builder' <86>Dec 6 03:03:59 userdel[1704768]: removed group 'builder' owned by 'builder' <86>Dec 6 03:03:59 userdel[1704768]: removed shadow group 'builder' owned by 'builder' <86>Dec 6 03:03:59 groupadd[1704777]: group added to /etc/group: name=builder, GID=616 <86>Dec 6 03:03:59 groupadd[1704777]: group added to /etc/gshadow: name=builder <86>Dec 6 03:03:59 groupadd[1704777]: new group: name=builder, GID=616 <86>Dec 6 03:03:59 useradd[1704781]: new user: name=builder, UID=616, GID=616, home=/usr/src, shell=/bin/bash warning: Macro %add_tcl_lib_path not found <13>Dec 6 03:04:05 rpmi: libpng16-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed <13>Dec 6 03:04:05 rpmi: xorg-proto-devel-2018.4-alt3 1527685079 installed <13>Dec 6 03:04:05 rpmi: libjpeg-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed <13>Dec 6 03:04:05 rpmi: libexpat-2.2.10-alt1 p9+261554.100.1.1 1605103332 installed <13>Dec 6 03:04:05 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed <13>Dec 6 03:04:05 rpmi: perl-libnet-1:3.11-alt1 1511423541 installed <13>Dec 6 03:04:05 rpmi: javapackages-tools-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed <13>Dec 6 03:04:05 rpmi: perl-Module-Runtime-0.016-alt1 1509549848 installed <13>Dec 6 03:04:05 rpmi: perl-HTTP-Date-6.02-alt1 1348645274 installed <13>Dec 6 03:04:05 rpmi: perl-Term-ANSIColor-4.06-alt1 1479407083 installed <13>Dec 6 03:04:05 rpmi: libICE-1.0.9-alt1 1409902719 installed <13>Dec 6 03:04:05 rpmi: libgdbm-1.8.3-alt10 1454943313 installed <13>Dec 6 03:04:05 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed <13>Dec 6 03:04:05 rpmi: libglvnd-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:05 rpmi: tex-common-0.2-alt4 1244804096 installed <13>Dec 6 03:04:06 rpmi: libopenblas-0.2.20-alt2 p9+229427.100.2.1 1558020504 installed <13>Dec 6 03:04:06 rpmi: perl-Unicode-Normalize-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Dec 6 03:04:06 rpmi: libpaper-1.1.26-alt1 sisyphus+221360.100.1.1 1549974198 installed <13>Dec 6 03:04:06 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520810 installed <13>Dec 6 03:04:06 rpmi: perl-Dist-CheckConflicts-0.11-alt1 1397076608 installed <13>Dec 6 03:04:06 rpmi: perl-Module-Implementation-0.09-alt1 1418836057 installed <13>Dec 6 03:04:06 rpmi: libjasper-2.0.22-alt1 p9+259398.100.5.1 1602695042 installed <13>Dec 6 03:04:06 rpmi: rpm-macros-info-install-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Dec 6 03:04:06 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550600768 installed <13>Dec 6 03:04:06 rpmi: liblksctp-1.0.17-alt2 1523113258 installed <13>Dec 6 03:04:06 rpmi: libnspr-1:4.28-alt1 p9+254920.20.18.1 1601209852 installed <13>Dec 6 03:04:06 rpmi: libidn2-2.2.0-alt1 p9+229971.100.2.1 1558696275 installed <13>Dec 6 03:04:06 rpmi: libpixman-3:0.38.4-alt1 sisyphus+228006.100.1.1 1556013486 installed <13>Dec 6 03:04:06 rpmi: libwayland-server-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed <13>Dec 6 03:04:06 rpmi: libtcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Dec 6 03:04:06 rpmi: tcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Dec 6 03:04:06 rpmi: libsqlite3-3.33.0-alt1 p9+258834.40.2.1 1601364885 installed <13>Dec 6 03:04:06 rpmi: python-module-sphinxcontrib-2.1.1-alt2.1.2 sisyphus+227529.1100.1.2 1555924423 installed <13>Dec 6 03:04:06 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed <13>Dec 6 03:04:06 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed <13>Dec 6 03:04:06 rpmi: perl-Devel-StackTrace-1:2.03-alt1 1511420922 installed <13>Dec 6 03:04:06 rpmi: perl-Sub-Exporter-Progressive-0.001013-alt1 1479395404 installed <13>Dec 6 03:04:06 rpmi: perl-File-Which-1.23-alt1 sisyphus.218871.100 1546337313 installed <13>Dec 6 03:04:06 rpmi: perl-Tie-RefHash-1.39-alt1 1316492563 installed <13>Dec 6 03:04:06 rpmi: perl-TimeDate-2.32-alt1 p9+252601.500.11.1 1592659283 installed <13>Dec 6 03:04:06 rpmi: perl-IO-Socket-IP-0.39-alt1 1494508514 installed <13>Dec 6 03:04:06 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed <13>Dec 6 03:04:06 rpmi: perl-Compress-Raw-Zlib-2.086-alt1 sisyphus+226395.100.1.2 1554269783 installed <13>Dec 6 03:04:06 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed <13>Dec 6 03:04:06 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed <13>Dec 6 03:04:06 rpmi: libwebp7-1.0.3-alt1 p9+234901.200.1.1 1563552213 installed <13>Dec 6 03:04:06 rpmi: libjbig-2.1-alt1 1401380921 installed <13>Dec 6 03:04:06 rpmi: libtiff5-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed <13>Dec 6 03:04:06 rpmi: libopenjpeg2.0-2.3.1-alt1 sisyphus+226454.100.1.1 1554284336 installed <13>Dec 6 03:04:06 rpmi: libquadmath0-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:06 rpmi: libgfortran5-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:07 rpmi: libicu64-1:6.4.2-alt2 p9+247371.14540.149.1 1590835182 installed <13>Dec 6 03:04:07 rpmi: libgraphite2-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed <13>Dec 6 03:04:07 rpmi: libharfbuzz-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed <13>Dec 6 03:04:07 rpmi: libfreetype-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed <13>Dec 6 03:04:07 rpmi: fontconfig-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed Updating fonts cache: <29>Dec 6 03:04:08 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>Dec 6 03:04:08 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed <13>Dec 6 03:04:08 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed <13>Dec 6 03:04:08 rpmi: libharfbuzz-icu-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed <13>Dec 6 03:04:08 rpmi: libgraphite2-devel-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed <13>Dec 6 03:04:08 rpmi: libquadmath8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:08 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed <13>Dec 6 03:04:08 rpmi: perl-autodie-2.29-alt1 1445013559 installed <13>Dec 6 03:04:08 rpmi: perl-File-HomeDir-1.004-alt1 1525450444 installed <13>Dec 6 03:04:08 rpmi: perl-Devel-GlobalDestruction-1:0.14-alt1 1479389769 installed <13>Dec 6 03:04:08 rpmi: perl-OLE-Storage_Lite-0.20-alt1 p9+252601.400.11.1 1592659257 installed <13>Dec 6 03:04:08 rpmi: lksctp-tools-1.0.17-alt2 1523113258 installed <13>Dec 6 03:04:08 rpmi: libpng-devel-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed <13>Dec 6 03:04:08 rpmi: perl-unicore-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Dec 6 03:04:08 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+221481.100.1.1 1550127189 installed <13>Dec 6 03:04:08 rpmi: libopenblas-devel-0.2.20-alt2 p9+229427.100.2.1 1558020504 installed <13>Dec 6 03:04:08 rpmi: libOpenGL-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:08 rpmi: libgdbm-devel-1.8.3-alt10 1454943313 installed <13>Dec 6 03:04:08 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed <13>Dec 6 03:04:08 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed <13>Dec 6 03:04:08 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed <13>Dec 6 03:04:08 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed <13>Dec 6 03:04:08 rpmi: java-common-1.6.0-alt1 p9+234085.100.1.1 1562573623 installed <13>Dec 6 03:04:08 rpmi: rpm-build-tcl-0.5.1-alt1 1519671307 installed <13>Dec 6 03:04:09 rpmi: tcl-devel-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Dec 6 03:04:09 rpmi: rpm-macros-java-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed <13>Dec 6 03:04:09 rpmi: perl-Algorithm-Diff-1.1903-alt1 1418755800 installed <13>Dec 6 03:04:09 rpmi: perl-Unicode-EastAsianWidth-1.40-alt1 sisyphus.217785.100 1544703272 installed <13>Dec 6 03:04:09 rpmi: libtre5-0.8.0-alt2.1 1334590818 installed <13>Dec 6 03:04:09 rpmi: libpcre16-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Dec 6 03:04:09 rpmi: pcretest-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Dec 6 03:04:09 rpmi: libpcsclite-1.9.0-alt1 p9+260393.100.3.1 1604003766 installed <13>Dec 6 03:04:09 rpmi: javazi-2019c-alt1 p9+242136.100.1.1 1575295029 installed <13>Dec 6 03:04:09 rpmi: libgif-4.1.6-alt3 1299634266 installed <13>Dec 6 03:04:09 rpmi: libalsa-1:1.1.9-alt2 sisyphus+229323.100.1.1 1557826762 installed <13>Dec 6 03:04:09 rpmi: libgtk+2-locales-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Dec 6 03:04:09 rpmi: libfribidi-1.0.7-alt1 p9+238309.200.1.1 1569787041 installed <13>Dec 6 03:04:09 rpmi: libatk-locales-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed <13>Dec 6 03:04:09 rpmi: libatk-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed <13>Dec 6 03:04:09 rpmi: icon-theme-hicolor-0.17-alt2 p9+248347.100.1.1 1584981172 installed <13>Dec 6 03:04:09 rpmi: shared-mime-info-1.13.1-alt1 p9+238204.100.1.1 1569496447 installed <13>Dec 6 03:04:09 rpmi: libgdk-pixbuf-locales-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed <13>Dec 6 03:04:09 rpmi: gsettings-desktop-schemas-data-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed <13>Dec 6 03:04:09 rpmi: libgio-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed <13>Dec 6 03:04:09 rpmi: gsettings-desktop-schemas-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed <13>Dec 6 03:04:09 rpmi: libgdk-pixbuf-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed <13>Dec 6 03:04:09 rpmi: gtk-update-icon-cache-3.24.11-alt1 p9+260591.300.12.1 1606214030 installed <13>Dec 6 03:04:09 rpmi: libkpathsea6-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Dec 6 03:04:09 rpmi: libptexenc1-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Dec 6 03:04:09 rpmi: libsynctex2-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Dec 6 03:04:09 rpmi: libtexlua5-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Dec 6 03:04:09 rpmi: zziplib-0.13.69-alt3 p9+240930.100.1.1 1574080033 installed <13>Dec 6 03:04:09 rpmi: liblcms2-2.9-alt1 1516411888 installed <13>Dec 6 03:04:09 rpmi: publicsuffix-list-dafsa-20201117-alt1 p9+262027.100.2.1 1605874289 installed <13>Dec 6 03:04:09 rpmi: libpsl-0.21.1-alt1 p9+255207.100.1.1 1595355041 installed <13>Dec 6 03:04:09 rpmi: libnghttp2-1.41.0-alt1 p9+256449.100.1.1 1597829543 installed <13>Dec 6 03:04:09 rpmi: libbrotlicommon-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed <13>Dec 6 03:04:09 rpmi: libbrotlidec-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed <13>Dec 6 03:04:09 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed <13>Dec 6 03:04:09 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268594 installed <13>Dec 6 03:04:09 rpmi: libwayland-client-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed <13>Dec 6 03:04:09 rpmi: libpciaccess-1:0.14-alt1 1528969624 installed <13>Dec 6 03:04:09 rpmi: libdrm-1:2.4.102-alt1 p9+252863.100.1.1 1591372623 installed <13>Dec 6 03:04:09 rpmi: libgbm-4:20.1.8-alt1 p9+260591.240.12.1 1606213200 installed <13>Dec 6 03:04:09 rpmi: t1utils-1.41-alt1 1502978415 installed <13>Dec 6 03:04:09 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267504 installed <13>Dec 6 03:04:09 rpmi: libqqwing-1.3.4-alt2 1436192940 installed <13>Dec 6 03:04:09 rpmi: qqwing-1.3.4-alt2 1436192940 installed <13>Dec 6 03:04:09 rpmi: python-module-iniconfig-1.0.0-alt1 sisyphus+227494.1100.1.3 1555839106 installed <13>Dec 6 03:04:09 rpmi: python-module-apipkg-1.5-alt1 1531926894 installed <13>Dec 6 03:04:09 rpmi: python-module-imagesize-1.1.0-alt1 sisyphus+229015.100.2.1 1557233756 installed <13>Dec 6 03:04:09 rpmi: python-sphinx-objects.inv-1:2.3.8.20190514-alt1 p9+229421.100.1.1 1557927689 installed <13>Dec 6 03:04:09 rpmi: libxapian-1.4.15-alt1 p9+258827.100.1.1 1601305414 installed <13>Dec 6 03:04:09 rpmi: python-module-google-0.4.2-alt2.1 sisyphus+228356.1500.3.1 1556633038 installed <13>Dec 6 03:04:09 rpmi: python-module-markupsafe-1.1.1-alt1 p9+254838.60.14.1 1602882123 installed <13>Dec 6 03:04:09 rpmi: python-module-enum34-1.1.6-alt3 1527251693 installed <13>Dec 6 03:04:09 rpmi: libnumpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed <13>Dec 6 03:04:10 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388758 installed <13>Dec 6 03:04:10 rpmi: liblapack-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed <13>Dec 6 03:04:10 rpmi: python-modules-curses-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:10 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed <13>Dec 6 03:04:10 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed <13>Dec 6 03:04:10 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed <13>Dec 6 03:04:10 rpmi: libdatrie-0.2.9-alt1_6 1511686677 installed <13>Dec 6 03:04:10 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed <13>Dec 6 03:04:10 rpmi: libsombok-2.4.0-alt1_8 sisyphus+226104.100.1.1 1554121176 installed <13>Dec 6 03:04:10 rpmi: perl-Unicode-Map-0.112-alt7.1 sisyphus+219907.5000.1.1 1548349925 installed <13>Dec 6 03:04:10 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed <13>Dec 6 03:04:10 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed <13>Dec 6 03:04:10 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed <13>Dec 6 03:04:10 rpmi: perl-XML-RegExp-0.04-alt1 1348526543 installed <13>Dec 6 03:04:10 rpmi: perl-DBI-1.642-alt1.1 sisyphus+219907.3200.1.1 1548345175 installed <13>Dec 6 03:04:10 rpmi: perl-Package-Stash-XS-0.29-alt1.1 sisyphus+219907.3400.1.1 1548345296 installed <13>Dec 6 03:04:10 rpmi: perl-Package-Stash-0.38-alt1 sisyphus.218845.100 1546250118 installed <13>Dec 6 03:04:10 rpmi: perl-Sub-Identify-0.14-alt1.2 sisyphus+219907.3700.1.1 1548345423 installed <13>Dec 6 03:04:10 rpmi: perl-Variable-Magic-0.62-alt1.2 sisyphus+219907.3600.1.1 1548345381 installed <13>Dec 6 03:04:10 rpmi: perl-B-Hooks-EndOfScope-0.24-alt1 1524680298 installed <13>Dec 6 03:04:10 rpmi: perl-namespace-clean-0.27-alt1 1464272543 installed <13>Dec 6 03:04:10 rpmi: perl-namespace-autoclean-0.28-alt1 1444994071 installed <13>Dec 6 03:04:10 rpmi: perl-Sub-Quote-2.006003-alt1 sisyphus+224895.100.1.1 1552434926 installed <13>Dec 6 03:04:10 rpmi: perl-Role-Tiny-2.000006-alt1 1513709006 installed <13>Dec 6 03:04:10 rpmi: perl-MRO-Compat-0.13-alt2 p9+261964.200.3.1 1606316246 installed <13>Dec 6 03:04:10 rpmi: perl-Class-Data-Inheritable-0.08-alt2 1316996762 installed <13>Dec 6 03:04:10 rpmi: perl-Exception-Class-1.44-alt1 1513614520 installed <13>Dec 6 03:04:10 rpmi: perl-PadWalker-2.3-alt1.2 sisyphus+219907.3500.1.1 1548345336 installed <13>Dec 6 03:04:10 rpmi: perl-Devel-Caller-2.06-alt2.2 sisyphus+219907.4000.1.1 1548345464 installed <13>Dec 6 03:04:10 rpmi: perl-Devel-LexAlias-0.05-alt3_17 sisyphus+219907.4100.1.1 1548345510 installed <13>Dec 6 03:04:10 rpmi: perl-Eval-Closure-0.14-alt1 1465147597 installed <13>Dec 6 03:04:10 rpmi: perl-Params-ValidationCompiler-0.30-alt1 1533170707 installed <13>Dec 6 03:04:10 rpmi: perl-Mail-Sendmail-0.80-alt1 1504118031 installed <13>Dec 6 03:04:10 rpmi: perl-Mail-Sender-1:0.903-alt1 1479576662 installed <13>Dec 6 03:04:10 rpmi: perl-Email-Date-Format-1.005-alt1 1413796337 installed <13>Dec 6 03:04:10 rpmi: ppp-common-0.5.1-alt1 1244040597 installed <13>Dec 6 03:04:10 rpmi: sendmail-common-1.7-alt3 1353029717 installed <13>Dec 6 03:04:10 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed <13>Dec 6 03:04:10 rpmi: perl-IPC-System-Simple-1.25-alt2_1 1388863478 installed <13>Dec 6 03:04:10 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>Dec 6 03:04:10 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>Dec 6 03:04:10 rpmi: perl-File-Copy-Recursive-0.44-alt1 1525447381 installed <13>Dec 6 03:04:10 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+219907.4500.1.1 1548349730 installed <13>Dec 6 03:04:10 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed <13>Dec 6 03:04:10 rpmi: perl-Compress-Raw-Bzip2-2.086-alt1 sisyphus+226394.100.1.2 1554269409 installed <13>Dec 6 03:04:10 rpmi: libdb4.7-devel-4.7.25-alt9 1490438456 installed <13>Dec 6 03:04:10 rpmi: perl-devel-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Dec 6 03:04:10 rpmi: perl-Test-Fatal-0.014-alt1 1418768336 installed <13>Dec 6 03:04:10 rpmi: perl-Specio-0.43-alt1 sisyphus.215861.100 1540964587 installed <13>Dec 6 03:04:10 rpmi: hd2u-1.0.3-alt2 1400842666 installed <13>Dec 6 03:04:10 rpmi: perl-Filter-1.59-alt1.1 sisyphus+219907.400.1.1 1548343225 installed <13>Dec 6 03:04:10 rpmi: perl-Encode-3.01-alt1 sisyphus+224923.100.1.1 1552474113 installed <13>Dec 6 03:04:10 rpmi: perl-URI-1.76-alt1 sisyphus+220243.100.1.1 1548863244 installed <13>Dec 6 03:04:10 rpmi: perl-HTML-Parser-3.72-alt1.2 sisyphus+219907.600.1.1 1548343407 installed <13>Dec 6 03:04:10 rpmi: perl-IO-Compress-2.086-alt1 sisyphus+226399.100.2.1 1554270186 installed <13>Dec 6 03:04:10 rpmi: perl-Net-HTTP-6.18-alt1 1526560501 installed <13>Dec 6 03:04:10 rpmi: perl-Pod-Simple-3.35-alt1 1482098090 installed <13>Dec 6 03:04:10 rpmi: perl-Pod-Usage-1.69-alt1 1464274721 installed <13>Dec 6 03:04:10 rpmi: perl-podlators-4.11-alt1 1525935408 installed <13>Dec 6 03:04:10 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>Dec 6 03:04:10 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>Dec 6 03:04:10 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed <13>Dec 6 03:04:10 rpmi: perl-HTTP-Message-6.18-alt1 1528288416 installed <13>Dec 6 03:04:10 rpmi: perl-HTTP-Cookies-6.04-alt1 1504116575 installed <13>Dec 6 03:04:10 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>Dec 6 03:04:10 rpmi: perl-libwww-6.39-alt1 sisyphus+229237.100.1.1 1557650051 installed <13>Dec 6 03:04:10 rpmi: perl-XML-Parser-2.44-alt2.2 sisyphus+219907.1300.1.1 1548343654 installed <13>Dec 6 03:04:10 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed <13>Dec 6 03:04:10 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed <13>Dec 6 03:04:10 rpmi: perl-XML-DOM-1.46-alt1 1474815568 installed <13>Dec 6 03:04:10 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed <13>Dec 6 03:04:10 rpmi: perl-HTML-Form-6.04-alt1 sisyphus+225750.100.1.1 1553678430 installed <13>Dec 6 03:04:10 rpmi: perl-WWW-Mechanize-1.91-alt1 sisyphus+219761.100.1.2 1548132822 installed <13>Dec 6 03:04:10 rpmi: perl-XML-Writer-0.625-alt1 1402417374 installed <13>Dec 6 03:04:10 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+223919.100.1.1 1551893088 installed <13>Dec 6 03:04:10 rpmi: perl-MIME-Types-2.17-alt1 1517533413 installed <13>Dec 6 03:04:10 rpmi: perl-Text-CSV_XS-1.39-alt1 sisyphus+225184.100.1.2 1552965519 installed <13>Dec 6 03:04:10 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed <13>Dec 6 03:04:10 rpmi: perl-MIME-Charset-1.012.2-alt1 1494353584 installed <13>Dec 6 03:04:10 rpmi: perl-Unicode-LineBreak-2019.001-alt1.1 sisyphus+219907.4700.1.1 1548349872 installed <13>Dec 6 03:04:10 rpmi: perl-YAML-Tiny-1.73-alt1 1520430664 installed <13>Dec 6 03:04:10 rpmi: perl-libintl-1.31-alt1.1 sisyphus+219907.6300.1.1 1548352427 installed <13>Dec 6 03:04:10 rpmi: libteckit-2.5.1-alt2.1 1319227424 installed <13>Dec 6 03:04:10 rpmi: libteckit-utils-2.5.1-alt2.1 1319227424 installed <13>Dec 6 03:04:10 rpmi: rgb-1.0.6-alt3 p9+229442.100.1.1 1557941137 installed <13>Dec 6 03:04:10 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed <13>Dec 6 03:04:10 rpmi: mailx-8.1.2-alt7 1366314831 installed <13>Dec 6 03:04:10 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed <13>Dec 6 03:04:10 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed <13>Dec 6 03:04:10 rpmi: libX11-locales-3:1.6.7-alt2 p9+258208.100.1.1 1600333167 installed <13>Dec 6 03:04:10 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949347 installed <13>Dec 6 03:04:10 rpmi: libxcb-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed <13>Dec 6 03:04:10 rpmi: libX11-3:1.6.7-alt2 p9+258208.100.1.1 1600333167 installed <13>Dec 6 03:04:10 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed <13>Dec 6 03:04:10 rpmi: libXrender-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed <13>Dec 6 03:04:10 rpmi: libXt-1.1.4-alt1 1369984716 installed <13>Dec 6 03:04:10 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed <13>Dec 6 03:04:10 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed <13>Dec 6 03:04:10 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614842 installed <13>Dec 6 03:04:10 rpmi: libXpm-3.5.12-alt1 sisyphus+223149.400.2.1 1551268300 installed <13>Dec 6 03:04:10 rpmi: libXi-1.7.9-alt2 sisyphus+226377.100.1.2 1554260258 installed <13>Dec 6 03:04:10 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949282 installed <13>Dec 6 03:04:10 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949136 installed <13>Dec 6 03:04:12 rpmi: libxcb-devel-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed <13>Dec 6 03:04:12 rpmi: libX11-devel-3:1.6.7-alt2 p9+258208.100.1.1 1600333167 installed <13>Dec 6 03:04:12 rpmi: libXrender-devel-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed <13>Dec 6 03:04:12 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed <13>Dec 6 03:04:12 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed <13>Dec 6 03:04:12 rpmi: libXaw-1.0.12-alt1 1391072621 installed <13>Dec 6 03:04:12 rpmi: libgd3-2.2.5-alt3 sisyphus+226800.200.2.1 1554649314 installed <13>Dec 6 03:04:12 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949214 installed <13>Dec 6 03:04:12 rpmi: perl-Tk-804.034-alt1.2 sisyphus+219907.4300.1.1 1548345831 installed <13>Dec 6 03:04:12 rpmi: libtk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Dec 6 03:04:12 rpmi: tk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Dec 6 03:04:12 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438593 installed <13>Dec 6 03:04:12 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949698 installed <13>Dec 6 03:04:12 rpmi: libXxf86vm-1.1.4-alt2 1527672159 installed <13>Dec 6 03:04:12 rpmi: libGLX-mesa-4:20.1.8-alt1 p9+260591.240.12.1 1606213200 installed <13>Dec 6 03:04:12 rpmi: libEGL-mesa-4:20.1.8-alt1 p9+260591.240.12.1 1606213200 installed <13>Dec 6 03:04:12 rpmi: libEGL-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:12 rpmi: libGLX-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:12 rpmi: libGL-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:12 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed <13>Dec 6 03:04:12 rpmi: libpango-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed <13>Dec 6 03:04:12 rpmi: libglvnd-devel-7:1.3.1-alt0.p9 p9+251991.160.19.1 1590834868 installed <13>Dec 6 03:04:12 rpmi: libEGL-devel-4:20.1.8-alt1 p9+260591.240.12.1 1606213200 installed <13>Dec 6 03:04:12 rpmi: libGL-devel-4:20.1.8-alt1 p9+260591.240.12.1 1606213200 installed <13>Dec 6 03:04:12 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268223 installed <13>Dec 6 03:04:12 rpmi: libXtst-1.2.3-alt1 p9+261891.100.2.1 1606149065 installed <13>Dec 6 03:04:12 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed <13>Dec 6 03:04:12 rpmi: xprop-1.2.4-alt1 sisyphus+225764.100.1.1 1553680701 installed <13>Dec 6 03:04:12 rpmi: xdg-utils-1.1.3-alt7 p9+259359.100.1.1 1602061025 installed <13>Dec 6 03:04:12 rpmi: liblz4-1:1.9.2-alt1 p9+238696.500.1.1 1570228072 installed <13>Dec 6 03:04:12 rpmi: libgpg-error-1.36-alt1 p9+261942.140.4.1 1606237682 installed <13>Dec 6 03:04:12 rpmi: libgcrypt20-1.8.5-alt3 p9+261942.200.4.1 1606237844 installed <13>Dec 6 03:04:12 rpmi: libxslt-1.1.34-alt1.p9.1 p9+261811.300.3.1 1605513910 installed <13>Dec 6 03:04:12 rpmi: libsystemd-1:243.9-alt1 p9+258476.300.4.1 1601997124 installed <13>Dec 6 03:04:12 rpmi: libdbus-1.12.16-alt2 p9+240607.100.1.1 1573553670 installed <13>Dec 6 03:04:12 rpmi: libavahi-0.8-alt1 p9+258828.100.4.1 1601912047 installed <13>Dec 6 03:04:12 rpmi: libcups-2.3.1-alt1 p9+247593.200.5.1 1585155224 installed <13>Dec 6 03:04:13 rpmi: libgtk+2-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Dec 6 03:04:13 rpmi: libgail-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Dec 6 03:04:13 rpmi: libgs-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Dec 6 03:04:14 rpmi: ghostscript-common-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Dec 6 03:04:14 rpmi: ghostscript-classic-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Dec 6 03:04:14 rpmi: ghostscript-module-X-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Dec 6 03:04:14 rpmi: gcc-fortran-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed <13>Dec 6 03:04:14 rpmi: libgfortran8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:15 rpmi: gcc8-fortran-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:15 rpmi: gcc-c++-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed <13>Dec 6 03:04:15 rpmi: libstdc++8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:16 rpmi: gcc8-c++-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Dec 6 03:04:17 rpmi: libicu65-1:6.5.1-alt1 p9+247371.14560.149.1 1590835589 installed <13>Dec 6 03:04:17 rpmi: icu-utils-1:6.5.1-alt1 p9+247371.14560.149.1 1590835589 installed <13>Dec 6 03:04:17 rpmi: libicu-devel-1:6.5.1-alt1 p9+247371.14560.149.1 1590835589 installed <13>Dec 6 03:04:17 rpmi: xml-utils-1:2.9.10-alt4 p9+261133.100.1.1 1604676294 installed <13>Dec 6 03:04:17 rpmi: rpm-build-gir-0.7.3-alt2 p9+234356.40.2.1 1562933848 installed <13>Dec 6 03:04:17 rpmi: ed-1:0.2-alt10 1449768441 installed <13>Dec 6 03:04:17 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed <13>Dec 6 03:04:17 rpmi: dialog-1.3.20171209-alt1 1529583087 installed <13>Dec 6 03:04:17 rpmi: libruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:17 rpmi: libp11-kit-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed <13>Dec 6 03:04:17 rpmi: libtasn1-4.14-alt1 p9+235792.100.2.1 1565425233 installed <13>Dec 6 03:04:17 rpmi: libyaml2-0.2.2-alt1 sisyphus+229134.100.1.1 1557342720 installed <13>Dec 6 03:04:17 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587848 installed <13>Dec 6 03:04:17 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Dec 6 03:04:17 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Dec 6 03:04:17 rpmi: libnss-3.56.0-alt1 p9+254920.30.20.1 1601657858 installed <13>Dec 6 03:04:17 rpmi: ca-certificates-2020.06.29-alt1 p9+258899.100.3.1 1601998604 installed <13>Dec 6 03:04:17 rpmi: ca-trust-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed <13>Dec 6 03:04:17 rpmi: p11-kit-trust-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed <13>Dec 6 03:04:17 rpmi: libcrypto1.1-1.1.1g-alt1 p9+250580.100.5.1 1588175208 installed <13>Dec 6 03:04:17 rpmi: libssl1.1-1.1.1g-alt1 p9+250580.100.5.1 1588175208 installed <13>Dec 6 03:04:17 rpmi: libpython3-3.7.4-alt3 p9+249932.100.2.1 1587126956 installed <13>Dec 6 03:04:17 rpmi: python3-3.7.4-alt3 p9+249932.100.2.1 1587126956 installed <13>Dec 6 03:04:18 rpmi: python3-base-3.7.4-alt3 p9+249932.100.2.1 1587126956 installed <86>Dec 6 03:04:18 groupadd[1727714]: group added to /etc/group: name=_keytab, GID=499 <86>Dec 6 03:04:18 groupadd[1727714]: group added to /etc/gshadow: name=_keytab <86>Dec 6 03:04:18 groupadd[1727714]: new group: name=_keytab, GID=499 <13>Dec 6 03:04:18 rpmi: libkrb5-1.17.2-alt1 p9+262110.100.3.1 1606242396 installed <13>Dec 6 03:04:18 rpmi: glib2-devel-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed <13>Dec 6 03:04:18 rpmi: libharfbuzz-devel-2.6.2-alt1 p9+238790.200.1.1 1570435797 installed <13>Dec 6 03:04:18 rpmi: libfreetype-devel-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed <13>Dec 6 03:04:18 rpmi: fontconfig-devel-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed <13>Dec 6 03:04:18 rpmi: python3-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed <13>Dec 6 03:04:18 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed <13>Dec 6 03:04:18 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed <13>Dec 6 03:04:18 rpmi: libtirpc-1.0.3-alt1 1532008015 installed <13>Dec 6 03:04:18 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed <13>Dec 6 03:04:18 rpmi: python-modules-encodings-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:18 rpmi: python-modules-compiler-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:18 rpmi: python-modules-email-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:18 rpmi: python-modules-unittest-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:18 rpmi: python-modules-nis-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-xml-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-ctypes-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed <13>Dec 6 03:04:19 rpmi: python-module-pkg_resources-1:40.8.0-alt2 sisyphus+229158.200.2.1 1557735221 installed <13>Dec 6 03:04:19 rpmi: python-modules-multiprocessing-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-logging-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-json-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-module-jinja2-2.11.2-alt1 p9+254838.40.14.1 1602882082 installed <13>Dec 6 03:04:19 rpmi: python-modules-hotshot-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-module-webencodings-0.5.1-alt1.1 1517943573 installed <13>Dec 6 03:04:19 rpmi: python-module-chardet-3.0.4-alt1 sisyphus+227476.1700.1.2 1555756717 installed <13>Dec 6 03:04:19 rpmi: python-tools-2to3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-module-future-0.16.0-alt2 sisyphus+228356.200.3.3 1556645013 installed <13>Dec 6 03:04:19 rpmi: python-module-pyglet-1.3.0-alt4.a1.hg20150730.1.1.1 1460413686 installed <13>Dec 6 03:04:19 rpmi: python-module-whoosh-2.7.4-alt1 1527697941 installed <13>Dec 6 03:04:19 rpmi: python-modules-bsddb-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-strict-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-modules-distutils-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:19 rpmi: python-module-numpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed <13>Dec 6 03:04:19 rpmi: python-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed <13>Dec 6 03:04:19 rpmi: python-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed <13>Dec 6 03:04:19 rpmi: python-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed <13>Dec 6 03:04:19 rpmi: python-module-docutils-0.14-alt2 1535729778 installed <13>Dec 6 03:04:19 rpmi: python-module-idna-2.8-alt1 sisyphus+227494.400.1.3 1555838720 installed <13>Dec 6 03:04:19 rpmi: python-module-pycparser-2.19-alt1 sisyphus+228366.1000.2.3 1556706938 installed <13>Dec 6 03:04:19 rpmi: python-module-cffi-1.12.3-alt1 sisyphus+229040.200.3.1 1557316502 installed <13>Dec 6 03:04:20 rpmi: python-module-asn1crypto-0.24.0-alt1 sisyphus+227473.1300.1.2 1555756512 installed <13>Dec 6 03:04:20 rpmi: python-module-ntlm-1.1.0-alt1.2 sisyphus+228512.100.1.1 1556654575 installed <13>Dec 6 03:04:20 rpmi: python-module-pytz-1:2016.10-alt1 1484291011 installed <13>Dec 6 03:04:20 rpmi: python-module-babel-1:2.6.0-alt1 sisyphus+228351.2400.6.2 1556652168 installed <13>Dec 6 03:04:20 rpmi: python-module-PyStemmer-1.0.1-alt1.2.1 1321387369 installed <13>Dec 6 03:04:20 rpmi: python-module-snowballstemmer-1.2.0-alt2.1 1457859319 installed <13>Dec 6 03:04:20 rpmi: python-module-simplejson-3.15.0-alt1.qa1 sisyphus+225625.16100.91.1 1555293606 installed <13>Dec 6 03:04:20 rpmi: python-module-ipaddress-1.0.18-alt1.1 sisyphus+227494.1700.1.3 1555839523 installed <13>Dec 6 03:04:20 rpmi: python-module-cryptography-2.6.1-alt1 sisyphus+225625.24400.91.1 1555299604 installed <13>Dec 6 03:04:20 rpmi: python-module-OpenSSL-18.0.0-alt1 1532996168 installed <13>Dec 6 03:04:20 rpmi: python-module-ndg-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed <13>Dec 6 03:04:20 rpmi: python-module-ndg-httpsclient-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed <13>Dec 6 03:04:20 rpmi: python-module-backports-3.5.0.1-alt1.1.1 1517645428 installed <13>Dec 6 03:04:20 rpmi: python-module-backports.ssl_match_hostname-3.5.0.1-alt1.1.1 1517645428 installed <13>Dec 6 03:04:20 rpmi: python-module-urllib3-2:1.25.6-alt1 p9+250567.200.5.1 1590420860 installed <13>Dec 6 03:04:20 rpmi: python-module-requests-2.23.0-alt1 p9+250567.400.5.1 1590420890 installed <13>Dec 6 03:04:20 rpmi: python-module-typing-3.6.6-alt2 sisyphus+220108.100.1.1 1548749697 installed <13>Dec 6 03:04:20 rpmi: python-modules-sqlite3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Dec 6 03:04:20 rpmi: python-module-SQLAlchemy-1.2.15-alt1 sisyphus+225625.4500.91.1 1555285684 installed <13>Dec 6 03:04:20 rpmi: python-module-py-1.8.0-alt2 sisyphus+228349.1400.4.1 1556631070 installed <13>Dec 6 03:04:20 rpmi: python-module-mpmath-0.19-alt1.git20150621.1.1.1.1 sisyphus+227503.2100.1.3 1555860908 installed <13>Dec 6 03:04:21 rpmi: python-module-sympy-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed <13>Dec 6 03:04:21 rpmi: python-module-sympy-tests-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed <13>Dec 6 03:04:21 rpmi: python-module-xapian-1.4.15-alt1 p9+258827.200.2.1 1601308059 installed <13>Dec 6 03:04:21 rpmi: python-module-sphinxcontrib-websupport-1.0.1-alt5 p9+247680.340.15.1 1585331199 installed <13>Dec 6 03:04:21 rpmi: python-module-alabaster-0.7.6-alt3 sisyphus+228351.700.4.1 1556637370 installed <13>Dec 6 03:04:21 rpmi: python-module-Pygments-2.2.0-alt2 1526455576 installed <13>Dec 6 03:04:21 rpmi: python-module-sphinx-1:1.6.5-alt8 p9+250806.100.2.1 1588178467 installed <86>Dec 6 03:04:21 groupadd[1729179]: group added to /etc/group: name=sasl, GID=498 <86>Dec 6 03:04:21 groupadd[1729179]: group added to /etc/gshadow: name=sasl <86>Dec 6 03:04:21 groupadd[1729179]: new group: name=sasl, GID=498 <13>Dec 6 03:04:21 rpmi: libsasl2-3-2.1.27-alt2.1 p9+256192.100.1.1 1597226707 installed <13>Dec 6 03:04:21 rpmi: libldap-2.4.54-alt0.M90P.1 p9+260357.200.2.1 1603585219 installed <13>Dec 6 03:04:21 rpmi: libcurl-7.71.0-alt1 p9+253931.100.3.1 1595484139 installed <13>Dec 6 03:04:21 rpmi: libpoppler90-0.80.0-alt1 p9+237607.100.1.1 1568643072 installed <13>Dec 6 03:04:21 rpmi: python3-module-genshi-0.7-alt2 sisyphus+229363.100.1.1 1557847321 installed <13>Dec 6 03:04:21 rpmi: python3-module-webencodings-0.5.1-alt1.1 1517943573 installed <13>Dec 6 03:04:21 rpmi: python3-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed <13>Dec 6 03:04:22 rpmi: python3-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed <13>Dec 6 03:04:22 rpmi: python3-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed <13>Dec 6 03:04:22 rpmi: python3-module-javapackages-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed <13>Dec 6 03:04:22 rpmi: rpm-build-java-1:5.0.0-alt1_12jpp8 sisyphus+228348.2100.3.3 1556657006 installed <13>Dec 6 03:04:22 rpmi: openssl-1.1.1g-alt1 p9+250580.100.5.1 1588175208 installed <13>Dec 6 03:04:22 rpmi: ruby-rubygems-update-3.0.4-alt1 p9+247371.35300.135.1 1590436206 installed <13>Dec 6 03:04:22 rpmi: gem-did-you-mean-1.3.0-alt2.1 p9+247371.40400.161.1 1591376055 installed <13>Dec 6 03:04:22 rpmi: gem-minitest-5.14.0-alt1.1 p9+247371.67710.170.1 1592235999 installed <13>Dec 6 03:04:22 rpmi: ruby-net-telnet-0.2.0-alt1 sisyphus+219345.2700.8.1 1547631566 installed <13>Dec 6 03:04:22 rpmi: gem-rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed <13>Dec 6 03:04:22 rpmi: ruby-xmlrpc-0.3.0-alt1 sisyphus+219345.3300.8.1 1547631818 installed <13>Dec 6 03:04:22 rpmi: gem-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:22 rpmi: ri-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Dec 6 03:04:22 rpmi: rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Dec 6 03:04:22 rpmi: ruby-rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Dec 6 03:04:22 rpmi: rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed <13>Dec 6 03:04:22 rpmi: erb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:22 rpmi: irb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:23 rpmi: gem-bundler-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed <13>Dec 6 03:04:23 rpmi: gem-test-unit-3.3.5-alt0.1 p9+247371.60440.162.1 1591424158 installed <13>Dec 6 03:04:23 rpmi: gem-power-assert-1.1.7-alt1 p9+247371.60200.162.1 1591424056 installed <13>Dec 6 03:04:23 rpmi: ruby-stdlibs-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:23 rpmi: bundle-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed <13>Dec 6 03:04:23 rpmi: ruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Dec 6 03:04:23 rpmi: perl-Net-SSLeay-1.86_09-alt2 sisyphus+227568.100.1.1 1555676534 installed <13>Dec 6 03:04:23 rpmi: perl-IO-Socket-SSL-2.066-alt1 sisyphus+223890.100.1.1 1551873760 installed <13>Dec 6 03:04:23 rpmi: perl-Net-HTTPS-6.18-alt1 1526560501 installed <13>Dec 6 03:04:23 rpmi: perl-LWP-Protocol-https-6.07-alt1 1494527383 installed <13>Dec 6 03:04:23 rpmi: perl-Net-SMTP-SSL-1.04-alt1 1479470835 installed <13>Dec 6 03:04:23 rpmi: perl-MailTools-2.20-alt1 1517533205 installed <13>Dec 6 03:04:23 rpmi: perl-MIME-Lite-3.030-alt1 1383865152 installed <13>Dec 6 03:04:23 rpmi: perl-Log-Dispatch-2.68-alt2 sisyphus.218872.100 1546338428 installed <13>Dec 6 03:04:23 rpmi: perl-Log-Log4perl-1.49-alt1 1489613295 installed <13>Dec 6 03:04:23 rpmi: ca-trust-java-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed <13>Dec 6 03:04:26 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Dec 6 03:04:26 rpmi: java-1.8.0-openjdk-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Dec 6 03:04:27 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Dec 6 03:04:27 rpmi: gambit-4.9.3-alt1 sisyphus+220998.100.1.4 1549742897 installed <13>Dec 6 03:04:27 rpmi: foomatic-db-engine-4.0.12-alt1 1449527980 installed <13>Dec 6 03:04:27 rpmi: ghostscript-utils-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Dec 6 03:04:28 rpmi: texlive-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Dec 6 03:04:39 rpmi: texlive-collection-basic-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Dec 6 03:04:39 rpmi: texlive-texmf-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Dec 6 03:05:32 rpmi: texlive-dist-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Dec 6 03:05:32 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed <13>Dec 6 03:05:32 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed <13>Dec 6 03:05:32 rpmi: libcurl-devel-7.71.0-alt1 p9+253931.100.3.1 1595484139 installed <13>Dec 6 03:05:32 rpmi: libpango-devel-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed <13>Dec 6 03:05:32 rpmi: gcc-c++-8-alt2 p9+246536.100.3.1 1582643803 installed <13>Dec 6 03:05:32 rpmi: gcc-fortran-8-alt2 p9+246536.100.3.1 1582643803 installed <13>Dec 6 03:05:32 rpmi: tk-devel-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Dec 6 03:05:32 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed <13>Dec 6 03:05:32 rpmi: makeinfo-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Dec 6 03:05:32 rpmi: liblapack-devel-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed <13>Dec 6 03:05:32 rpmi: libpcre-devel-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Dec 6 03:05:32 rpmi: libtre-devel-0.8.0-alt2.1 1334590818 installed <13>Dec 6 03:05:32 rpmi: libtiff-devel-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed <13>Dec 6 03:05:32 rpmi: texi2dvi-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Dec 6 03:05:32 rpmi: libjpeg-devel-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed <13>Dec 6 03:05:32 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686325 installed <13>Dec 6 03:05:32 rpmi: liblzma-devel-5.2.4-alt1 sisyphus+221902.5700.4.1 1550600683 installed <13>Dec 6 03:05:32 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-3.5.3-alt1.nosrc.rpm Installing R-base-3.5.3-alt1.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.27317 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-3.5.3 + echo 'Source #0 (R-3.5.3.tar):' Source #0 (R-3.5.3.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-3.5.3.tar + cd R-3.5.3 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-3.5.3-alt1.patch):' Patch #0 (R-3.5.3-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/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/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.27317 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.5.3 + export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=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 '' ']' ++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g' ++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' + ASFLAGS= + export ASFLAGS + export lt_cv_deplibs_check_method=pass_all + lt_cv_deplibs_check_method=pass_all + xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess + sort -u + xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n' + xargs -ri dirname -- '{}' + readlink -e -- ./configure + ./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-3.5' 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... 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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 f95 option to produce PIC... -fPIC checking if f95 PIC flag -fPIC works... yes checking if f95 static flag -static works... no checking if f95 supports -c -o file.o... yes checking if f95 supports -c -o file.o... (cached) yes checking whether the f95 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 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 dl.h usability... no checking dl.h presence... no checking for dl.h... no 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... unsupported checking how to get verbose linking output from f95... -v checking for Fortran 77 libraries of f95... -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 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking whether f95 appends underscores to external names... yes checking whether f95 appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether f95 and x86_64-alt-linux-gcc agree on int and double... yes checking whether f95 and x86_64-alt-linux-gcc agree on double complex... yes checking for f95 option to support OpenMP... unsupported checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes checking for x86_64-alt-linux-g++ option to support OpenMP... unsupported 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 whether C runtime needs -D__NO_MATH_INLINES... no 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 option providing pthread_kill... -pthread checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint 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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 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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 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate 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... unsupported checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for 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... no using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/f77_f2c config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules R is now configured for x86_64-alt-linux-gnu Source directory: . Installation directory: /usr C compiler: x86_64-alt-linux-gcc -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Fortran 77 compiler: f95 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Default C++ compiler: x86_64-alt-linux-g++ -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 90/95 compiler: x86_64-alt-linux-gfortran -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 -j8 make[1]: Nothing to be done for 'R'. make[1]: Nothing to be done for 'R'. make[2]: Nothing to be done for 'R'. make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts' creating src/scripts/R.fe make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/scripts' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/include' mkdir -p -- ../../include make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/include' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/include/R_ext' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making regcomp.d from regcomp.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making regerror.d from regerror.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-ast.d from tre-ast.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making regexec.d from regexec.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-match-approx.d from tre-match-approx.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-compile.d from tre-compile.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-match-backtrack.d from tre-match-backtrack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-match-parallel.d from tre-match-parallel.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-stack.d from tre-stack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making xmalloc.d from xmalloc.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-mem.d from tre-mem.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' making tre-parse.d from tre-parse.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o ranlib libtre.a make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/extra/tre' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making integrate.d from integrate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making maxcol.d from maxcol.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making interv.d from interv.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making pretty.d from pretty.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making uncmin.d from uncmin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' making optim.d from optim.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbfa.f -o dpbfa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c interv.c -o interv.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c maxcol.c -o maxcol.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pretty.c -o pretty.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbsl.f -o dpbsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dchdc.f -o dchdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpofa.f -o dpofa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dposl.f -o dposl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpodi.f -o dpodi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpoco.f -o dpoco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrls.f -o dqrls.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc.f -o dqrdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -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-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrutl.f -o dqrutl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrco.f -o dtrco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrsl.f -o dtrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' f95 -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-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c uncmin.c -o uncmin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making mlutils.d from mlutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making d1mach.d from d1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making fmax2.d from fmax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making fmin2.d from fmin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making i1mach.d from i1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making fprec.d from fprec.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making fround.d from fround.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making ftrunc.d from ftrunc.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making fsign.d from fsign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making sign.d from sign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making imax2.d from imax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making imin2.d from imin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making log1p.d from log1p.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making chebyshev.d from chebyshev.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making lgammacor.d from lgammacor.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making gammalims.d from gammalims.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making stirlerr.d from stirlerr.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making bd0.d from bd0.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making gamma.d from gamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making lgamma.d from lgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making gamma_cody.d from gamma_cody.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making beta.d from beta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making lbeta.d from lbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making polygamma.d from polygamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making cospi.d from cospi.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making bessel_j.d from bessel_j.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making bessel_i.d from bessel_i.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making bessel_k.d from bessel_k.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making bessel_y.d from bessel_y.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making choose.d from choose.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making snorm.d from snorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making sexp.d from sexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dgamma.d from dgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pgamma.d from pgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qgamma.d from qgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rgamma.d from rgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dbeta.d from dbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pbeta.d from pbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qbeta.d from qbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rbeta.d from rbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dunif.d from dunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making punif.d from punif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qunif.d from qunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making runif.d from runif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnorm.d from dnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnorm.d from pnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnorm.d from qnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rnorm.d from rnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dlnorm.d from dlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making plnorm.d from plnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qlnorm.d from qlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rlnorm.d from rlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making df.d from df.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pf.d from pf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rf.d from rf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qf.d from qf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnf.d from dnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dt.d from dt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pt.d from pt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qt.d from qt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rt.d from rt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnt.d from dnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dchisq.d from dchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pchisq.d from pchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qchisq.d from qchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rchisq.d from rchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dbinom.d from dbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rnchisq.d from rnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pbinom.d from pbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qbinom.d from qbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dcauchy.d from dcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rmultinom.d from rmultinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pcauchy.d from pcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rbinom.d from rbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qcauchy.d from qcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rcauchy.d from rcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dexp.d from dexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pexp.d from pexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qexp.d from qexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rexp.d from rexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dgeom.d from dgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qgeom.d from qgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pgeom.d from pgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rgeom.d from rgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dhyper.d from dhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making phyper.d from phyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qhyper.d from qhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rhyper.d from rhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnbinom.d from dnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnbinom.d from pnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnbinom.d from qnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rnbinom.d from rnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dpois.d from dpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making ppois.d from ppois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qpois.d from qpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rpois.d from rpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dweibull.d from dweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pweibull.d from pweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qweibull.d from qweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rweibull.d from rweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dlogis.d from dlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making plogis.d from plogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qlogis.d from qlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making rlogis.d from rlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnchisq.d from dnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnchisq.d from pnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnchisq.d from qnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making dnbeta.d from dnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnbeta.d from pnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnbeta.d from qnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnf.d from pnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making pnt.d from pnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnf.d from qnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qnt.d from qnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making ptukey.d from ptukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making qtukey.d from qtukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making toms708.d from toms708.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making wilcox.d from wilcox.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' making signrank.d from signrank.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmax2.c -o fmax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c i1mach.c -o i1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ftrunc.c -o ftrunc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mlutils.c -o mlutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmin2.c -o fmin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fround.c -o fround.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sign.c -o sign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fprec.c -o fprec.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c imax2.c -o imax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c log1p.c -o log1p.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c imin2.c -o imin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fsign.c -o fsign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chebyshev.c -o chebyshev.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gammalims.c -o gammalims.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgammacor.c -o lgammacor.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stirlerr.c -o stirlerr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bd0.c -o bd0.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgamma.c -o lgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c beta.c -o beta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gamma.c -o gamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lbeta.c -o lbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cospi.c -o cospi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sexp.c -o sexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c choose.c -o choose.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgamma.c -o dgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c snorm.c -o snorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c polygamma.c -o polygamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_i.c -o bessel_i.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_y.c -o bessel_y.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_k.c -o bessel_k.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_j.c -o bessel_j.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbeta.c -o dbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rgamma.c -o rgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pbeta.c -o pbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dunif.c -o dunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qunif.c -o qunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qgamma.c -o qgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c punif.c -o punif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c runif.c -o runif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbeta.c -o rbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pgamma.c -o pgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnorm.c -o rnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnorm.c -o dnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dlnorm.c -o dlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plnorm.c -o plnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qlnorm.c -o qlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnorm.c -o qnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlnorm.c -o rlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c df.c -o df.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnorm.c -o pnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rf.c -o rf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pf.c -o pf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qf.c -o qf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnf.c -o dnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dt.c -o dt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dchisq.c -o dchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pt.c -o pt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rt.c -o rt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnt.c -o dnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pchisq.c -o pchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qchisq.c -o qchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rchisq.c -o rchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qbeta.c -o qbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnchisq.c -o rnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pbinom.c -o pbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbinom.c -o dbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qt.c -o qt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dcauchy.c -o dcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pcauchy.c -o pcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qbinom.c -o qbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rmultinom.c -o rmultinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qcauchy.c -o qcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dexp.c -o dexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rcauchy.c -o rcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbinom.c -o rbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pexp.c -o pexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rexp.c -o rexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qexp.c -o qexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgeom.c -o dgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pgeom.c -o pgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rgeom.c -o rgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qgeom.c -o qgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dhyper.c -o dhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c phyper.c -o phyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qhyper.c -o qhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnbinom.c -o rnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnbinom.c -o pnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnbinom.c -o dnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ppois.c -o ppois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnbinom.c -o qnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpois.c -o dpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dweibull.c -o dweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pweibull.c -o pweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rhyper.c -o rhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rweibull.c -o rweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qpois.c -o qpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qweibull.c -o qweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dlogis.c -o dlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpois.c -o rpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlogis.c -o rlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plogis.c -o plogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qlogis.c -o qlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnchisq.c -o dnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnf.c -o pnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnbeta.c -o dnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnchisq.c -o qnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnbeta.c -o qnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnbeta.c -o pnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnf.c -o qnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnchisq.c -o pnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnt.c -o pnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnt.c -o qnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qtukey.c -o qtukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ptukey.c -o ptukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c signrank.c -o signrank.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c wilcox.c -o wilcox.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c toms708.c -o toms708.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o 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-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making Rembedded.d from Rembedded.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making dynload.d from dynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making X11.d from X11.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making system.d from system.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making sys-unix.d from sys-unix.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' making sys-std.d from sys-std.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rembedded.c -o Rembedded.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dynload.c -o dynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c X11.c -o X11.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c system.c -o system.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-unix.c -o sys-unix.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-std.c -o sys-std.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o ranlib libunix.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.5.3"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making CommandLineArgs.d from CommandLineArgs.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making Rdynload.d from Rdynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making RNG.d from RNG.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making Renviron.d from Renviron.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making agrep.d from agrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making altrep.d from altrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making apply.d from apply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making arithmetic.d from arithmetic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making array.d from array.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making attrib.d from attrib.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making bind.d from bind.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making builtin.d from builtin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making character.d from character.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making coerce.d from coerce.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making colors.d from colors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making complex.d from complex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making context.d from context.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making cum.d from cum.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making connections.d from connections.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making dcf.d from dcf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making datetime.d from datetime.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making debug.d from debug.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making deparse.d from deparse.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making devices.d from devices.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making dotcode.d from dotcode.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making dounzip.d from dounzip.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making dstruct.d from dstruct.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making duplicate.d from duplicate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making edit.d from edit.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making engine.d from engine.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making envir.d from envir.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making errors.d from errors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making format.d from format.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making gevents.d from gevents.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making eval.d from eval.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making gram-ex.d from gram-ex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making gram.d from gram.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making graphics.d from graphics.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making grep.d from grep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making identical.d from identical.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making inlined.d from inlined.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making inspect.d from inspect.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making internet.d from internet.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making iosupport.d from iosupport.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making lapack.d from lapack.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making localecharset.d from localecharset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making list.d from list.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making logic.d from logic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making mapply.d from mapply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making match.d from match.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making main.d from main.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making names.d from names.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making memory.d from memory.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making objects.d from objects.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making options.d from options.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making paste.d from paste.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making plot.d from plot.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making plot3d.d from plot3d.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making printvector.d from printvector.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making print.d from print.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making platform.d from platform.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making printarray.d from printarray.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making plotmath.d from plotmath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making printutils.d from printutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making radixsort.d from radixsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making qsort.d from qsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making random.d from random.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making raw.d from raw.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making rlocale.d from rlocale.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making registration.d from registration.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making relop.d from relop.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making scan.d from scan.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making saveload.d from saveload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making seq.d from seq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making sort.d from sort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making split.d from split.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making source.d from source.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making sprintf.d from sprintf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making serialize.d from serialize.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making startup.d from startup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making subassign.d from subassign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making subscript.d from subscript.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making subset.d from subset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making summary.d from summary.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making times.d from times.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making sysutils.d from sysutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making unique.d from unique.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making alloca.d from alloca.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making version.d from version.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making g_alab_her.d from g_alab_her.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making Rmain.d from Rmain.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making g_cntrlify.d from g_cntrlify.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making g_fontdb.d from g_fontdb.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making g_her_glyph.d from g_her_glyph.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making strncasecmp.d from strncasecmp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making strdup.d from strdup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making util.d from util.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' making mkdtemp.d from mkdtemp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c builtin.c -o builtin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c attrib.c -o attrib.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bind.c -o bind.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c array.c -o array.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c arithmetic.c -o arithmetic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coerce.c -o coerce.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o deparse.c: In function 'deparse2buff': deparse.c:1443:8: warning: 'doquote' may be used uninitialized in this function [-Wmaybe-uninitialized] if(doquote) ^ make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dotcode.c -o dotcode.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gevents.c -o gevents.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gram-ex.c -o gram-ex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c identical.c -o identical.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c errors.c -o errors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c engine.c -o engine.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c inlined.c -o inlined.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c inspect.c -o inspect.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lapack.c -o lapack.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c iosupport.c -o iosupport.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c internet.c -o internet.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c connections.c -o connections.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c list.c -o list.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c localecharset.c -o localecharset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mapply.c -o mapply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c match.c -o match.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c main.c -o main.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c envir.c -o envir.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c logic.c -o logic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c names.c -o names.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gram.c -o gram.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c options.c -o options.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c paste.c -o paste.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c objects.c -o objects.o make[3]: 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-I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c platform.c -o platform.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qsort.c -o qsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c registration.c -o registration.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: 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-I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c source.c -o source.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -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-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c saveload.c -o saveload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' 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-I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c version.c -o version.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sysutils.c -o sysutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: 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g_cntrlify.c -o g_cntrlify.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xxxpr.f -o xxxpr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subset.c -o subset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unique.c -o unique.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subassign.c -o subassign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c eval.c -o eval.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' x86_64-alt-linux-gcc -shared -pthread -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.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 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/bin/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/lib make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rmain.c -o Rmain.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' x86_64-alt-linux-gcc -Wl,--export-dynamic -pthread -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o -lR make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' making rotated.d from rotated.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making Rsock.d from Rsock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' making rbitmap.d from rbitmap.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making Rhttpd.d from Rhttpd.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' making Lapack.d from Lapack.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making internet.d from internet.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making libcurl.d from libcurl.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making sock.d from sock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making nanohttp.d from nanohttp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making nanoftp.d from nanoftp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' making sockconn.d from sockconn.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' making devX11.d from devX11.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o nanoftp.o nanohttp.o sock.o sockconn.o -lcurl -lR make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' mkdir -p -- /usr/src/RPM/BUILD/R-3.5.3/modules make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbitmap.c -o rbitmap.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rotated.c -o rotated.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Lapack.c -o Lapack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o lapack.so Lapack.o -lR -llapack -lopenblas -lgfortran -lm -lquadmath make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devX11.c -o devX11.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o R_X11.so devX11.o rotated.o rbitmap.o -ltiff -ljpeg -lpng16 -lz -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -I/usr/include/libpng16 -I. -I../../../src/include -I../../../src/include -I/usr/include/pango-1.0 -I/usr/include/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 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dataentry.c -o dataentry.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' x86_64-alt-linux-gcc -shared -L"../../../lib" -L/usr/local/lib64 -o R_de.so dataentry.o -lSM -lICE -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -lX11 -lXext -lX11 -lXt -lXmu -lR -lm make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/modules/X11' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library' mkdir -p -- ../../library make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/profile' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/translations' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' building package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making md5.d from md5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making text.d from text.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making Rmd5.d from Rmd5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making http.d from http.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making install.d from install.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making signals.d from signals.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making getfmts.d from getfmts.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making gramLatex.d from gramLatex.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' making gramRd.d from gramRd.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rmd5.c -o Rmd5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c http.c -o http.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c signals.c -o signals.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c md5.c -o md5.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c install.c -o install.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c getfmts.c -o getfmts.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c text.c -o text.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gramLatex.c -o gramLatex.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gramRd.c -o gramRd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/compiler' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' mkdir -p -- ../../../library/utils/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making sock.d from sock.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making size.d from size.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' making io.d from io.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sock.c -o sock.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c size.c -o size.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c io.c -o io.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o utils.so init.o io.o size.o sock.o stubs.o utils.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/utils' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' mkdir -p -- ../../../library/grDevices/afm mkdir -p -- ../../../library/grDevices/enc mkdir -p -- ../../../library/grDevices/icc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making chull.d from chull.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making axis_scales.d from axis_scales.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making devices.d from devices.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making colors.d from colors.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making devCairo.d from devCairo.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making devQuartz.d from devQuartz.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making devPicTeX.d from devPicTeX.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' making devPS.d from devPS.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stubs.c -o stubs.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c axis_scales.c -o axis_scales.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devCairo.c -o devCairo.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devQuartz.c -o devQuartz.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chull.c -o chull.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devPS.c -o devPS.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src' make[7]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[7]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo' x86_64-alt-linux-gcc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/include/pango-1.0 -I/usr/include/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 -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-3.5.3/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo' x86_64-alt-linux-gcc -shared -L"../../../../../lib" -L/usr/local/lib64 -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -ltiff -ljpeg -lpng16 -lz -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lharfbuzz -lpng16 -lz -lcairo -L"../../../../../lib" -lR -lm make[9]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices/src/cairo' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grDevices' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making stem.d from stem.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making base.d from base.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making par.d from par.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making plot.d from plot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making plot3d.d from plot3d.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' making graphics.d from graphics.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stem.c -o stem.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c base.c -o base.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c par.c -o par.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/graphics' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making kmeans.d from kmeans.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making ansari.d from ansari.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making bandwidths.d from bandwidths.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making chisqsim.d from chisqsim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making d2x2xk.d from d2x2xk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making kendall.d from kendall.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making fexact.d from fexact.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making line.d from line.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making ks.d from ks.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making swilk.d from swilk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making prho.d from prho.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making smooth.d from smooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making ksmooth.d from ksmooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making loessc.d from loessc.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making monoSpl.d from monoSpl.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making isoreg.d from isoreg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making dblcen.d from dblcen.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making Srunmed.d from Srunmed.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making distance.d from distance.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making hclust-utils.d from hclust-utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making nls.d from nls.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making HoltWinters.d from HoltWinters.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making PPsum.d from PPsum.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making rWishart.d from rWishart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making arima.d from arima.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making burg.d from burg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making filter.d from filter.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making mAR.d from mAR.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making pacf.d from pacf.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making starma.d from starma.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making family.d from family.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making port.d from port.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making sbart.d from sbart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making approx.d from approx.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making loglin.d from loglin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making massdist.d from massdist.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making lowess.d from lowess.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making lm.d from lm.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making complete_cases.d from complete_cases.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making cov.d from cov.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making fft.d from fft.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making deriv.d from deriv.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making fourier.d from fourier.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making model.d from model.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making optim.d from optim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making integrate.d from integrate.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making zeroin.d from zeroin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making optimize.d from optimize.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making rcont.d from rcont.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making random.d from random.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making influence.d from influence.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' making distn.d from distn.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kmeans.c -o kmeans.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c prho.c -o prho.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c line.c -o line.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ks.c -o ks.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ksmooth.c -o ksmooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c monoSpl.c -o monoSpl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c smooth.c -o smooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dblcen.c -o dblcen.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c isoreg.c -o isoreg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessc.c -o loessc.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nls.c -o nls.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c filter.c -o filter.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c family.c -o family.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c massdist.c -o massdist.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loglin.c -o loglin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.o loessf.f:59:14: j=DBLE(j)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1893:14: 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:1398:20: i=phi(pi(ii)) 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:927:12: lg=DBLE(lg)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:522:22: 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:1204:13: ifloor=x 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:834:22: 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:1582:18: 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:472:25: 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:472:39: 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:827:31: subroutine ehg197(deg,tau,d,f,dk,trl) 1 Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument] loessf.f:1984:31: 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:1984:47: 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:1984:53: 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:1497:50: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1497:53: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1648:30: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1648:33: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1667:39: 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:1667:42: 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:1699:30: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1699:33: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1721:33: subroutine lowesr(yy,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1721:36: 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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o portsrc.f:6446:0: NCOMP = NCOMP + 1 Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:6357:0: 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:5340:0: 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:5477:0: IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310 Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10115:0: V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA) Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10032:0: 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:10027:0: LK = DMAX1(LK, PHI*W(PHIPIN)) Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10169:0: IF (KA .GE. KAMIN) GO TO 340 Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11936:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11939:0: V(DST0) = DNWTST Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2392:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2391:0: 60 V(DST0) = DS0 Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:7913:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:7912:0: 90 V(DST0) = DS0 Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8391:0: 210 IV(FDH) = HES Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:3464:0: IF (LIV .LT. MIV2) GO TO 300 Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:11772:0: 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:440:0: 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-3.5.3/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making class_support.d from class_support.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making methods_list_dispatch.d from methods_list_dispatch.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making slot.d from slot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making tests.d from tests.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c class_support.c -o class_support.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c slot.c -o slot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tests.c -o tests.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/methods' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making gpar.d from gpar.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making grid.d from grid.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making just.d from just.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making layout.d from layout.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making matrix.d from matrix.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making register.d from register.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making unit.d from unit.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making state.d from state.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making util.d from util.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' making viewport.d from viewport.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gpar.c -o gpar.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c register.c -o register.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c just.c -o just.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c state.c -o state.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c layout.c -o layout.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c viewport.c -o viewport.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unit.c -o unit.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c grid.c -o grid.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' 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-3.5.3/src/library/grid/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/grid' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/splines' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/stats4' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' making init.d from init.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' making tcltk_unix.d from tcltk_unix.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' making tcltk.d from tcltk.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/include -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tcltk.c -o tcltk.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/lib64 -ltcl8.6 -lpthread -L/usr/lib64 -ltk8.6 -lX11 -lm -L../../../../lib -lR make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' mkdir -p -- ../../../../library/tcltk/libs make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' byte-compiling package 'tcltk' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/tcltk' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' building package 'parallel' mkdir -p -- ../../../library/parallel mkdir -p -- ../../../library/parallel/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' mkdir -p -- ../../../library/parallel/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' making rngstream.d from rngstream.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' making fork.d from fork.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rngstream.c -o rngstream.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fork.c -o fork.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' mkdir -p -- ../../../../library/parallel/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' byte-compiling package 'parallel' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/parallel' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library' installing parsed NAMESPACE files make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library' make[1]: Nothing to be done for 'R'. make: Entering directory '/usr/src/RPM/BUILD/R-3.5.3' you should 'make docs' now ... make: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3' configuring Java ... Java interpreter : /usr/lib/jvm/java/jre/bin/java Java version : 1.8.0_212 Java home path : /usr/lib/jvm/java Java compiler : /usr/lib/jvm/java/bin/javac Java headers gen.: /usr/lib/jvm/java/bin/javah Java archive tool: /usr/lib/jvm/java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm make[2]: Entering directory '/usr/src/tmp/Rjavareconf.66IJxE' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c conftest.c -o conftest.o x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib/jvm/java/jre/lib/amd64/server -ljvm -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[2]: Leaving directory '/usr/src/tmp/Rjavareconf.66IJxE' JAVA_HOME : /usr/lib/jvm/java Java library path: $(JAVA_HOME)/jre/lib/amd64/server JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm Updating Java configuration in /usr/src/RPM/BUILD/R-3.5.3 Done. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc' creating doc/NEWS make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc' creating doc/NEWS.pdf make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' creating doc/manual/version.texi make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' creating doc/manual/R-FAQ.html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory 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lower.tri html ls html make.names html make.unique html mapply html margin.table html mat.or.vec html match html match.arg html match.call html match.fun html matmult html matrix html maxCol html mean html memCompress html memory.profile html merge html message html missing html mode html name html names html nargs html nchar html nlevels html noquote html norm html normalizePath html notyet html nrow html ns-dblcolon html ns-hooks html ns-internal html ns-load html ns-reflect html ns-topenv html numeric html numeric_version html octmode html on.exit html options html order html outer html parse html paste html path.expand html pcre_config html pmatch html polyroot html pos.to.env html pretty html print html Rd warning: /usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/src/library/tools/man/check_packages_in_dir.Rd:121: 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 update_pkg_po html vignetteDepends html vignetteEngine html writePACKAGES html xgettext html converting help for package 'utils' BATCH html INSTALL html PkgUtils html Question html REMOVE html RHOME html RShowDoc html RSiteSearch 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 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 chooseBioCmirror html chooseCRANmirror html citEntry html citation html cite 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 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 menu html methods html mirrorAdmin html modifyList html news 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 recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories 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 write.table html zip html COMPILE html LINK html memory.size html nsl 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 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 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 recordGraphics html recordplot html rgb html rgb2hsv html trans3d html xfig html xy.coords html xyTable html xyz.coords html png html quartz html quartzFonts html savePlot html x11 html x11Fonts 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 Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html npk html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Classes_Details html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html Introduction html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html Methods_Details html Methods_for_Nongenerics html Methods_for_S3 html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html removeMethod html representation html selectSuperClasses html setAs html setClass html setClassUnion html setGeneric html setGroupGeneric html setIs html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html calcStringMetric html current.viewport html dataViewport html depth html drawDetails html editDetails html explode html gEdit html gPath html getNames html gpar html grid-defunct html grid-internal html grid-package html grid.DLapply html grid.add html grid.bezier html grid.cap html grid.circle html grid.clip html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grep html grid.grill html grid.grob html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobName html grobWidth html grobX html legendGrob html makeContent html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html valid.just html validDetails html viewport html viewports html vpPath html widthDetails html xDetails html xsplinePoints html converting help for package 'splines' asVector html backSpline html bs html interpSpline html ns html periodicSpline html polySpline html predict.bSpline html predict.bs html splineDesign html splineKnots html splineOrder html splines-package html xyVector html converting help for package 'stats4' coef-methods html confint-methods html logLik-methods html mle-class html mle html plot-methods html profile-methods html profile.mle-class html show-methods html stats4-package html summary-methods html summary.mle-class html update-methods html vcov-methods html converting help for package 'tcltk' TclInterface html TkCommands html TkWidgetcmds html TkWidgets html tclServiceMode html tcltk-defunct html tcltk-package html tkProgressBar html tkStartGUI html tk_choose.dir html tk_choose.files html tk_messageBox html tk_select.list html tkpager html converting help for package 'compiler' compile html converting help for package 'parallel' RngStream html clusterApply html detectCores html makeCluster html parallel-package html splitIndices html children html mcaffinity html mcfork html mclapply html mcparallel html pvec html make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package MASS make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package lattice make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package codetools make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package foreign make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package KernSmooth make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package rpart make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package nnet make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package spatial make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpyYENci/R.INSTALL1fbb145864929b/nnet/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpyYENci/R.INSTALL1fbb145864929b/nnet/src' make[3]: Entering directory '/usr/src/tmp/RtmpyYENci/R.INSTALL1fbb145864929b/nnet/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpyYENci/R.INSTALL1fbb145864929b/nnet/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html nnet html predict.nnet html which.is.max html ** building package indices ** testing if installed package can be loaded * DONE (nnet) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpaLBmYl/R.INSTALL1fbb526d64bf0/spatial/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html ppregion html predict.trls html prmat html semat html surf.gls html surf.ls html trls.influence html trmat html variogram html ** building package indices ** testing if installed package can be loaded * DONE (spatial) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgedi.f -o dgedi.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgefa.f -o dgefa.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin2D.f -o linbin2D.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpbeBDJe/R.INSTALL1fbb0d6699dfe5/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html bkfe html dpih html dpik html dpill html locpoly html ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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 make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbfopen.c -o dbfopen.o make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c minitab.c -o minitab.o make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c spss.c -o spss.o make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stataread.c -o stataread.o make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpGszFAe/R.INSTALL1fbb0873ae0e1e/foreign/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpart.c -o rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown.c -o rundown.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown2.c -o rundown2.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c surrogate.c -o surrogate.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c usersplit.c -o usersplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpaumRze/R.INSTALL1fbb1023788c39/rpart/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder html stagec html summary.rpart html text.rpart html xpred.rpart html ** 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-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' make[3]: Entering directory '/usr/src/tmp/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpXaIMLe/R.INSTALL1fbb01657e3e60/MASS/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html Animals html Boston html Cars93 html Cushings html DDT html GAGurine html Insurance html MASS-internal html Melanoma html Null html OME html Pima.tr html Rabbit html Rubber html SP500 html Sitka html Sitka89 html Skye html Traffic html UScereal html UScrime html VA html abbey html accdeaths html addterm html anorexia html anova.negbin html area html bacteria html bandwidth.nrd html bcv html beav1 html beav2 html biopsy html birthwt html boxcox html cabbages html caith html cats html cement html chem html con2tr html confint html contr.sdif html coop html corresp html cov.rob html cov.trob html cpus html crabs html deaths html denumerate html dose.p html drivers html dropterm html eagles html epil html eqscplot html farms html fgl html fitdistr html forbes html fractions html galaxies html gamma.dispersion html gamma.shape.glm html gehan html genotype html geyser html gilgais html ginv html glm.convert html glm.nb html glmmPQL html hills html hist.scott html housing html huber html hubers html immer html isoMDS html kde2d html lda html ldahist html leuk html lm.gls html lm.ridge html loglm html loglm1 html logtrans html lqs html mammals html mca html mcycle html menarche html michelson html minn38 html motors html muscle html mvrnorm html negative.binomial html newcomb html nlschools html npk html npr1 html oats html painters html pairs.lda html parcoord html petrol html phones html plot.lda html plot.mca html plot.profile html polr html predict.glmmPQL html predict.lda html predict.lqs html predict.mca html predict.qda html profile.glm html qda html quine html rational html renumerate html rlm html rms.curv html rnegbin html road html rotifer html sammon html ships html shoes html shrimp html shuttle html snails html stdres html steam html stepAIC html stormer html studres html summary.loglm html summary.negbin html summary.rlm html survey html synth.tr html theta.md html topo html truehist html ucv html waders html whiteside html width.SJ html write.matrix html wtloss html ** building package indices ** testing if installed package can be loaded * DONE (MASS) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package cluster make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package class make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' make[3]: Entering directory '/usr/src/tmp/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' make[3]: Entering directory '/usr/src/tmp/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmp8mWvKe/R.INSTALL1fbb045356ab90/lattice/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' finding HTML links ... done Lattice html Rows html USMortality html axis.default html banking html barchart.table html barley html cloud html draw.colorkey html draw.key html environmental html ethanol html histogram html interaction html lattice.options html latticeParseFormula html level.colors html levelplot html llines html lset html make.groups html melanoma html oneway html packet.panel.default html panel.axis html panel.barchart html panel.bwplot html panel.cloud html panel.densityplot html panel.dotplot html panel.functions html panel.histogram html panel.levelplot html panel.loess html panel.number html panel.pairs html panel.parallel html panel.qqmath html panel.qqmathline html panel.smoothScatter html panel.spline html panel.stripplot html panel.superpose html panel.violin html panel.xyplot html prepanel.default html prepanel.functions html print.trellis html qq html qqmath html rfs html shingles html simpleKey html simpleTheme html singer html splom html strip.default html tmd html trellis.device html trellis.object html trellis.par.get html update.trellis html utilities.3d html xyplot html xyplot.ts html ** building package indices ** testing if installed package can be loaded * DONE (lattice) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package Matrix make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package nlme make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpOkEjnQ/R.INSTALL1fc1231cd56c93/class/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpOkEjnQ/R.INSTALL1fc1231cd56c93/class/src' make[3]: Entering directory '/usr/src/tmp/RtmpOkEjnQ/R.INSTALL1fc1231cd56c93/class/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpOkEjnQ/R.INSTALL1fc1231cd56c93/class/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html batchSOM html condense html knn html knn.cv html knn1 html lvq1 html lvq2 html lvq3 html lvqinit html lvqtest html multiedit html olvq1 html reduce.nn html somgrid html ** building package indices ** testing if installed package can be loaded * DONE (class) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o make[3]: Leaving directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o make[3]: Leaving directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mona.c -o mona.o mona.c: In function 'clmona_': mona.c:261:10: warning: 'nelbb' may be used uninitialized in this function [-Wmaybe-uninitialized] ner[k] = nelbb; ~~~~~~~^~~~~~~ mona.c:248:7: warning: 'lcc' may be used uninitialized in this function [-Wmaybe-uninitialized] int lcc, nelbb; ^~~ mona.c:234:6: warning: 'jtelz' may be used uninitialized in this function [-Wmaybe-uninitialized] int jres = kb - ka + 1 - jtel2, ^~~~ mona.c:234:6: warning: 'jtel' may be used uninitialized in this function [-Wmaybe-uninitialized] mona.c:227:18: warning: 'jma' may be used uninitialized in this function [-Wmaybe-uninitialized] if (x[nel + jma * x_dim1] == 1) { ~~~~^~~~~~~~ mona.c:211:8: warning: 'd' may be used uninitialized in this function [-Wmaybe-uninitialized] jtel = c + d; ~~~~~^~~~~~~ mona.c:211:8: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized] mona.c:212:9: warning: 'b' may be used uninitialized in this function [-Wmaybe-uninitialized] jtelz = a + b; ~~~~~~^~~~~~~ mona.c:212:9: warning: 'a' may be used uninitialized in this function [-Wmaybe-uninitialized] make[3]: Leaving directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html agnes.object html agriculture html animals html bannerplot html chorSub html clara html clara.object html clusGap html clusplot.default html Rd warning: /usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic clusplot.partition html cluster-internal html coef.hclust html daisy html diana html dissimilarity.object html ellipsoidhull html Rd warning: /usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/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/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic fanny html fanny.object html flower html lower.to.upper.tri.inds html mona html mona.object html pam html pam.object html partition.object html plantTraits html plot.agnes html Rd warning: /usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic plot.diana html plot.mona html plot.partition html pltree html pluton html predict.ellipsoid html print.agnes html print.clara html print.diana html print.dissimilarity html Rd warning: /usr/src/tmp/RtmpqVe6pQ/R.INSTALL1fc12115c26916/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic print.fanny html print.mona html print.pam html ruspini html silhouette html sizeDiss html summary.agnes html summary.clara html summary.diana html summary.mona html summary.pam html twins.object html volume.ellipsoid html votes.repub html xclara html ** building package indices ** testing if installed package can be loaded * DONE (cluster) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o make[3]: Leaving directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' f95 -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o make[3]: Leaving directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpPFQVCY/R.INSTALL1fc1b12651d628/nlme/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html ACF.lme html Alfalfa html Assay html BodyWeight html Cefamandole html Coef html Covariate html Covariate.varFunc html Dialyzer html Dim html Dim.corSpatial html Dim.corStruct html Dim.pdMat html Earthquake html Extract.pdMat html Fatigue html Gasoline html Glucose html Glucose2 html Gun html IGF html Initialize html Initialize.corStruct html Initialize.glsStruct html Initialize.lmeStruct html Initialize.reStruct html Initialize.varFunc html LDEsysMat html Machines html MathAchSchool html MathAchieve html Matrix html Matrix.pdMat html Matrix.reStruct html Meat html Milk html Muscle html Names html Names.formula html Names.pdBlocked html Names.pdMat html Names.reStruct html Nitrendipene html Oats html Orthodont html Ovary html Oxboys html Oxide html PBG html Phenobarb html Pixel html Quinidine html Rail html RatPupWeight html Relaxin html Remifentanil html Soybean html Spruce html Tetracycline1 html Tetracycline2 html VarCorr html Variogram html Variogram.corExp html Variogram.corGaus html Variogram.corLin html Variogram.corRatio html Variogram.corSpatial html Variogram.corSpher html Variogram.default html Variogram.gls html Variogram.lme html Wafer html Wheat html Wheat2 html allCoef html anova.gls html anova.lme html as.matrix.corStruct html as.matrix.pdMat html as.matrix.reStruct html asOneFormula html asTable html augPred html balancedGrouped html bdf html coef.corStruct html coef.gnls html coef.lmList html coef.lme html coef.modelStruct html coef.pdMat html coef.reStruct html coef.varFunc html collapse html collapse.groupedData html compareFits html comparePred html corAR1 html corARMA html corCAR1 html corClasses html corCompSymm html corExp html corFactor html corFactor.corStruct html corGaus html corLin html corMatrix html corMatrix.corStruct html corMatrix.pdMat html corMatrix.reStruct html corNatural html corRatio html corSpatial html corSpher html corSymm html ergoStool html fdHess html fitted.glsStruct html fitted.gnlsStruct html fitted.lmList html fitted.lme html fitted.lmeStruct html fitted.nlmeStruct html fixed.effects html fixef.lmList html formula.pdBlocked html formula.pdMat html formula.reStruct html gapply html getCovariate html getCovariate.corStruct html getCovariate.data.frame html getCovariate.varFunc html getCovariateFormula html getData html getData.gls html getData.lmList html getData.lme html getGroups html getGroups.corStruct html getGroups.data.frame html getGroups.gls html getGroups.lmList html getGroups.lme html getGroups.varFunc html getGroupsFormula html getResponse html getResponseFormula html getVarCov html gls-internal html gls html glsControl html glsObject html glsStruct html gnls html gnlsControl html gnlsObject html gnlsStruct html groupedData html gsummary html intervals html intervals.gls html intervals.lmList html intervals.lme html isBalanced html isInitialized html lmList html lmList.groupedData html lme html lme.groupedData html lme.lmList html lmeControl html lmeObject html lmeStruct html logDet html logDet.corStruct html logDet.pdMat html logDet.reStruct html logLik.corStruct html logLik.glsStruct html logLik.gnls html logLik.gnlsStruct html logLik.lmList html logLik.lme html logLik.lmeStruct html logLik.reStruct html logLik.varFunc html model.matrix.reStruct html needUpdate html needUpdate.modelStruct html nlme html nlme.nlsList html nlmeControl html nlmeObject html nlmeStruct html nlsList html nlsList.selfStart html pairs.compareFits html pairs.lmList html pairs.lme html pdBlocked html pdClasses html pdCompSymm html pdConstruct html pdConstruct.pdBlocked html pdDiag html pdFactor html pdFactor.reStruct html pdIdent html pdLogChol html pdMat html pdMatrix html pdMatrix.reStruct html pdNatural html pdSymm html phenoModel html plot.ACF html plot.Variogram html plot.augPred html plot.compareFits html plot.gls html plot.intervals.lmList html plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html pooledSD html predict.gls html predict.gnls html predict.lmList html predict.lme html predict.nlme html print.summary.pdMat html print.varFunc html qqnorm.gls html qqnorm.lme html quinModel html random.effects html ranef.lmList html ranef.lme html reStruct html recalc html recalc.corStruct html recalc.modelStruct html recalc.reStruct html recalc.varFunc html residuals.gls html residuals.glsStruct html residuals.gnlsStruct html residuals.lmList html residuals.lme html residuals.lmeStruct html residuals.nlmeStruct html simulate.lme html solve.pdMat html solve.reStruct html splitFormula html summary.corStruct html summary.gls html summary.lmList html summary.lme html summary.modelStruct html summary.nlsList html summary.pdMat html summary.varFunc html update.modelStruct html update.varFunc html varClasses html varComb html varConstPower html 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-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' ( cd Lib ; make clean ) make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' ( cd Source ; make clean ) ( cd Source ; make clean ) make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile ) make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/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-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/CHOLMOD/Lib' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/COLAMD/Source' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.5.3/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/AMD/Source' make[4]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/SuiteSparse_config' ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src/SuiteSparse_config' make[3]: Entering directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/Matrix/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html KhatriRao html LU-class html Matrix-class html Matrix html MatrixClass html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html Rd warning: /usr/src/tmp/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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/Rtmp5YhUEY/R.INSTALL1fc1af3c9ecb7/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 Loading required package: Matrix ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package survival make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package mgcv make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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:531:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized] if (start[p1] < dtime) break; ^ make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit5.c -o agfit5.o make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxexact.c -o coxexact.o make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gchol.c -o gchol.o make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c norisk.c -o norisk.o norisk.c: In function 'norisk': norisk.c:12:23: warning: 'p1' may be used uninitialized in this function [-Wmaybe-uninitialized] int i, j, istrat, p1, p2; ^~ make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pystep.c -o pystep.o make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tmerge.c -o tmerge.o make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfitci.c -o survfitci.o survfitci.c: In function 'survfitci': survfitci.c:216:37: warning: 'umat' may be used uninitialized in this function [-Wmaybe-uninitialized] umat[j][k] -= hmat[oldstate][k]* p[oldstate]/ ws[oldstate]; ~~~~^~~ survfitci.c:46:38: warning: 'usave' may be used uninitialized in this function [-Wmaybe-uninitialized] double **pmat, **vmat, *cumhaz, *usave; ^~~~~ make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' make[3]: Entering directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/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 survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'survival' finding HTML links ... done Surv html 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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/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/Rtmps1v3yx/R.INSTALL1fcebc7dc100b/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic clogit html cluster html colon html concordance html cox.zph html coxph html coxph.control html coxph.detail html coxph.object html coxph.wtest html diabetic html dsurvreg html finegray html flchain html frailty html genfan html heart html is.ratetable html kidney html levels.Surv html lines.survfit html logLik.coxph html logan html lung html mgus html mgus2 html model.frame.coxph html model.matrix.coxph html myeloid html neardate html nwtco html ovarian html pbc html pbcseq html plot.aareg html plot.cox.zph html plot.survfit html predict.coxph html predict.survreg html print.aareg html print.summary.coxph html print.summary.survexp html print.summary.survfit html print.survfit html pspline html pyears html quantile.survfit html ratetable html ratetableDate html rats html rats2 html residuals.coxph html residuals.survreg html retinopathy html rhDNase html ridge html solder html stanford2 html statefig html strata html summary.aareg html summary.coxph html summary.pyears html summary.survexp html summary.survfit html survConcordance html survSplit html survdiff html survexp html survexp.fit html survexp.object html survexp.us html survfit html survfit.coxph html survfit.formula html survfit.matrix html survfit.object html survfitcoxph.fit html survival-internal html survobrien html survreg html survreg.control html survreg.distributions html survreg.object html survregDtest html tcut html tmerge html tobin html transplant html udca html untangle.specials html uspop2 html vcov.coxph html veteran html xtfrm.Surv html yates html yates_setup html ** 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-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' begin installing recommended package boot make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'boot' finding HTML links ... done EEF.profile html Imp.Estimates html abc.ci html acme html aids html aircondit html amis html aml html beaver html bigcity html boot-practicals html boot html boot.array html boot.ci html brambles html breslow html calcium html cane html capability html catsM html cav html cd4 html cd4.nested html censboot html channing html claridge html cloth html co.transfer html coal html control html corr html cum3 html cv.glm html darwin html dogs html downs.bc html ducks html empinf html envelope html exp.tilt html fir html freq.array html frets html glm.diag html glm.diag.plots html gravity html hirose html imp.weights html inv.logit html islay html jack.after.boot html k3.linear html linear.approx html lines.saddle.distn html logit html manaus html melanoma html motor html neuro html nitrofen html nodal html norm.ci html nuclear html paulsen html plot.boot html poisons html polar html print.boot html print.bootci html print.saddle.distn html print.simplex html remission html saddle html saddle.distn html saddle.distn.object html salinity html simplex html simplex.object html smooth.f html sunspot html survival html tau html tilt.boot html tsboot html tuna html urine html var.linear html wool html ** building package indices ** testing if installed package can be loaded * DONE (boot) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/library/Recommended' * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** libs make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/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/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxph.c -o coxph.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mgcv.c -o mgcv.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c misc.c -o misc.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mvn.c -o mvn.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c magic.c -o magic.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qp.c -o qp.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c soap.c -o soap.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tprs.c -o tprs.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c discrete.c -o discrete.o discrete.c: In function 'Xbd': discrete.c:368: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (xbdcalloc) discrete.c:391: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (xbdcalloc) discrete.c:413: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (xbdcalloc) 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:1308:5: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized] XWXijs(XWX+tpsu[rb] + (ptrdiff_t) nxwx * tpsu[cb],rb,cb,r,c,X,k,ks,m,p,*nx,*n,ts, dt,*nt,w,ws, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tri,off,work + tid * q,worki + tid * (ptrdiff_t) qi,nxwx,ht, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sm + tid * (ptrdiff_t) *n,SMstack + 3 * tid * (ptrdiff_t) *n ); /* compute r,c block */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -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/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -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:1744:9: warning: unused variable 'j' [-Wunused-variable] int i,j,n1; ^ mat.c: In function 'chol_up': mat.c:1869:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (*n>1) R[1] = -2.0;return; /* signals error */ ^~ mat.c:1869:29: 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 */ ^~~~~~ make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.5.3/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gdi.c -o gdi.o make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.5.3/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 -L/usr/src/RPM/BUILD/R-3.5.3/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/src' installing to /usr/src/RPM/BUILD/R-3.5.3/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'mgcv' finding HTML links ... done Beta html FFdes html Predict.matrix html Predict.matrix.cr.smooth html Predict.matrix.soap.film html Rrank html Sl.initial.repara html Sl.repara html Sl.setup html Tweedie html anova.gam html bam html Rd warning: /usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/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/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/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/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/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 columb html concurvity html coxph html coxpht html dDeta html exclude.too.far html extract.lme.cov html family.mgcv html fix.family.link html fixDependence html formXtViX html formula.gam html fs.test html full.score html gam html gam.check html gam.control html gam.convergence html gam.fit html gam.fit3 html gam.fit5.post.proc html gam.models html gam.outer html gam.reparam html gam.scale html gam.selection html gam.side html gam.vcomp html gam2objective html gamObject html gamSim html gamlss.etamu html gamlss.gH html gamm html gaulss html get.var html gevlss html ginla html identifiability html in.out html inSide html influence.gam html initial.sp html interpret.gam html jagam html k.check html ldTweedie html ldetS html linear.functional.terms html logLik.gam html ls.size html magic html magic.post.proc html mgcv-FAQ html mgcv-package html mgcv-parallel html Rd warning: /usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/man/mgcv-parallel.Rd:11: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic mini.roots html missing.data html model.matrix.gam html mono.con html mroot html multinom html mvn html negbin html new.name html notExp html notExp2 html null.space.dimension html ocat html one.se.rule html pcls html pdIdnot html pdTens html pen.edf html place.knots html plot.gam html polys.plot html predict.bam html Rd warning: /usr/src/tmp/RtmpDDS4yx/R.INSTALL1fcebb6d2f7b20/mgcv/man/predict.bam.Rd:76: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic predict.gam html print.gam html qq.gam html rTweedie html random.effects html residuals.gam html rig html rmvn html s html scat html sdiag html single.index html slanczos html smooth.construct html smooth.construct.ad.smooth.spec html smooth.construct.bs.smooth.spec html smooth.construct.cr.smooth.spec html smooth.construct.ds.smooth.spec html smooth.construct.fs.smooth.spec html smooth.construct.gp.smooth.spec html smooth.construct.mrf.smooth.spec html smooth.construct.ps.smooth.spec html smooth.construct.re.smooth.spec html smooth.construct.so.smooth.spec html smooth.construct.sos.smooth.spec html smooth.construct.t2.smooth.spec html smooth.construct.tensor.smooth.spec html smooth.construct.tp.smooth.spec html smooth.terms html smooth2random html smoothCon html sp.vcov html spasm.construct html step.gam html summary.gam html t2 html te html tensor.prod.model.matrix html totalPenaltySpace html trichol html trind.generator html twlss html uniquecombs html vcov.gam html vis.gam html ziP html ziplss html ** building package indices ** testing if installed package can be loaded * DONE (mgcv) Making 'packages.html' ... done make[2]: Leaving directory 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Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [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] No file R-data.vrs. (Concept index) [31] No file R-data.cps. [32] ) (see the transcript file for additional information) Output written on R-data.pdf (35 pages, 270376 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [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] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 309921 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.t2d/pdf/xtr/R-data.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-data.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-data.aux) Underfull \hbox (badness 10000) in paragraph at lines 87--87 [][]@textbf DBI Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 87--87 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 87--87 @texttt package=DBI[]@textrm )[][]| Overfull \hbox (8.53186pt too wide) in paragraph at lines 88--88 [][]@textbf dataframes2xls Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 88--88 @texttt org / Overfull \hbox (67.73643pt too wide) in paragraph at lines 88--88 @texttt package=dataframes2xls[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 89--89 [][]@textbf foreign Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 89--89 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 89--89 @texttt package=foreign[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 90--90 [][]@textbf gdata Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 90--90 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 90--90 @texttt package=gdata[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 91--91 [][]@textbf ncdf4 Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 91--91 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 91--91 @texttt package=ncdf4[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 92--92 [][]@textbf rJava Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 92--92 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 92--92 @texttt package=rJava[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 93--93 [][]@textbf RJDBC Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 93--93 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 93--93 @texttt package=RJDBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 94--94 [][]@textbf RMySQL Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 94--94 @texttt org / Overfull \hbox (21.74693pt too wide) in paragraph at lines 94--94 @texttt package=RMySQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 95--95 [][]@textbf RNetCDF Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 95--95 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 95--95 @texttt package=RNetCDF[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 96--96 [][]@textbf RODBC Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 96--96 @texttt org / Overfull \hbox (15.99825pt too wide) in paragraph at lines 96--96 @texttt package=RODBC[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 97--97 [][]@textbf ROracle Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 97--97 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 97--97 @texttt package=ROracle[]@textrm )[][]| Overfull \hbox (2.70708pt too wide) in paragraph at lines 98--98 [][]@textbf RPostgreSQL Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 98--98 @texttt org / Overfull \hbox (50.49037pt too wide) in paragraph at lines 98--98 @texttt package=RPostgreSQL[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 101--101 [][]@textbf RSQLite Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 101--101 @texttt org / Overfull \hbox (27.49562pt too wide) in paragraph at lines 101--101 @texttt package=RSQLite[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 103--103 [][]@textbf WriteXLS Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 103--103 @texttt org / Overfull \hbox (33.24431pt too wide) in paragraph at lines 103--103 @texttt package=WriteXLS[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 104--104 [][]@textbf XLConnect Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 104--104 @texttt org / Overfull \hbox (38.993pt too wide) in paragraph at lines 104--104 @texttt package=XLConnect[]@textrm )[][]| Underfull \hbox (badness 10000) in paragraph at lines 105--105 [][]@textbf XML Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt CRAN . Underfull \hbox (badness 10000) in paragraph at lines 105--105 @texttt org / Overfull \hbox (4.50087pt too wide) in paragraph at lines 105--105 @texttt package=XML[]@textrm )[][]| [1] [2] Chapter 1 [3] Writing index file R-data.cp [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] ) (see the transcript file for additional information) Output written on R-data.pdf (37 pages, 309926 bytes). Transcript written on R-data.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (51 pages, 366402 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382734 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] [20] Chapter 5 [21] [22] [23] [24] [25] Chapter 6 [26] [27] Chapter 7 [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] Writing index file R-FAQ.fn [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3389--3397 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [43] Chapter 8 [44] Chapter 9 [45] [46] Chapter 10 [47] [48] [49] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (53 pages, 382729 bytes). Transcript written on R-FAQ.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16] [17] Chapter 4 [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29] [30] Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37] [38] [39] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3350--3350 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52] [53] Appendix C [54] [55] [56] [57] [58] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5010--5010 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 5016--5016 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [59] [60] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5118--5118 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5156--5156 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [61] [62] [63] [64] [65] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5595--5595 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [66] [67] [68] [69] Appendix D [70] [71] [72] (Function and variable index) [73] No file R-admin.vrs. (Concept index) [74] No file R-admin.cps. (Environment variable index) [75] No file R-admin.ens. [76] ) (see the transcript file for additional information) Output written on R-admin.pdf (79 pages, 477577 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16] [17] Chapter 4 [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34] [35] Appendix A [36] [37] [38] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3350--3350 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [39] [40] [41] [42] [43] [44] [45] [46] Appendix B [47] [48] [49] [50] [51] [52] Appendix C [53] [54] [55] [56] [57] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5010--5010 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 5016--5016 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [58] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5118--5118 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5156--5156 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [60] [61] [62] [63] [64] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5595--5595 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [65] [66] [67] [68] Appendix D [69] [70] [71] (Function and variable index) [72] (Concept index) [73] (Environment variable index) [74] [75] ) (see the transcript file for additional information)pdfTeX warning (dest): name {76} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (80 pages, 522359 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] Underfull \hbox (badness 7685) in paragraph at lines 1293--1297 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 1510--1514 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [16] [17] Chapter 4 [18] [19] Underfull \hbox (badness 10000) in paragraph at lines 1888--1900 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [20] Chapter 5 [21] Chapter 6 [22] [23] [24] [25] [26] [27] [28] [29] Chapter 7 [30] [31] [32] Chapter 8 [33] Chapter 9 [34] [35] Appendix A [36] [37] [38] Overfull \hbox (27.8098pt too wide) in paragraph at lines 3350--3350 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [39] [40] [41] [42] [43] [44] [45] [46] Appendix B [47] [48] [49] [50] [51] [52] Appendix C [53] [54] [55] [56] [57] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5010--5010 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (50.80455pt too wide) in paragraph at lines 5016--5016 []@texttt CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.s dk/usr/include"[] [58] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5118--5118 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5156--5156 []@texttt export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconf ig:/usr/lib/pkgconfig[] [60] [61] [62] [63] [64] Overfull \hbox (119.7888pt too wide) in paragraph at lines 5595--5595 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [65] [66] [67] [68] Appendix D [69] [70] [71] (Function and variable index) [72] (Concept index) [73] (Environment variable index) [74] [75] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (80 pages, 522364 bytes). Transcript written on R-admin.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11 [56] Chapter 12 [57] [58] (Function and variable index) [59] No file R-ints.vrs. (Concept index) [60] No file R-ints.cps. [61] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on R-ints.pdf (64 pages, 393196 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11 [56] Chapter 12 [57] [58] (Function and variable index) [59] [60] (Concept index) [61] [62] ) (see the transcript file for additional information) Output written on R-ints.pdf (66 pages, 442734 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-ints.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 1455--1455 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 1456--1456 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (45.05586pt too wide) in paragraph at lines 1457--1457 [] @texttt length(meth.Ops <- nM$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Chapter 9 [53] [54] Chapter 10 [55] Chapter 11 [56] Chapter 12 [57] [58] (Function and variable index) [59] [60] (Concept index) [61] [62] ) (see the transcript file for additional information) Output written on R-ints.pdf (66 pages, 442742 bytes). Transcript written on R-ints.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] No file R-lang.vrs. (Concept Index) [52] No file R-lang.cps. Appendix A [53] [54] ) (see the transcript file for additional information) Output written on R-lang.pdf (57 pages, 326359 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374818 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-lang.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 4342--4344 []@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be found by [46] [47] [48] [49] [50] (Function and Variable Index) [51] [52] (Concept Index) [53] Appendix A [54] [55] ) (see the transcript file for additional information) Output written on R-lang.pdf (60 pages, 374826 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' collecting LaTeX docs for package 'mgcv' ... Converting parsed Rd's to LaTeX .............. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] No file R-intro.vrs. Appendix E [94] No file R-intro.cps. Appendix F [95] [96] ) (see the transcript file for additional information) Output written on R-intro.pdf (99 pages, 578714 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 628355 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-intro.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-intro.toc) (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13] [14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24] Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] [34] [35] [36] [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45] [46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] Chapter 13 [76] [77] Chapter 14 [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 6647--6652 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and Underfull \hbox (badness 7064) in paragraph at lines 6647--6652 @texttt \\?\UNC\server\dir1\dir2\file[]@textrm ) are not sup-ported, but they may work in [80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89] [90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97] Appendix F [98] [99] ) (see the transcript file for additional information) Output written on R-intro.pdf (105 pages, 637484 bytes). Transcript written on R-intro.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2312--2312 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2314--2314 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2573--2575 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29] [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2700--2700 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4694--4694 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4696--4696 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4697--4697 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4712--4712 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] [58] [59] [60] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5354--5354 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6876--6883 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7053--7059 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91] Chapter 4 [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 8348--8357 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [97] [98] [99] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8625--8626 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [100] [101] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8758--8758 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8786--8788 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [102] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8918--8918 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10066--10066 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [117] [118] [119] [120] [121] [122] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10645--10645 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11478--11480 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12511--12511 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14315--14321 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [166] [167] Chapter 8 [168] [169] [170] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14727--14727 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [171] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14786--14786 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15289--15296 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15412--15416 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [180] No file R-exts.vrs. (Concept index) [181] No file R-exts.cps. [182] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (185 pages, 891784 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2312--2312 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2314--2314 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2573--2575 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29] [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2700--2700 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4694--4694 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4696--4696 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4697--4697 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4712--4712 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5354--5354 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6876--6883 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7053--7059 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91] Chapter 4 [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 8348--8357 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [97] [98] [99] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8625--8626 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [100] [101] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8758--8758 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8786--8788 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [102] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8918--8918 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10066--10066 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [117] [118] [119] [120] [121] [122] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10645--10645 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11478--11480 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12511--12511 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14315--14321 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [166] [167] Chapter 8 [168] [169] [170] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14727--14727 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [171] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14786--14786 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15289--15296 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15412--15416 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [180] [181] [182] Overfull \vbox (6.89986pt too high) has occurred while \output is active (Concept index) [183] [184] [185] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (191 pages, 954185 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2312--2312 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2314--2314 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2573--2575 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29] [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2700--2700 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4694--4694 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4696--4696 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4697--4697 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4712--4712 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] [58] [59] [60] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5354--5354 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6876--6883 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7053--7059 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91] Chapter 4 [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 8348--8357 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [97] [98] [99] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8625--8626 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [100] [101] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8758--8758 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8786--8788 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [102] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8918--8918 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10066--10066 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [117] [118] [119] [120] [121] [122] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10645--10645 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11478--11480 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12511--12511 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14315--14321 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [166] [167] Chapter 8 [168] [169] [170] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14727--14727 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [171] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14786--14786 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15289--15296 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15412--15416 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [180] [181] [182] Overfull \vbox (6.89986pt too high) has occurred while \output is active (Concept index) [183] [184] [185] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (191 pages, 964893 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2312--2312 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2314--2314 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2573--2575 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29] [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2700--2700 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4694--4694 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4696--4696 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4697--4697 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4712--4712 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5354--5354 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6876--6883 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7053--7059 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91] Chapter 4 [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 8348--8357 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [97] [98] [99] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8625--8626 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [100] [101] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8758--8758 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8786--8788 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [102] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8918--8918 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10066--10066 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [117] [118] [119] [120] [121] [122] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10645--10645 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11478--11480 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12511--12511 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14315--14321 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [166] [167] Chapter 8 [168] [169] [170] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14727--14727 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [171] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14786--14786 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15289--15296 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15412--15416 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [180] [181] [182] Overfull \vbox (6.89986pt too high) has occurred while \output is active (Concept index) [183] [184] [185] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (191 pages, 954186 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.texi (/usr/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2017-08-23.19]: pdf, fonts, markup, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) Writing index file R-exts.vr (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.5.3/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 493--496 []@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] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2312--2312 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (31.98314pt too wide) in paragraph at lines 2314--2314 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [26] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2573--2575 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [29] [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2700--2700 [] @texttt CXX="$(CXX11) $(CXX11STD)" CXXFLAGS="$(CXX11FLAGS) $(CXX 11PICFLAGS)")[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4694--4694 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4696--4696 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4697--4697 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] Overfull \hbox (55.2397pt too wide) in paragraph at lines 4712--4712 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [53] [54] [55] [56] [57] [58] [59] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5354--5354 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [60] [61] [62] [63] [64] [65] Chapter 2 [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] Underfull \hbox (badness 10000) in paragraph at lines 6876--6883 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [78] [79] Underfull \hbox (badness 10000) in paragraph at lines 7053--7059 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [80] [81] [82] [83] Chapter 3 [84] [85] [86] [87] [88] [89] [90] [91] Chapter 4 [92] [93] [94] [95] [96] Underfull \hbox (badness 10000) in paragraph at lines 8348--8357 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [97] [98] [99] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8625--8626 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [100] [101] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8758--8758 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8786--8788 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [102] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8918--8918 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [103] [104] [105] [106] Chapter 5 [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10066--10066 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [117] [118] [119] [120] [121] [122] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10645--10645 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] Underfull \hbox (badness 10000) in paragraph at lines 11478--11480 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12511--12511 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [145] [146] Chapter 6 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Warning: unbalanced parentheses in @def... [160] [161] [162] [163] [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 14315--14321 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [166] [167] Chapter 8 [168] [169] [170] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14727--14727 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [171] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14786--14786 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [172] [173] [174] [175] [176] [177] Underfull \hbox (badness 10000) in paragraph at lines 15289--15296 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [178] [179] Underfull \hbox (badness 10000) in paragraph at lines 15412--15416 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [180] [181] [182] Overfull \vbox (6.89986pt too high) has occurred while \output is active (Concept index) [183] [184] [185] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (191 pages, 954173 bytes). Transcript written on R-exts.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' PDF/LaTeX documentation: full reference index ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-04-01> patch level 2 Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\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 [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\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 [38] [39] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40] [41] [42] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] [61] [62] [63] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \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 [64] [65] Underfull \hbox (badness 4595) in paragraph at lines 4280--4283 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [66] [67] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4435--4435 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [68] Underfull \hbox (badness 1199) in paragraph at lines 4465--4471 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4476--4479 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [69] Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4556--4561 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [70] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [75] [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\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 [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 1796) in paragraph at lines 5845--5853 []\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 : / / [89] [90] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6041--6041 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6042--6042 []\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}[] [91] [92] [93] Underfull \hbox (badness 1635) in paragraph at lines 6208--6211 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6212--6215 []\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 Underfull \hbox (badness 1102) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6243--6251 []\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 [94] [95] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [96] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \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 [99] [100] Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110] [111] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112] [113] [114] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [115] [116] Underfull \hbox (badness 8132) in paragraph at lines 7836--7840 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7836--7840 \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 Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\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 1062) in paragraph at lines 7855--7865 [][]\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 [117] Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891 []\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") Underfull \hbox (badness 7451) in paragraph at lines 7926--7936 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7926--7936 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124] [125] [126] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8805--8809 []\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 [130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [131] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [132] [133] Underfull \hbox (badness 5403) in paragraph at lines 9039--9041 []\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 9058--9060 []\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 [134] Underfull \hbox (badness 1132) in paragraph at lines 9130--9137 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [135] Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\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 [136] [137] [138] [139] [140] [141] [142] [143] [144] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\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 [145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\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 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146] [147] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\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 [148] [149] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ [150] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [152] [153] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [154] Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [157] Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158] [159] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\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 [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\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 [170] Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \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 [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\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 [174] Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175] [176] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [177] [178] [179] Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [180] [181] [182] [183] [184] [185] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186] [187] [188] [189] Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190] [191] Underfull \hbox (badness 2221) in paragraph at lines 13178--13187 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [192] [193] [194] [195] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 13704--13706 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [200] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [201] Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [202] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\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 , [203] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- [205] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [206] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210] [211] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497 []\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 14500--14500 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [212] Underfull \hbox (badness 1168) in paragraph at lines 14584--14588 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14584--14588 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [213] Underfull \hbox (badness 6944) in paragraph at lines 14679--14682 [][][]\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 , [214] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 14838--14840 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14884--14892 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14899--14903 []\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 [217] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\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 [218] Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\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, Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14979--14987 []\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 Underfull \hbox (badness 3601) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [220] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [232] [233] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\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 Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\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 , [234] [235] [236] [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [242] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [243] [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\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))) [248] [249] [250] [251] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252] [253] [254] Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257] [258] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\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 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259] [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\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 17942--17942 []\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):[] [261] [262] [263] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\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 [264] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\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 18246--18262 [][][]\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 , [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 4699) in paragraph at lines 18660--18663 []\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 , [271] [272] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [273] [274] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1430) in paragraph at lines 19331--19336 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 19331--19336 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [282] Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [283] Underfull \hbox (badness 10000) in paragraph at lines 19452--19459 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19452--19459 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19468--19470 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [284] Underfull \hbox (badness 1975) in paragraph at lines 19540--19543 []\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 [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\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 [291] Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [292] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\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 [293] Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\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 20153--20157 [][]\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 [294] [295] Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\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 , [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\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 [298] Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\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 20442--20447 \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 20442--20447 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [299] [300] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303] [304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\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 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305] Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306] Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\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 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307] Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [309] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\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 Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\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 1939) in paragraph at lines 21384--21390 \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 names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [313] [314] [315] [316] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317] [318] [319] [320] [321] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\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 22006--22006 [] \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 22009--22009 []\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)[] [322] [323] Underfull \hbox (badness 1655) in paragraph at lines 22133--22137 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [324] [325] [326] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\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. [327] [328] [329] [330] [331] [332] [333] [334] Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\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 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \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 ; [343] [344] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\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 [345] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\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 5077) in paragraph at lines 23672--23678 \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 10000) in paragraph at lines 23682--23685 []\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 23682--23685 \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 [346] [347] Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348] [349] [350] [351] Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\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 [352] [353] [354] [355] [356] [357] [358] Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\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 24549--24553 \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 [359] Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\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 24642--24648 \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 [360] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \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:[] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\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 Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365] [366] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367] [368] [369] [370] Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372] [373] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374] [375] [376] Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\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 25948--25954 \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 25948--25954 \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 [377] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\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 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378] Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\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 10000) in paragraph at lines 26061--26068 \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 Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379] [380] [381] [382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\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 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \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)] [383] [384] [385] [386] [387] Underfull \hbox (badness 4341) in paragraph at lines 26729--26731 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26765--26771 [][][]\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 [388] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787 []\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 26799--26799 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [389] [390] [391] [392] [393] [394] [395] Underfull \hbox (badness 10000) in paragraph at lines 27233--27237 []\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, [396] Underfull \hbox (badness 1796) in paragraph at lines 27299--27302 []\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 [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 27499--27502 []\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 [400] [401] [402] [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 1226) in paragraph at lines 28131--28136 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [409] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176 [] \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))[] [410] [411] [412] [413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442 []\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 28453--28453 []\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 28459--28459 []\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 28460--28460 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [414] Underfull \hbox (badness 7415) in paragraph at lines 28538--28542 []\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 [415] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [416] Underfull \hbox (badness 2418) in paragraph at lines 28718--28729 []\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 [417] [418] Underfull \hbox (badness 1248) in paragraph at lines 28852--28859 \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 28852--28859 \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 / [419] [420] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [421] Underfull \hbox (badness 1337) in paragraph at lines 29065--29068 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 29131--29142 []\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 Underfull \hbox (badness 10000) in paragraph at lines 29143--29146 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [423] [424] Underfull \hbox (badness 1117) in paragraph at lines 29238--29244 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 4048) in paragraph at lines 29616--29621 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29616--29621 \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 , [431] [432] [433] [434] [435] [436] [437] [438] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [439] [440] [441] [442] Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443] [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\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 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452] [453] [454] [455] [456] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [457] [458] [459] Underfull \hbox (badness 3375) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/ ptm/m/n/10 , are in-valid, e.g., du- Underfull \hbox (badness 2359) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal Underfull \hbox (badness 2582) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call [460] [461] [462] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [463] [464] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [465] [466] [467] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469] Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\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 [470] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [474] [475] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] Underfull \hbox (badness 1735) in paragraph at lines 33605--33611 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [488] Underfull \hbox (badness 4303) in paragraph at lines 33621--33624 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [489] [490] [491] [492] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [494] [495] [496] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [497] Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; Underfull \hbox (badness 2512) in paragraph at lines 34251--34253 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [498] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [499] [500] [501] [502] [503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [511] [512] [513] Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\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 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515] Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \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 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \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 35534--35541 \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 [516] [517] [518] [519] [520] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [522] [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [525] [526] [527] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529] [530] [531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532] [533] [534] [535] [536] [537] [538] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [539] Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 37192--37192 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [540] [541] [542] [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\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. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \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 [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \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 [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\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 [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\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 [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\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 [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\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 [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\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 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\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., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437 [] \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 39439--39439 [] \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),[] [574] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441 [] \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 39454--39456 []\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 [575] Underfull \hbox (badness 10000) in paragraph at lines 39534--39537 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39652--39656 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39714--39718 [][][]\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 \ [][]$\T1/pcr/m/n/10 https : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40132--40139 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40188--40197 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40188--40197 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40198--40206 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40198--40206 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40198--40206 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40264--40272 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40273--40276 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40330--40332 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40339--40339 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40556--40558 []\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 [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40678--40678 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40680--40680 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41042--41044 []\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 [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41208--41211 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41215--41223 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41215--41223 \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 Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41224--41228 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41245--41250 [][][]\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; [600] Underfull \hbox (badness 3895) in paragraph at lines 41307--41319 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41307--41319 \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 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41492--41495 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41629--41629 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42096--42096 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42105--42105 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42222--42225 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42226--42233 []\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 [614] Underfull \hbox (badness 4726) in paragraph at lines 42252--42256 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42252--42256 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42441--42443 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42545--42545 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42620--42620 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42628--42628 []\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 ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42758--42763 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42758--42763 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42758--42763 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42774--42779 []\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 [622] Underfull \hbox (badness 1603) in paragraph at lines 42793--42797 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42864--42870 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 42899--42899 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42993--42995 []\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 . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43355--43359 []\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 [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43395--43395 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43416--43420 []\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 [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \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 [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1472) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\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. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \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 [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] Overfull \vbox (4.29591pt too high) has occurred while \output is active [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 2376) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\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 [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \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 [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \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 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \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 [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\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 [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\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 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\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 Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\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 Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\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 [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\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 [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \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 Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\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 / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\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 Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \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 [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\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 [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\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 / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\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 [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\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- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\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 [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\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 Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\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 [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \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 [852] [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\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 [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\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 [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\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 [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \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 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\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. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\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 [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\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 [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\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 [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\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 [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\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)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \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 [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\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- [971] [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\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 [975] [976] [977] [978] [979] [980] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [981] [982] [983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [984] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\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 , [985] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\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 [986] [987] [988] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\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 [989] [990] [991] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\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- [992] [993] [994] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [995] [996] [997] [998] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [999] [1000] [1001] [1002] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1003] [1004] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1005] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\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 [1006] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1007] [1008] [1009] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1010] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1023] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\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- [1024] [1025] [1026] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\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 [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1046] [1047] [1048] [1049] [1050] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\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 [1051] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\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 , [1052] [1053] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\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 [1054] [1055] [1056] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1057]) (./methods-pkg.tex [1058] Chapter 7. [1059] [1060] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1061] [1062] [1063] 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- [1064] [1065] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1066] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1067] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1068] [1069] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1085] [1086] [1087] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1088] [1089] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1090] [1091] [1092] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1093] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1094] [1095] [1096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1097] [1098] [1099] [1100] [1101] [1102] [1103] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1106] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1107] [1108] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") [1109] Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1113] [1114] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1115] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1116] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1117] [1118] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1119] 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 , [1120] [1121] [1122] 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 [1123] [1124] [1125] [1126] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1127] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1128] [1129] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1130] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1131] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1132] [1133] [1134] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1135] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1136] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1137] [1138] [1139] [1140] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1141] [1142] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1143] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1144] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1145] 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 [1146] Underfull \vbox (badness 10000) has occurred while \output is active [1147] [1148] [1149]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1150] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1151] [1152] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1153]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1154] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1155] [1156] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1157] [1158] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1171] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1172] [1173] [1174] [1175] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1176] [1177] [1178] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1179] [1180] Underfull \vbox (badness 2302) has occurred while \output is active [1181] 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[] [1182] [1183] [1184] [1185] 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[] [1186] 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][] [1187] 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][] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1197] [1198] [1199] [1200]) (./parallel-pkg.tex 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 [1201] 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 [1202] [1203] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1204] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1205] [1206] 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 [1207] [1208] [1209] [1210] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\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 742--751 \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 [1211] [1212] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1213] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1214] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1215] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1216] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\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 [1217] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\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)[] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\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 [1220] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\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 [1221] [1222]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1223] [1224] [1225] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1230] [1231] [1232] [1233] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1234] [1235] [1236]) (./stats-pkg.tex Chapter 10. [1237] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1238] [1239] [1240] [1241] [1242] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\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 [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1258] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1259] [1260] [1261] [1262] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1263] [1264] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1265] [1266] [1267] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1268] [1269] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1270] [1271] [1272] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1273] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1274] [1275] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1276] [1277] [1278] [1279] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1280] [1281] [1282] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1283] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1284] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1285] [1286] [1287] [1288] [1289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1290] [1291] [1292] [1293] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1294] [1295] [1296] [1297] [1298] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1299] [1300] [1301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1302] [1303] [1304] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1305] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1306] [1307] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1308] [1309] [1310] [1311] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\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))[] [1312] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1313] [1314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\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 [1315] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1316] [1317] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\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 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \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 , [1318] [1319] [1320] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1321] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1322] [1323] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1324] [1325] [1326] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1327] [1328] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\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 [1329] [1330] [1331] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1332] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\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 6468--6473 \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, [1333] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\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 [1334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1335] [1336] [1337] [1338] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1345] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1346] [1347] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\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 , ..., [1354] [1355] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1356] [1357] [1358] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1366] [1367] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1368] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1369] [1370] [1371] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1372] [1373] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \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 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1374] [1375] [1376] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1377] [1378] [1379] [1380] [1381] [1382] [1383] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\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); [1384] [1385] [1386] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\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 [1387] [1388] [1389] [1390] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1391] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1392] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\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 [1393] [1394] [1395] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ [1396] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1397] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \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 (= [1398] [1399] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \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 [1400] [1401] [1402] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1403] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \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 11337--11341 []\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 [1405] [1406] [1407] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1408] [1409] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1410] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1411] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1412] [1413] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1414] [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1416] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1417] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1418] [1419] [1420] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\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 [1421] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\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 [1422] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1423] [1424] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1425] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\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 Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\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 12731--12735 \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 [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1437] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\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 , [1440] [1441] [1442] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1443] [1444] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \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 , [1445] [1446] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1449] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\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 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1451] [1452] [1453] [1454] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\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 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1455] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\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 , [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1474] [1475] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \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 [1476] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\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 16097--16106 \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 16097--16106 \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 [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\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[] [1486] [1487] [1488] [1489] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1498] [1499] Underfull \vbox (badness 10000) has occurred while \output is active [1500] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1501] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1502] [1503] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\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 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1504] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\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 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1513] Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \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 18529--18531 []\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 [1514] [1515] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \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 [1516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\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 18698--18698 []\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 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1517] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\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 18756--18767 \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 [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1519] [1520] [1521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1522] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\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 [1523] [1524] [1525] [1526] [1527] [1528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1529] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \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 (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1530] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\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 [1531] [1532] [1533] [1534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1535] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\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 [1536] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1537] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\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)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1539] [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1541] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1542] Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1543] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \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 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1557] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\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 21342--21348 []\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 , [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1575] [1576] [1577] [1578] [1579] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1588] [1589] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\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 [1590] [1591] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1592] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\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 Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\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 [1593] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1595] [1596] [1597] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\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 Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\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 [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1602] [1603] [1604] [1605] [1606] [1607] [1608] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\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 , [1609] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1610] [1611] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\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 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1613] [1614] [1615] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\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 . [1616] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1617] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1618] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\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 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1619] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1620] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1622] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1623] [1624] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1632] [1633] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\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 26293--26293 []\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 [1634] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\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 [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \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 26402--26402 [] \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 26411--26411 [] \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 26412--26412 [] \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 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1636] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\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 Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \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 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1637] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\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 [1638] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \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 26581--26581 [] \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 26591--26591 [] \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 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\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 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1640] [1641] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1642] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\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 [1643] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1644] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\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 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1645] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\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 27023--27023 []\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 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \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 27092--27097 []\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 [1647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\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 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1648] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\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 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\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 27216--27216 []\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 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1657] [1658] [1659] [1660] [1661] [1662] [1663] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\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 [1664] [1665] [1666] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\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 [1667] [1668] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\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 [1669] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\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 [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1671] [1672] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\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) [1673] [1674] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1677] [1678] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\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 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1679] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1680] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1681] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1682] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1683] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\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 [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1692] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1693] [1694] [1695] [1696] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1697] [1698] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\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:[] [1699] [1700] [1701] [1702] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1711] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1712] [1713] [1714] [1715] [1716] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1717] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\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 [1718] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\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 "")[] [1719]) (./stats4-pkg.tex [1720] Chapter 11. [1721] [1722] [1723] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1727] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1728] [1729]) (./tcltk-pkg.tex [1730] Chapter 12. [1731] [1732] [1733] [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1735] [1736] [1737] Underfull \vbox (badness 10000) has occurred while \output is active [1738] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1750]) (./tools-pkg.tex Chapter 13. [1751] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1752] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1753] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1754] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1755] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\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 [1756] [1757] [1758] [1759] [1760] [1761] [1762] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1763] [1764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 960--960 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1765] [1766] Underfull \hbox (badness 1635) in paragraph at lines 1060--1062 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1767] Underfull \hbox (badness 5431) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1138--1148 \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- [1768] Underfull \hbox (badness 1014) in paragraph at lines 1160--1162 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1166--1168 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1769] Underfull \hbox (badness 10000) in paragraph at lines 1211--1214 []\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 [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 1360--1363 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1381--1383 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1772] [1773] [1774] [1775] [1776] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1683--1683 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1693--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1693--1698 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1897 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1780] [1781] [1782] [1783] Underfull \hbox (badness 1142) in paragraph at lines 2165--2171 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2199--2199 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1784] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2200--2200 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2227--2234 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2227--2234 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2227--2234 \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 [1785] Underfull \hbox (badness 1342) in paragraph at lines 2279--2285 \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 [1786] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2355--2355 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2368--2374 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2368--2374 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1787] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2401--2401 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2410--2410 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2427--2427 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1788] [1789] [1790] [1791] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1792] Underfull \hbox (badness 2486) in paragraph at lines 2737--2745 []\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 [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 1072) in paragraph at lines 3115--3117 []\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 [1798] [1799] [1800] [1801] [1802] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3451--3451 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1803] [1804] [1805] [1806] Underfull \hbox (badness 4108) in paragraph at lines 3695--3702 []\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 [1807] [1808] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3795--3795 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3798--3798 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3815--3817 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3832--3838 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1809] [1810] Underfull \hbox (badness 7832) in paragraph at lines 3954--3957 []\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 [1811] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4029--4029 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1812] Underfull \hbox (badness 1137) in paragraph at lines 4052--4054 []\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 [1813] [1814] [1815] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4226--4226 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4237--4240 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4253--4258 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4261--4267 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4261--4267 \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 [1816] Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1817] [1818] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4474--4474 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4486--4489 []\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 ', [1819] Underfull \hbox (badness 1742) in paragraph at lines 4490--4500 \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 4525--4531 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4525--4531 \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 ', Underfull \hbox (badness 1571) in paragraph at lines 4553--4557 []\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 [1820] [1821] [1822]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1823] [1824] [1825] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1826] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1827] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1828] [1829] [1830] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\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 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\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 620--626 \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- [1832] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1833] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \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 [1834] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1835] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1836] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1837] [1838] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1839] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1840] [1841] [1842] [1843] [1844] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1845] [1846] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1847] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1848] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1849] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1850] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1851] [1852] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \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")[] [1853] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1854] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1855] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\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; [1856] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\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 Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1857] [1858] [1859] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\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 [1864] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2941--2941 []\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 '[] [1865] Underfull \hbox (badness 2452) in paragraph at lines 3017--3020 []\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 [1866] [1867] [1868] [1869] [1870] [1871] [1872] Underfull \hbox (badness 1072) in paragraph at lines 3499--3507 []\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 [1873] Underfull \hbox (badness 1231) in paragraph at lines 3548--3554 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3555--3560 []\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 3555--3560 \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 3555--3560 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1874] [1875] Underfull \hbox (badness 4660) in paragraph at lines 3677--3680 \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 3701--3703 []\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 [1876] [1877] [1878] Underfull \hbox (badness 1565) in paragraph at lines 3886--3890 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3907--3913 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1879] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3969--3969 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3997--4004 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1880] [1881] [1882] [1883] [1884] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4324--4324 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1901] Underfull \hbox (badness 10000) in paragraph at lines 5432--5434 []\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 [1902] Underfull \hbox (badness 1502) in paragraph at lines 5481--5486 []\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 5481--5486 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 5654--5663 []\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 5654--5663 \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 [1905] Underfull \hbox (badness 2150) in paragraph at lines 5717--5720 []\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 5733--5736 []\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 [1906] [1907] Underfull \hbox (badness 3118) in paragraph at lines 5854--5856 []\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 [1908] Underfull \hbox (badness 2409) in paragraph at lines 5887--5891 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1909] Underfull \hbox (badness 5091) in paragraph at lines 5991--5993 []\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 Overfull \hbox (44.55087pt too wide) in paragraph at lines 6007--6012 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6020--6027 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1910] Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., [1911] Underfull \hbox (badness 10000) in paragraph at lines 6137--6141 []\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 6151--6158 []\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 6151--6158 \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 6151--6158 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1912] Underfull \hbox (badness 1314) in paragraph at lines 6210--6217 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 6251--6256 [][][]\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 , [1913] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6274--6274 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6310--6314 []\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 6324--6327 []\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 [1914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6371--6371 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1915] [1916] Underfull \hbox (badness 4132) in paragraph at lines 6490--6492 []\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 [1917] [1918] [1919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1920] [1921] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1922] Underfull \hbox (badness 10000) in paragraph at lines 6831--6833 []\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 [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 6972--6974 []\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 6977--6979 []\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 [1925] [1926] [1927] Underfull \hbox (badness 1859) in paragraph at lines 7200--7203 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1928] Underfull \hbox (badness 1655) in paragraph at lines 7282--7285 []\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 7293--7293 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297 []\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 7305--7305 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1930] Underfull \hbox (badness 10000) in paragraph at lines 7390--7394 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1931] [1932] [1933] [1934] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7654--7654 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655 [] \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 7656--7656 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1935] Underfull \hbox (badness 10000) in paragraph at lines 7684--7686 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7698--7700 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7706--7711 []\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, [1936] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7752--7752 [] \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 7753--7753 [] \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[] [1937] [1938] Underfull \hbox (badness 10000) in paragraph at lines 7882--7887 []\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 7882--7887 [][]\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 10000) in paragraph at lines 7889--7892 []\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 7889--7892 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1939] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8005--8005 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177 [] \T1/pcr/m/n/9 "S original, "),[] [1943] Underfull \hbox (badness 1789) in paragraph at lines 8300--8302 []\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 [1944] Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1945] [1946] Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1948] [1949] [1950] [1951] Underfull \hbox (badness 5203) in paragraph at lines 8869--8872 []\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 [1952] [1953] [1954] Underfull \hbox (badness 1776) in paragraph at lines 9095--9102 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1955] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1956] [1957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1958] [1959] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461 []\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[] [1960] [1961] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1962] Underfull \hbox (badness 1077) in paragraph at lines 9627--9630 []\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 [1963] [1964] [1965] [1966] [1967] [1968] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1969] Underfull \hbox (badness 10000) in paragraph at lines 10154--10156 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1970] [1971] Underfull \hbox (badness 2181) in paragraph at lines 10277--10281 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10277--10281 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10289--10293 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [1972] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10311--10311 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1973] [1974] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1975] Underfull \hbox (badness 1917) in paragraph at lines 10566--10569 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10566--10569 \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 [1976] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589 []\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 '[] [1977] Underfull \hbox (badness 8075) in paragraph at lines 10652--10654 []\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 [1978] Underfull \hbox (badness 6725) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10702--10711 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10702--10711 \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 [1979] Underfull \hbox (badness 3646) in paragraph at lines 10828--10830 [][][]$\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 / [1980] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 11047--11051 []\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 11078--11084 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1984] Underfull \hbox (badness 2012) in paragraph at lines 11173--11179 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1985] Underfull \hbox (badness 2096) in paragraph at lines 11186--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11189--11191 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11196--11199 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11200--11203 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1986] Underfull \hbox (badness 1009) in paragraph at lines 11272--11283 []\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 [1987] Underfull \hbox (badness 2846) in paragraph at lines 11359--11369 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11515--11518 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1990] Underfull \hbox (badness 2158) in paragraph at lines 11594--11597 []\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 [1991] [1992] [1993] Underfull \hbox (badness 3333) in paragraph at lines 11774--11776 []\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- [1994] [1995] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1996] Underfull \hbox (badness 5970) in paragraph at lines 11972--11975 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11972--11975 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11983--11992 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1997] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12065--12065 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12067--12067 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1998] [1999] [2000] Underfull \hbox (badness 10000) in paragraph at lines 12235--12237 []\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 [2001] [2002] Underfull \hbox (badness 4492) in paragraph at lines 12392--12399 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12392--12399 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12392--12399 \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 [2003] [2004] [2005] Underfull \hbox (badness 2020) in paragraph at lines 12555--12571 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12555--12571 \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 [2006] Underfull \hbox (badness 2809) in paragraph at lines 12675--12679 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12675--12679 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12690--12694 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 [][][]$\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 . Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2007] [2008] [2009] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2010] [2011] [2012] [2013] [2014] [2015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13273--13275 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13286--13290 \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 Overfull \hbox (36.87935pt too wide) in paragraph at lines 13300--13304 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \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[][][] [2016] Underfull \hbox (badness 1052) in paragraph at lines 13312--13314 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13363--13368 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13371--13374 [][][]\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 , [2017] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2018] [2019] [2020] Underfull \hbox (badness 10000) in paragraph at lines 13613--13616 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13629--13629 []\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:[] [2021] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13696--13696 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2022] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13718--13718 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13737--13737 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2023] Underfull \hbox (badness 1454) in paragraph at lines 13764--13768 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13789--13792 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13834--13836 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2024] Underfull \hbox (badness 3271) in paragraph at lines 13846--13850 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex Chapter 15. [2029] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2030] [2031] [2032] [2033] [2034] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2035] [2036] [2037] [2038]) (./MASS-pkg.tex Chapter 16. [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2073] [2074] [2075] [2076] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\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 [2077] [2078] [2079] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \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 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2080] [2081] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\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 Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2082] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2085] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\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 [2098] [2099] [2100] [2101] [2102] [2103] [2104] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2105] [2106] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2107] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2113] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2122] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\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") [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \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 \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2125] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\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 [2126] [2127] [2128] [2129] Underfull \vbox (badness 10000) has occurred while \output is active [2130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2131] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2132] [2133] [2134] [2135] [2136] [2137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2138] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\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 ) = [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2140] [2141] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \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 [2142] [2143] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2144] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2145] [2146] [2147] [2148] [2149] [2150] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\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 Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2151] [2152] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\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 [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2173] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\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), [2174] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]) (./Matrix-pkg.tex [2188] 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 [2189] 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 [2190] 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 [2191] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2192] [2193] 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) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2194] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2195] [2196] 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:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2197] 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 . [2198] [2199] [2200] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2201] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2202]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \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 \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2203pdfTeX 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' ] [2204] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\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 [2206] 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 [2207] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2208] Underfull \hbox (badness 6445) 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 3861) 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 Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \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 [2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \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 \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 \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 \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 \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2210] 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 [2211] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2212] 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 [2213] [2214] [2215] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2218] Underfull \hbox (badness 4713) 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 [2219] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2220] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2221] Underfull \hbox (badness 2707) 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 ; [2222] 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 [2223] 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 [2224] 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 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of 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 3803) 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 [2225] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class 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 [2226] [2227] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his 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 pre fer-able to (and more ef-fi-cient than) [2228] Underfull \hbox (badness 1168) 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 [2229] [2230] Underfull \hbox (badness 4967) 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 [2231] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2232] [2233] 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 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2234] Underfull \hbox (badness 4967) 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 Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2235] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2236] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2237] 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 [2238] 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 - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2239] [2240] [2241] [2242] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2243] [2244] 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():[] [2245] [2246] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2247] [2248] 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 , [2249] 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))[] [2250] 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 '[] [2251] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2252] 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")) ||[] [2253] 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[] [2254] 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 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2255] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2256] 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,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2257] [2258] [2259] 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[] [2260] 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"[] [2261] 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 [2262] 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)))[] [2263] 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 [2264] Underfull \hbox (badness 2809) 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 [2265] 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., [2266] 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 [2267] Underfull \hbox (badness 1184) 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 [2268] 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., [2269] 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[] [2270] 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 [2271] 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[] [2272] [2273] 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''), [2274] 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 ``e mpty'' [][]sparse-Ma-trix[][][], as does [2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) 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 [2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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 \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 \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2277] 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 [2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.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 - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2279] [2280] 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 [2281] Underfull \hbox (badness 2809) 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 [2282] 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/ ptm/m/n/10 should be done, af-ter [2283] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\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 [2285] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\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 7911--7916 \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 7919--7922 []\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., [2286] [2287] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2289] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\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 8241--8241 []\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 8242--8242 []\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 8355--8365 []\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 , [2290] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\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 [2291] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\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., [2292] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\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., [2293] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\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 [2294] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2295] [2296] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\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![] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\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 [2301] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\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"[] [2302] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2303] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\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 Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2307] [2308] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\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 [2309] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2311] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2312] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2313] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \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 [2314] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\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 [2315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \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 10256--10256 [] \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 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2316] [2317] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2318] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\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 [2319] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\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 10574--10574 []\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 10575--10575 []\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 10580--10580 []\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 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\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 10607--10607 []\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 10633--10633 []\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 10635--10635 [] \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 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2321] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2322] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2323] [2324] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \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 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2325] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\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 11140--11146 \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 , [2326] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\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 [2327] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\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 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2328] [2329] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2330] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\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 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \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 [2331] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\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., [2332] [2333] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\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 11688--11692 []\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 11688--11692 \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 [2334] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2335] [2336] [2337] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\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 [2338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\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 12035--12035 []\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)[] [2339] [2340] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2341] [2342] [2343]) (./boot-pkg.tex [2344] Chapter 18. [2345] [2346] [2347] [2348] [2349] [2350] [2351] 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"), [2352] 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- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2353] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2354] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2355] 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 , [2356] 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 [2357] [2358] 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 [2359] 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 [2360] [2361] [2362] [2363] 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- [2364] [2365] [2366] [2367] [2368] 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), [2369] [2370] [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] 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),[] [2373] 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. [2374] [2375] [2376] 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 [2377] 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 , [2378] [2379] 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 [2380] [2381] [2382] [2383] [2384] 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,[] [2385] [2386] [2387] 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 , [2388] 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)) [2389] [2390] [2391] 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 [2392] [2393] [2394] [2395] [2396] [2397] [2398] 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)[] [2399] [2400] 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])[] [2401] [2402] [2403] 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 [2404] 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 [2405] [2406] 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 Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] 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 [2416] [2417] [2418] [2419] 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 [2420] 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])[] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] 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][] [2429] 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 [2430] 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 [2431] [2432] [2433] [2434] 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). [2435] [2436] 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[] [2437] [2438] [2439] 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 [2440] [2441] 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),[] [2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex [2450] Chapter 19. [2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex Chapter 20. [2467] Underfull \hbox (badness 3098) 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- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2468] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2469] 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]))[] [2470] [2471] Underfull \vbox (badness 10000) has occurred while \output is active [2472] [2473] 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, ...)[] [2474] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2475] 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)[] [2476] 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 [2477] [2478] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\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 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2479] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2481] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\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 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2482] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2483] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\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 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2484] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\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 [2485] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \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 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2486] [2487] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\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 1451--1454 [2488] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\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 1492--1492 []\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 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2489] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\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 [2490] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2491] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \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 [2492] [2493] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\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 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2494] [2495] [2496] [2497] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\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. [2498] [2499] [2500] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\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 , [2501] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\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 2403--2405 []\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 2426--2429 [][][]\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 , [2502] [2503] [2504] [2505] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\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 ):[] [2506] [2507] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2509] [2510] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2511] [2512] [2513] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2514] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\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 [2515] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] [2517] [2518] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\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 Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2519] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\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 , [2520] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which 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 Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\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 , [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\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 3844--3847 [][][]\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 , [2524] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\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 [2525] [2526] [2527] [2528] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \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 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2529] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2530] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\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 4250--4250 [] \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 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\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 4257--4257 [] \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 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\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 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\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 4653--4653 []\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 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2537] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2538]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2539] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2540] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2541] [2542] [2543]) (./foreign-pkg.tex [2544] Chapter 22. [2545] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2546] [2547] 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 , [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2549] [2550] [2551] 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,[] [2552] 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"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \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 [2553] 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 [2554] 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.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2555] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\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="")[] [2556] [2557] 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])[] [2558] [2559] 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) [2560] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2563] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2564] 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 , [2565] Underfull \hbox (badness 6725) 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 [2566]) (./lattice-pkg.tex Chapter 23. [2567] [2568] [2569] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2570] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2571] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2572] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2573] [2574] 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 [2575] [2576] [2577] [2578] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2579] 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 [2580] [2581] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2582] [2583] [2584] 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 , [2585] 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 , [2586] Underfull \vbox (badness 10000) has occurred while \output is active [2587] 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 [2588] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2589] 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 [2590] [2591] [2592] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2593] 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 [2594] [2595] [2596] 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"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2597] [2598] [2599] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2600] [2601] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2602] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2603] 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 Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \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 [2604] 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- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \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 [2605] [2606] 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),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2607] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x 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 [2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2612] 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"),[] [2613] [2614] [2615] [2616] [2617] 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))) [2618] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2619] [2620] 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) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\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 [2621] 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 [2622] [2623] 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 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\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 [2624] [2625] [2626] [2627] [2628] [2629] 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")[] [2630] [2631] 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 . [2632] [2633] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\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 [2634] [2635] [2636] [2637] [2638] [2639] 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 Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2640] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \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 Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2641] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\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 [2642] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2643] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \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),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2644] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2645] 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 Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \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 [2646] [2647] 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 , [2648] [2649] 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- [2650] [2651] 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 Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \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 [2652] [2653] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2654] 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 [2655] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2656] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2657] [2658] [2659] [2660] [2661] 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- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \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 [2662] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2663] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \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 [2664] 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 [2665] [2666] 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 [2667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2668] [2669] 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 Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2670] 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)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2671] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2672] [2673] [2674] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2675] 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 Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] 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 [2684] [2685] 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, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2686] 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 [2687] 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 [2688] 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 [2689] [2690] 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)[] [2691] [2692] 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)),[] [2693] Overfull \hbox (84.94879pt 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 (104.63074pt 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 [2694] [2695] [2696] [2697] [2698] [2699] [2700] Underfull \hbox (badness 4205) 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 4518) 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 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular 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 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2708]) (./mgcv-pkg.tex Chapter 24. [2709] [2710] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2711] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2712] [2713] [2714] [2715] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\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 , [2716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\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)+[] [2717] [2718] [2719] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\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 [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 697--698 []\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1 /pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then [2722] Underfull \hbox (badness 1158) in paragraph at lines 749--751 []\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 [2723] Underfull \hbox (badness 1259) in paragraph at lines 812--813 []\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). [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] [2726] [2727] [2728] [2729] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1160--1160 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1161--1161 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1167--1167 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2730] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1174--1174 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1176--1176 []\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),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1178--1178 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1209--1209 []\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)[] [2731] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1270--1270 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2732] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1281--1281 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1315--1315 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1818--1818 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2193--2201 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2210--2210 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2222--2225 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2235--2239 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2748] Underfull \hbox (badness 1043) in paragraph at lines 2261--2266 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] Underfull \hbox (badness 1043) in paragraph at lines 2424--2430 \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 [2751] [2752] Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\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 , [2753] Underfull \vbox (badness 10000) has occurred while \output is active [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3216--3216 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2764] [2765] [2766] [2767] [2768] [2769] Underfull \hbox (badness 5189) in paragraph at lines 3580--3584 []\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 [2770] [2771] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3697--3697 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2772] [2773] [2774] Underfull \hbox (badness 1184) in paragraph at lines 3866--3870 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2775] [2776] [2777] [2778] [2779] [2780] [2781] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4312--4312 [] \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)+[] [2782] [2783] [2784] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4462--4462 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2785] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4556--4556 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2786] Underfull \hbox (badness 1142) in paragraph at lines 4587--4591 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2787] Underfull \hbox (badness 10000) in paragraph at lines 4656--4665 []\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 [2788] [2789] Underfull \hbox (badness 5970) in paragraph at lines 4773--4779 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4773--4779 [][]\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 . [2790] Underfull \vbox (badness 10000) has occurred while \output is active [2791] [2792] [2793] Underfull \hbox (badness 1577) in paragraph at lines 5053--5056 []\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 5060--5061 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2794] [2795] [2796] [2797] [2798] [2799] [2800] Underfull \hbox (badness 6708) in paragraph at lines 5449--5450 []\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 [2801] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5498--5498 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2802] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5523--5523 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5552--5552 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] Underfull \vbox (badness 10000) has occurred while \output is active [2803] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5605--5605 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2804] [2805] [2806] [2807] [2808] [2809] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5929--5929 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5931--5931 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5952--5956 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2810] [2811] [2812] [2813] [2814] [2815] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6267--6267 []\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) [2816] [2817] [2818] [2819] Underfull \vbox (badness 10000) has occurred while \output is active [2820] Underfull \vbox (badness 10000) has occurred while \output is active [2821] [2822] [2823] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6696--6696 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6723--6723 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1242) in paragraph at lines 7266--7267 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2833] [2834] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7353--7353 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2835] [2836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7416--7416 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7435--7435 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] Underfull \vbox (badness 10000) has occurred while \output is active [2855] [2856] Underfull \hbox (badness 10000) in paragraph at lines 8655--8658 []\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 8655--8658 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8655--8658 \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 . [2857] Underfull \hbox (badness 10000) in paragraph at lines 8711--8714 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8711--8714 \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 [2858] [2859] [2860] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8931--8931 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8932--8932 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8935--8935 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2861] [2862] [2863] Underfull \hbox (badness 1629) in paragraph at lines 9093--9098 \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 [2864] [2865] [2866] [2867] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2868] [2869] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9468--9468 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2870] [2871] [2872] [2873] Underfull \vbox (badness 10000) has occurred while \output is active [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9736--9736 [] \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[] [2875] Underfull \hbox (badness 1205) in paragraph at lines 9774--9776 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9774--9776 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9780--9785 []\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 [2876] Underfull \hbox (badness 1205) in paragraph at lines 9864--9866 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9864--9866 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2877] Underfull \hbox (badness 10000) in paragraph at lines 9933--9936 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9933--9936 [][]\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, [2878] [2879] Underfull \hbox (badness 1253) in paragraph at lines 10063--10065 []\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, [2880] [2881] [2882] [2883] Underfull \hbox (badness 1946) in paragraph at lines 10241--10248 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10241--10248 \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 10241--10248 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10249--10252 []\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 10249--10252 \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. [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10315--10315 []\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 10344--10347 []\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 , [2885] [2886] [2887] [2888] [2889] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10631--10631 []\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) [2890] [2891] [2892] [2893] [2894] [2895] Underfull \hbox (badness 3861) in paragraph at lines 10972--10975 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10979--10979 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10992--10996 []\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- [2896] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\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- [2897] [2898] [2899] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11173--11173 [] \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 11184--11189 []\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 [2900] Underfull \hbox (badness 1803) in paragraph at lines 11261--11265 \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 11273--11285 \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 11290--11294 \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 11290--11294 \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 , [2901] [2902] [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] Underfull \hbox (badness 6876) in paragraph at lines 11485--11491 [][][]\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 11526--11527 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2905] [2906] Underfull \hbox (badness 10000) in paragraph at lines 11643--11644 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2907] [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11697--11697 [] \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 11709--11709 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11720--11720 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11721--11721 [] \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 11726--11726 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11732--11732 [] \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 11733--11733 [] \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:[] [2910] Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 \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 [2911] [2912] Underfull \hbox (badness 10000) in paragraph at lines 11930--11931 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12011--12011 []\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 12012--12012 []\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[] [2914] [2915] [2916] Underfull \hbox (badness 10000) in paragraph at lines 12162--12163 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2917] [2918] [2919] [2920] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12401--12401 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2921] Underfull \hbox (badness 10000) in paragraph at lines 12462--12464 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2922] [2923] Underfull \vbox (badness 10000) has occurred while \output is active [2924] Underfull \hbox (badness 10000) in paragraph at lines 12621--12624 []\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 12621--12624 \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 12621--12624 \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" [2925] [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12703--12703 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12748--12754 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12748--12754 \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- [2927] [2928] [2929] Underfull \vbox (badness 10000) has occurred while \output is active [2930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12962--12962 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 13065--13073 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13091--13092 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2933] [2934] [2935] [2936] Underfull \hbox (badness 3396) in paragraph at lines 13352--13355 [][][]\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 [2937] Underfull \hbox (badness 10000) in paragraph at lines 13397--13399 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2938] [2939] [2940] [2941] Underfull \hbox (badness 10000) in paragraph at lines 13621--13624 []\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 13621--13624 \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 [2942] Underfull \hbox (badness 10000) in paragraph at lines 13654--13658 [][][]\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 13654--13658 [][]\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 13654--13658 [][]\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 , [2943] [2944] [2945] [2946] [2947] Underfull \hbox (badness 2158) in paragraph at lines 13944--13944 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2948] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14023--14023 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2949] [2950] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14157--14157 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2951] [2952] [2953] Underfull \hbox (badness 4846) in paragraph at lines 14288--14291 []\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 [2954] [2955] [2956] [2957] [2958] Underfull \vbox (badness 10000) has occurred while \output is active [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2967] [2968] [2969] [2970] [2971] [2972] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15477--15477 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2973] [2974] [2975] [2976] [2977] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15771--15771 []\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 15772--15772 []\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 15784--15784 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2978] [2979] [2980]) (./nlme-pkg.tex Chapter 25. [2981] 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 [2982] 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 [2983] [2984] [2985] [2986] [2987] 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,[] [2988] [2989] 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 --------------------------- ---------------[] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] 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"),[] [2998] 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 [2999] [3000] [3001] [3002] [3003] [3004] [3005] 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 , [3006] 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 [3007] [3008] [3009] [3010] [3011] 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 , [3012] 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")[] [3013] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3014] [3015] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\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 , [3016] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\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 , [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\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 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\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 , [3061] [3062] [3063] [3064] [3065] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3066] [3067] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\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 , [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \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 [3077] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\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 , [3078] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\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 , [3079] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\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 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3080] [3081] [3082] [3083] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\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 , [3084] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\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 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3085] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\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 , [3090] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\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 [3091] [3092] [3093] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\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 , [3094] [3095] [3096] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\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 7407--7415 \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 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\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 , [3097] [3098] [3099] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\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 [3100] [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3106] [3107] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\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 8157--8174 [][]\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 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3108] [3109] [3110] [3111] [3112] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3114] [3115] [3116] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\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 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3126] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\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 [3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3131] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\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 9743--9746 []\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 9743--9746 \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 [3132] [3133] [3134] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3135] [3136] [3137] [3138] [3139] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\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 [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3143] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3144] [3145] [3146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3147] [3148] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\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[][][] [3149] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\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 Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\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 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3150] [3151] [3152] [3153] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\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 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\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 , [3170] [3171] [3172] [3173] [3174] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\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 [3175] [3176] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\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 , [3177] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\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 , [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3192] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\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 Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\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 13728--13735 \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 [3193] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\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 13792--13795 \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 [3194] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3195] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\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 Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \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 , [3196] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\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 , [3197] [3198] [3199] [3200] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3201] [3202] [3203] [3204] [3205] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \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 [3225] [3226] [3227] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3232] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\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 , [3233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3241] [3242] [3243] [3244] [3245] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \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 17147--17156 \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" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3246] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \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 , [3247] [3248] [3249] [3250] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\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 , [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\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 17993--18003 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \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 [3259] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \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 [3260] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \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 [3261] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\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 18221--18226 \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 [3262] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \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 [3263] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\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 18317--18326 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \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 [3264] [3265] [3266] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \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 [3267] [3268] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \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 [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3277] 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,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3278] [3279] [3280] 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,[] [3281] 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)[] [3282] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3283] 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,[] [3284]) (./rpart-pkg.tex Chapter 27. [3285] [3286] [3287] [3288] 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, ...)[] [3289] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3290] [3291] [3292] 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 [3293] [3294] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3295] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3296] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3297] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3298] [3299] [3300] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\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 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3301] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\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 [3302] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\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 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3303] [3304] [3305] [3306] [3307] [3308] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\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 ', [3309] [3310] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3311] [3312] [3313]) (./spatial-pkg.tex [3314] Chapter 28. [3315] [3316] [3317] [3318] [3319] [3320] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333]) (./survival-pkg.tex [3334] Chapter 29. [3335] [3336] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3337] [3338]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \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 \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3339] [3340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3342] [3343] Underfull \vbox (badness 10000) has occurred while \output is active [3344] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3345] [3346] 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,[] [3347] [3348] [3349] 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[] [3350] [3351] 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) [3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3353] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3354] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\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 , [3360] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3367] [3368] [3369] [3370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3371] [3372] [3373] [3374] [3375] Underfull \vbox (badness 2393) has occurred while \output is active [3376] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \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 2862--2864 []\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 [3377] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\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 [3378] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \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 )))[] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3384] [3385] [3386] [3387] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \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 )))[] [3388] Underfull \vbox (badness 10000) has occurred while \output is active [3389] [3390] [3391] [3392] [3393] [3394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3395] [3396] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3397] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\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[] [3398] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3399] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3400] [3401] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\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 [3402] [3403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3404] [3405] [3406] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3407] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\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 4910--4910 []\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 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3408] [3409] [3410] [3411] [3412] Underfull \vbox (badness 2126) has occurred while \output is active [3413] [3414] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \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 [3415] [3416] [3417] [3418] [3419] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\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 5700--5700 []\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 \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3420] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\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 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3427] [3428] [3429] [3430] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \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 ),[] [3431] [3432] Underfull \vbox (badness 10000) has occurred while \output is active [3433] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\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 [3434] [3435] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3437] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3438] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3439] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3440] [3441] [3442] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\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 , [3443] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3448] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3450] [3451] [3452] [3453] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3454] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3455] [3456] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \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 [3457] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3458] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3459] [3460] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \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 )[] [3461] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \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 )[] [3462] [3463] [3464] [3465] [3466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3467] [3468] [3469] [3470] [3471] [3472]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3473] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3474] [3475] [3476]) No file fullrefman.ind. 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(/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf-dist/tex/latex/url/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\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 Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \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, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\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 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [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] Underfull \hbox (badness 2359) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 860--860 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1147--1150 []\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 [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1381--1387 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\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 [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\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 [38] [39] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40] [41] [42] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] [61] [62] [63] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \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 [64] [65] Underfull \hbox (badness 4595) in paragraph at lines 4280--4283 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [66] [67] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4435--4435 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [68] Underfull \hbox (badness 1199) in paragraph at lines 4465--4471 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4476--4479 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [69] Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4556--4561 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [70] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [75] [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\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 [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 1796) in paragraph at lines 5845--5853 []\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 : / / [89] [90] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6041--6041 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6042--6042 []\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}[] [91] [92] [93] Underfull \hbox (badness 1635) in paragraph at lines 6208--6211 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6212--6215 []\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 Underfull \hbox (badness 1102) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6243--6251 []\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 [94] [95] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [96] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \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 [99] [100] Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110] [111] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112] [113] [114] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [115] [116] Underfull \hbox (badness 8132) in paragraph at lines 7836--7840 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7836--7840 \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 Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\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 1062) in paragraph at lines 7855--7865 [][]\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 [117] Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891 []\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") Underfull \hbox (badness 7451) in paragraph at lines 7926--7936 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7926--7936 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124] [125] [126] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8805--8809 []\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 [130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [131] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [132] [133] Underfull \hbox (badness 5403) in paragraph at lines 9039--9041 []\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 9058--9060 []\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 [134] Underfull \hbox (badness 1132) in paragraph at lines 9130--9137 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [135] Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\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 [136] [137] [138] [139] [140] [141] [142] [143] [144] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\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 [145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\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 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146] [147] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\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 [148] [149] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \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 _ [150] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [152] [153] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [154] Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [157] Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158] [159] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\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 [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\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 [170] Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \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 [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\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 [174] Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175] [176] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [177] [178] [179] Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [180] [181] [182] [183] [184] [185] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186] [187] [188] [189] Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190] [191] Underfull \hbox (badness 2221) in paragraph at lines 13178--13187 \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 [192] [193] [194] [195] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\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 [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 13704--13706 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [200] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\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 , [201] Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [202] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\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 , [203] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- [205] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [206] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210] [211] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497 []\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 14500--14500 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [212] Underfull \hbox (badness 1168) in paragraph at lines 14584--14588 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14584--14588 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [213] Underfull \hbox (badness 6944) in paragraph at lines 14679--14682 [][][]\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 , [214] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 14838--14840 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14884--14892 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14899--14903 []\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 [217] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\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 [218] Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\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, Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14979--14987 []\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 Underfull \hbox (badness 3601) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [220] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [232] [233] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\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 Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\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 , [234] [235] [236] [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [242] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [243] [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\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))) [248] [249] [250] [251] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252] [253] [254] Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257] [258] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\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 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259] [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\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 17942--17942 []\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):[] [261] [262] [263] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\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 [264] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\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 18246--18262 [][][]\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 , [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 4699) in paragraph at lines 18660--18663 []\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 , [271] [272] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [273] [274] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1430) in paragraph at lines 19331--19336 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 19331--19336 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [282] Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [283] Underfull \hbox (badness 10000) in paragraph at lines 19452--19459 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19452--19459 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19468--19470 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [284] Underfull \hbox (badness 1975) in paragraph at lines 19540--19543 []\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 [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\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 [291] Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\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 / [292] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\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 [293] Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\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 20153--20157 [][]\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 [294] [295] Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\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 , [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\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 [298] Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\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 20442--20447 \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 20442--20447 \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 20442--20447 \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 [299] [300] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\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 [302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303] [304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\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 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305] Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306] Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\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 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307] Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [309] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\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 Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\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 1939) in paragraph at lines 21384--21390 \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 names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [313] [314] [315] [316] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317] [318] [319] [320] [321] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\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 22006--22006 [] \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 22009--22009 []\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)[] [322] [323] Underfull \hbox (badness 1655) in paragraph at lines 22133--22137 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [324] [325] [326] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\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. [327] [328] [329] [330] [331] [332] [333] [334] Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\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 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \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 ; [343] [344] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\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 [345] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\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 5077) in paragraph at lines 23672--23678 \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 10000) in paragraph at lines 23682--23685 []\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 23682--23685 \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 [346] [347] Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348] [349] [350] [351] Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\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 [352] [353] [354] [355] [356] [357] [358] Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\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 24549--24553 \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 [359] Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\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 24642--24648 \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 [360] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \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:[] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\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 Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365] [366] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367] [368] [369] [370] Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372] [373] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374] [375] [376] Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\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 25948--25954 \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 25948--25954 \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 [377] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\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 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378] Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\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 10000) in paragraph at lines 26061--26068 \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 Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379] [380] [381] [382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\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 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \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)] [383] [384] [385] [386] [387] Underfull \hbox (badness 4341) in paragraph at lines 26729--26731 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26765--26771 [][][]\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 [388] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787 []\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 26799--26799 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [389] [390] [391] [392] [393] [394] [395] Underfull \hbox (badness 10000) in paragraph at lines 27233--27237 []\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, [396] Underfull \hbox (badness 1796) in paragraph at lines 27299--27302 []\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 [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 27499--27502 []\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 [400] [401] [402] [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 1226) in paragraph at lines 28131--28136 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [409] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176 [] \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))[] [410] [411] [412] [413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442 []\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 28453--28453 []\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 28459--28459 []\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 28460--28460 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [414] Underfull \hbox (badness 7415) in paragraph at lines 28538--28542 []\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 [415] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [416] Underfull \hbox (badness 2418) in paragraph at lines 28718--28729 []\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 [417] [418] Underfull \hbox (badness 1248) in paragraph at lines 28852--28859 \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 28852--28859 \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 / [419] [420] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [421] Underfull \hbox (badness 1337) in paragraph at lines 29065--29068 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 29131--29142 []\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 Underfull \hbox (badness 10000) in paragraph at lines 29143--29146 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [423] [424] Underfull \hbox (badness 1117) in paragraph at lines 29238--29244 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 4048) in paragraph at lines 29616--29621 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29616--29621 \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 , [431] [432] [433] [434] [435] [436] [437] [438] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [439] [440] [441] [442] Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443] [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\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 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452] [453] [454] [455] [456] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [457] [458] [459] Underfull \hbox (badness 3375) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/ ptm/m/n/10 , are in-valid, e.g., du- Underfull \hbox (badness 2359) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal Underfull \hbox (badness 2582) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call [460] [461] [462] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [463] [464] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [465] [466] [467] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469] Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\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 [470] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [474] [475] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] Underfull \hbox (badness 1735) in paragraph at lines 33605--33611 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [488] Underfull \hbox (badness 4303) in paragraph at lines 33621--33624 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [489] [490] [491] [492] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [494] [495] [496] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [497] Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; Underfull \hbox (badness 2512) in paragraph at lines 34251--34253 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [498] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [499] [500] [501] [502] [503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [511] [512] [513] Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\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 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515] Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \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 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \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 35534--35541 \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 [516] [517] [518] [519] [520] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [522] [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [525] [526] [527] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529] [530] [531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532] [533] [534] [535] [536] [537] [538] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [539] Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 37192--37192 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [540] [541] [542] [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\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. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \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 [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \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 [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\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 [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\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 [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\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 [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\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 [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\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 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\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., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437 [] \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 39439--39439 [] \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),[] [574] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441 [] \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 39454--39456 []\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 [575] Underfull \hbox (badness 10000) in paragraph at lines 39534--39537 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39652--39656 [][][]\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 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39714--39718 [][][]\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 : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40132--40139 \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 40188--40197 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40188--40197 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40198--40206 []\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 40198--40206 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40198--40206 \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 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40264--40272 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40273--40276 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40330--40332 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40339--40339 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40556--40558 []\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 [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40678--40678 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40680--40680 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41042--41044 []\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 [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41208--41211 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41215--41223 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41215--41223 \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 Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41224--41228 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41245--41250 [][][]\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; [600] Underfull \hbox (badness 3895) in paragraph at lines 41307--41319 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41307--41319 \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 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41492--41495 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41629--41629 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42096--42096 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42105--42105 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42222--42225 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42226--42233 []\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 [614] Underfull \hbox (badness 4726) in paragraph at lines 42252--42256 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42252--42256 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42441--42443 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42545--42545 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42620--42620 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42628--42628 []\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 ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42758--42763 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42758--42763 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42758--42763 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42774--42779 []\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 [622] Underfull \hbox (badness 1603) in paragraph at lines 42793--42797 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42864--42870 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 42899--42899 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42993--42995 []\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 . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43355--43359 []\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 [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43395--43395 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43416--43420 []\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 [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \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 [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1472) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\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. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \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 [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] Overfull \vbox (4.29591pt too high) has occurred while \output is active [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 2376) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\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 [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \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 [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \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 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \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 [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\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 [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\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 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\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 Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\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 Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\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 [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\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 [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \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 Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\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 / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\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 Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \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 [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\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 [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\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 / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\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 [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\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- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\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 [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\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 Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\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 [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \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 [852] [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\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 [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\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 [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\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 [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\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 [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\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 [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \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 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\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. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\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 [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\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 [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\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 [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\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 [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\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)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \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 [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\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- [971] [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\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 [975] [976] [977] [978] [979] [980] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [981] [982] [983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [984] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\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 , [985] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\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 [986] [987] [988] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\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 [989] [990] [991] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\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- [992] [993] [994] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [995] [996] [997] [998] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [999] [1000] [1001] [1002] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1003] [1004] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1005] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\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 [1006] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1007] [1008] [1009] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1010] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1023] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\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- [1024] [1025] [1026] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\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 [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1046] [1047] [1048] [1049] [1050] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\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 [1051] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\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 , [1052] [1053] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\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 [1054] [1055] [1056] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1057]) (./methods-pkg.tex [1058] Chapter 7. [1059] [1060] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1061] [1062] [1063] 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- [1064] [1065] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1066] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1067] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1068] [1069] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1085] [1086] [1087] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1088] [1089] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1090] [1091] [1092] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1093] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1094] [1095] [1096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1097] [1098] [1099] [1100] [1101] [1102] [1103] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1106] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1107] [1108] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") [1109] Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1113] [1114] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1115] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1116] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1117] [1118] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1119] 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 , [1120] [1121] [1122] 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 [1123] [1124] [1125] [1126] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1127] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1128] [1129] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1130] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1131] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1132] [1133] [1134] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1135] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1136] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1137] [1138] [1139] [1140] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1141] [1142] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1143] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1144] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1145] 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 [1146] Underfull \vbox (badness 10000) has occurred while \output is active [1147] [1148] [1149]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1150] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1151] [1152] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1153]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1154] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1155] [1156] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1157] [1158] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1171] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1172] [1173] [1174] [1175] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1176] [1177] [1178] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1179] [1180] Underfull \vbox (badness 2302) has occurred while \output is active [1181] 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[] [1182] [1183] [1184] [1185] 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[] [1186] 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][] [1187] 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][] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1197] [1198] [1199] [1200]) (./parallel-pkg.tex 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 [1201] 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 [1202] [1203] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1204] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1205] [1206] 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 [1207] [1208] [1209] [1210] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\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 742--751 \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 [1211] [1212] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1213] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1214] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1215] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1216] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\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 [1217] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\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)[] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\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 [1220] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\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 [1221] [1222]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1223] [1224] [1225] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1230] [1231] [1232] [1233] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1234] [1235] [1236]) (./stats-pkg.tex Chapter 10. [1237] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1238] [1239] [1240] [1241] [1242] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\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 [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1258] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1259] [1260] [1261] [1262] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1263] [1264] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1265] [1266] [1267] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1268] [1269] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1270] [1271] [1272] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1273] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1274] [1275] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1276] [1277] [1278] [1279] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1280] [1281] [1282] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1283] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1284] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1285] [1286] [1287] [1288] [1289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1290] [1291] [1292] [1293] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1294] [1295] [1296] [1297] [1298] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1299] [1300] [1301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1302] [1303] [1304] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1305] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1306] [1307] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1308] [1309] [1310] [1311] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\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))[] [1312] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1313] [1314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\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 [1315] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1316] [1317] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\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 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \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 , [1318] [1319] [1320] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1321] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1322] [1323] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1324] [1325] [1326] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1327] [1328] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\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 [1329] [1330] [1331] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1332] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\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 6468--6473 \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, [1333] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\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 [1334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\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 6554--6554 []\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):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1335] [1336] [1337] [1338] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \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 [1345] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\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 [1346] [1347] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\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 = [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\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 , ..., [1354] [1355] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1356] [1357] [1358] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1366] [1367] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1368] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1369] [1370] [1371] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1372] [1373] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \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 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1374] [1375] [1376] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1377] [1378] [1379] [1380] [1381] [1382] [1383] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\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); [1384] [1385] [1386] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\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 [1387] [1388] [1389] [1390] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1391] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1392] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\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 [1393] [1394] [1395] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ [1396] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1397] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \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 (= [1398] [1399] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \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 [1400] [1401] [1402] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1403] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \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 11337--11341 []\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 [1405] [1406] [1407] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\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 [1408] [1409] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1410] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1411] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\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 11802--11804 []\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 [1412] [1413] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1414] [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1416] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1417] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1418] [1419] [1420] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\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 [1421] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\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 [1422] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1423] [1424] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1425] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\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 Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\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 12731--12735 \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 [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1437] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\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 , [1440] [1441] [1442] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1443] [1444] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \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 , [1445] [1446] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1449] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\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 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1451] [1452] [1453] [1454] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\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 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1455] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\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 , [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1474] [1475] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \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 [1476] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\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 16097--16106 \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 16097--16106 \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 [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\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[] [1486] [1487] [1488] [1489] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1498] [1499] Underfull \vbox (badness 10000) has occurred while \output is active [1500] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1501] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1502] [1503] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\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 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1504] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\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 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1513] Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \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 18529--18531 []\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 [1514] [1515] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \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 [1516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\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 18698--18698 []\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 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1517] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\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 18756--18767 \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 [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1519] [1520] [1521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1522] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\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 [1523] [1524] [1525] [1526] [1527] [1528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1529] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \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 (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1530] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\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 [1531] [1532] [1533] [1534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1535] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\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 [1536] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1537] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\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)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1539] [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1541] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1542] Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1543] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \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 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1557] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\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 21342--21348 []\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 , [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1575] [1576] [1577] [1578] [1579] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1588] [1589] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\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 [1590] [1591] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1592] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\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 Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\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 [1593] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1595] [1596] [1597] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\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 Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\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 [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1602] [1603] [1604] [1605] [1606] [1607] [1608] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\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 , [1609] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1610] [1611] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\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 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1613] [1614] [1615] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1616] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1617] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1618] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1619] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1620] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1622] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1623] [1624] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1632] [1633] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\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 26293--26293 []\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 [1634] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\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 [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \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 26402--26402 [] \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 26411--26411 [] \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 26412--26412 [] \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 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1636] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\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 Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \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 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1637] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\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 [1638] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \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 26581--26581 [] \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 26591--26591 [] \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 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\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 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1640] [1641] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1642] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\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 [1643] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1644] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\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 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1645] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\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 27023--27023 []\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 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \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 27092--27097 []\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 [1647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\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 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1648] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\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 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\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 27216--27216 []\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 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1657] [1658] [1659] [1660] [1661] [1662] [1663] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\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 [1664] [1665] [1666] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\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 [1667] [1668] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\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 [1669] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\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 [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1671] [1672] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\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) [1673] [1674] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1677] [1678] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\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 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1679] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1680] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1681] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1682] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1683] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\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 [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1692] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1693] [1694] [1695] [1696] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1697] [1698] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\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:[] [1699] [1700] [1701] [1702] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1711] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1712] [1713] [1714] [1715] [1716] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1717] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\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 [1718] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\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 "")[] [1719]) (./stats4-pkg.tex [1720] Chapter 11. [1721] [1722] [1723] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1727] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1728] [1729]) (./tcltk-pkg.tex [1730] Chapter 12. [1731] [1732] [1733] [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1735] [1736] [1737] Underfull \vbox (badness 10000) has occurred while \output is active [1738] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1750]) (./tools-pkg.tex Chapter 13. [1751] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1752] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1753] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1754] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1755] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\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 [1756] [1757] [1758] [1759] [1760] [1761] [1762] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1763] [1764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 960--960 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1765] [1766] Underfull \hbox (badness 1635) in paragraph at lines 1060--1062 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1767] Underfull \hbox (badness 5431) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1138--1148 \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- [1768] Underfull \hbox (badness 1014) in paragraph at lines 1160--1162 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1166--1168 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1769] Underfull \hbox (badness 10000) in paragraph at lines 1211--1214 []\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 [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 1360--1363 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1381--1383 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1772] [1773] [1774] [1775] [1776] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1683--1683 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1693--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1693--1698 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1897 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1780] [1781] [1782] [1783] Underfull \hbox (badness 1142) in paragraph at lines 2165--2171 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2199--2199 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1784] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2200--2200 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2227--2234 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2227--2234 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2227--2234 \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 [1785] Underfull \hbox (badness 1342) in paragraph at lines 2279--2285 \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 [1786] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2355--2355 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2368--2374 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2368--2374 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1787] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2401--2401 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2410--2410 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2427--2427 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1788] [1789] [1790] [1791] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1792] Underfull \hbox (badness 2486) in paragraph at lines 2737--2745 []\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 [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 1072) in paragraph at lines 3115--3117 []\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 [1798] [1799] [1800] [1801] [1802] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3451--3451 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1803] [1804] [1805] [1806] Underfull \hbox (badness 4108) in paragraph at lines 3695--3702 []\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 [1807] [1808] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3795--3795 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3798--3798 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3815--3817 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3832--3838 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1809] [1810] Underfull \hbox (badness 7832) in paragraph at lines 3954--3957 []\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 [1811] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4029--4029 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1812] Underfull \hbox (badness 1137) in paragraph at lines 4052--4054 []\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 [1813] [1814] [1815] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4226--4226 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4237--4240 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4253--4258 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4261--4267 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4261--4267 \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 [1816] Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1817] [1818] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4474--4474 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4486--4489 []\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 ', [1819] Underfull \hbox (badness 1742) in paragraph at lines 4490--4500 \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 4525--4531 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4525--4531 \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 ', Underfull \hbox (badness 1571) in paragraph at lines 4553--4557 []\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 [1820] [1821] [1822]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1823] [1824] [1825] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1826] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1827] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1828] [1829] [1830] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\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 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\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 620--626 \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- [1832] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1833] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \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 [1834] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1835] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1836] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1837] [1838] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1839] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1840] [1841] [1842] [1843] [1844] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1845] [1846] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1847] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1848] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1849] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1850] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1851] [1852] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \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")[] [1853] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1854] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1855] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\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; [1856] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\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 Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1857] [1858] [1859] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\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 [1864] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2941--2941 []\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 '[] [1865] Underfull \hbox (badness 2452) in paragraph at lines 3017--3020 []\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 [1866] [1867] [1868] [1869] [1870] [1871] [1872] Underfull \hbox (badness 1072) in paragraph at lines 3499--3507 []\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 [1873] Underfull \hbox (badness 1231) in paragraph at lines 3548--3554 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3555--3560 []\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 3555--3560 \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 3555--3560 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1874] [1875] Underfull \hbox (badness 4660) in paragraph at lines 3677--3680 \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 3701--3703 []\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 [1876] [1877] [1878] Underfull \hbox (badness 1565) in paragraph at lines 3886--3890 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3907--3913 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1879] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3969--3969 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3997--4004 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1880] [1881] [1882] [1883] [1884] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4324--4324 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1901] Underfull \hbox (badness 10000) in paragraph at lines 5432--5434 []\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 [1902] Underfull \hbox (badness 1502) in paragraph at lines 5481--5486 []\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 5481--5486 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 5654--5663 []\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 5654--5663 \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 [1905] Underfull \hbox (badness 2150) in paragraph at lines 5717--5720 []\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 5733--5736 []\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 [1906] [1907] Underfull \hbox (badness 3118) in paragraph at lines 5854--5856 []\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 [1908] Underfull \hbox (badness 2409) in paragraph at lines 5887--5891 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1909] Underfull \hbox (badness 5091) in paragraph at lines 5991--5993 []\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 Overfull \hbox (44.55087pt too wide) in paragraph at lines 6007--6012 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6020--6027 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1910] Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., [1911] Underfull \hbox (badness 10000) in paragraph at lines 6137--6141 []\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 6151--6158 []\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 6151--6158 \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 6151--6158 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1912] Underfull \hbox (badness 1314) in paragraph at lines 6210--6217 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 6251--6256 [][][]\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 , [1913] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6274--6274 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6310--6314 []\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 6324--6327 []\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 [1914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6371--6371 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1915] [1916] Underfull \hbox (badness 4132) in paragraph at lines 6490--6492 []\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 [1917] [1918] [1919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1920] [1921] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1922] Underfull \hbox (badness 10000) in paragraph at lines 6831--6833 []\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 [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 6972--6974 []\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 6977--6979 []\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 [1925] [1926] [1927] Underfull \hbox (badness 1859) in paragraph at lines 7200--7203 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1928] Underfull \hbox (badness 1655) in paragraph at lines 7282--7285 []\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 7293--7293 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297 []\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 7305--7305 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1930] Underfull \hbox (badness 10000) in paragraph at lines 7390--7394 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1931] [1932] [1933] [1934] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7654--7654 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655 [] \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 7656--7656 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1935] Underfull \hbox (badness 10000) in paragraph at lines 7684--7686 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7698--7700 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7706--7711 []\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, [1936] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7752--7752 [] \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 7753--7753 [] \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[] [1937] [1938] Underfull \hbox (badness 10000) in paragraph at lines 7882--7887 []\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 7882--7887 [][]\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 10000) in paragraph at lines 7889--7892 []\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 7889--7892 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1939] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8005--8005 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177 [] \T1/pcr/m/n/9 "S original, "),[] [1943] Underfull \hbox (badness 1789) in paragraph at lines 8300--8302 []\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 [1944] Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1945] [1946] Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1948] [1949] [1950] [1951] Underfull \hbox (badness 5203) in paragraph at lines 8869--8872 []\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 [1952] [1953] [1954] Underfull \hbox (badness 1776) in paragraph at lines 9095--9102 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1955] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1956] [1957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1958] [1959] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461 []\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[] [1960] [1961] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1962] Underfull \hbox (badness 1077) in paragraph at lines 9627--9630 []\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 [1963] [1964] [1965] [1966] [1967] [1968] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1969] Underfull \hbox (badness 10000) in paragraph at lines 10154--10156 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1970] [1971] Underfull \hbox (badness 2181) in paragraph at lines 10277--10281 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10277--10281 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10289--10293 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [1972] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10311--10311 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1973] [1974] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1975] Underfull \hbox (badness 1917) in paragraph at lines 10566--10569 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10566--10569 \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 [1976] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589 []\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 '[] [1977] Underfull \hbox (badness 8075) in paragraph at lines 10652--10654 []\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 [1978] Underfull \hbox (badness 6725) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10702--10711 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10702--10711 \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 [1979] Underfull \hbox (badness 3646) in paragraph at lines 10828--10830 [][][]$\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 / [1980] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 11047--11051 []\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 11078--11084 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1984] Underfull \hbox (badness 2012) in paragraph at lines 11173--11179 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1985] Underfull \hbox (badness 2096) in paragraph at lines 11186--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11189--11191 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11196--11199 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11200--11203 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1986] Underfull \hbox (badness 1009) in paragraph at lines 11272--11283 []\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 [1987] Underfull \hbox (badness 2846) in paragraph at lines 11359--11369 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11515--11518 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1990] Underfull \hbox (badness 2158) in paragraph at lines 11594--11597 []\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 [1991] [1992] [1993] Underfull \hbox (badness 3333) in paragraph at lines 11774--11776 []\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- [1994] [1995] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1996] Underfull \hbox (badness 5970) in paragraph at lines 11972--11975 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11972--11975 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11983--11992 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1997] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12065--12065 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12067--12067 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1998] [1999] [2000] Underfull \hbox (badness 10000) in paragraph at lines 12235--12237 []\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 [2001] [2002] Underfull \hbox (badness 4492) in paragraph at lines 12392--12399 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12392--12399 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12392--12399 \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$"\T1/ptm/m/n/10 ) and [2003] [2004] [2005] Underfull \hbox (badness 2020) in paragraph at lines 12555--12571 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12555--12571 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2006] Underfull \hbox (badness 2809) in paragraph at lines 12675--12679 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12675--12679 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12690--12694 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 [][][]$\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 . Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2007] [2008] [2009] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2010] [2011] [2012] [2013] [2014] [2015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13273--13275 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13286--13290 \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 Overfull \hbox (36.87935pt too wide) in paragraph at lines 13300--13304 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \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[][][] [2016] Underfull \hbox (badness 1052) in paragraph at lines 13312--13314 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13363--13368 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13371--13374 [][][]\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 , [2017] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2018] [2019] [2020] Underfull \hbox (badness 10000) in paragraph at lines 13613--13616 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13629--13629 []\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:[] [2021] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13696--13696 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2022] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13718--13718 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13737--13737 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2023] Underfull \hbox (badness 1454) in paragraph at lines 13764--13768 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13789--13792 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13834--13836 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2024] Underfull \hbox (badness 3271) in paragraph at lines 13846--13850 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex Chapter 15. [2029] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2030] [2031] [2032] [2033] [2034] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2035] [2036] [2037] [2038]) (./MASS-pkg.tex Chapter 16. [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2073] [2074] [2075] [2076] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\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 [2077] [2078] [2079] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \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 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2080] [2081] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\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 Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2082] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2085] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\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 [2098] [2099] [2100] [2101] [2102] [2103] [2104] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2105] [2106] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2107] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2113] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2122] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\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") [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \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 \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2125] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\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 [2126] [2127] [2128] [2129] Underfull \vbox (badness 10000) has occurred while \output is active [2130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2131] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2132] [2133] [2134] [2135] [2136] [2137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2138] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\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 ) = [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2140] [2141] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \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 [2142] [2143] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2144] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2145] [2146] [2147] [2148] [2149] [2150] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\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 Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2151] [2152] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\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 [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2173] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\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), [2174] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]) (./Matrix-pkg.tex [2188] 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 [2189] 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 [2190] 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 [2191] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2192] [2193] 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) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2194] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2195] [2196] 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:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2197] 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 . [2198] [2199] [2200] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2201] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2202]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \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 \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2203pdfTeX 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' ] [2204] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\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 [2206] 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 [2207] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2208] Underfull \hbox (badness 6445) 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 3861) 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 Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \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 [2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \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 \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 \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 \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 \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2210] 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 [2211] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2212] 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 [2213] [2214] [2215] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2218] Underfull \hbox (badness 4713) 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 [2219] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2220] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2221] Underfull \hbox (badness 2707) 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 ; [2222] 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 [2223] 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 [2224] 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 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of 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 3803) 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 [2225] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class 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 [2226] [2227] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his 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 pre fer-able to (and more ef-fi-cient than) [2228] Underfull \hbox (badness 1168) 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 [2229] [2230] Underfull \hbox (badness 4967) 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 [2231] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2232] [2233] 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 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2234] Underfull \hbox (badness 4967) 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 Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2235] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2236] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2237] 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 [2238] 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 - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2239] [2240] [2241] [2242] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2243] [2244] 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():[] [2245] [2246] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2247] [2248] 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 , [2249] 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))[] [2250] 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 '[] [2251] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2252] 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")) ||[] [2253] 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[] [2254] 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 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2255] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2256] 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,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2257] [2258] [2259] 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[] [2260] 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"[] [2261] 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 [2262] 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)))[] [2263] 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 [2264] Underfull \hbox (badness 2809) 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 [2265] 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., [2266] 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 [2267] Underfull \hbox (badness 1184) 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 [2268] 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., [2269] 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[] [2270] 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 [2271] 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[] [2272] [2273] 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''), [2274] 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 ``e mpty'' [][]sparse-Ma-trix[][][], as does [2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) 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 [2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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 \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 \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2277] 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 [2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.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 - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2279] [2280] 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 [2281] Underfull \hbox (badness 2809) 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 [2282] 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/ ptm/m/n/10 should be done, af-ter [2283] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\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 [2285] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\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 7911--7916 \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 7919--7922 []\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., [2286] [2287] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2289] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\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 8241--8241 []\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 8242--8242 []\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 8355--8365 []\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 , [2290] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\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 [2291] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\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., [2292] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\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., [2293] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\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 [2294] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2295] [2296] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\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![] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\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 [2301] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\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"[] [2302] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2303] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\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 Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2307] [2308] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\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 [2309] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2311] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2312] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2313] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \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 [2314] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\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 [2315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \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 10256--10256 [] \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 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2316] [2317] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2318] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\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 [2319] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\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 10574--10574 []\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 10575--10575 []\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 10580--10580 []\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 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\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 10607--10607 []\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 10633--10633 []\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 10635--10635 [] \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 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2321] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2322] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2323] [2324] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \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 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2325] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\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 11140--11146 \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 , [2326] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\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 [2327] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\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 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2328] [2329] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2330] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\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 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \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 [2331] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\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., [2332] [2333] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\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 11688--11692 []\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 11688--11692 \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 [2334] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2335] [2336] [2337] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\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 [2338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\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 12035--12035 []\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)[] [2339] [2340] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2341] [2342] [2343]) (./boot-pkg.tex [2344] Chapter 18. [2345] [2346] [2347] [2348] [2349] [2350] [2351] 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"), [2352] 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- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2353] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2354] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2355] 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 , [2356] 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 [2357] [2358] 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 [2359] 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 [2360] [2361] [2362] [2363] 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- [2364] [2365] [2366] [2367] [2368] 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), [2369] [2370] [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] 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),[] [2373] 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. [2374] [2375] [2376] 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 [2377] 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 , [2378] [2379] 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 [2380] [2381] [2382] [2383] [2384] 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,[] [2385] [2386] [2387] 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 , [2388] 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)) [2389] [2390] [2391] 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 [2392] [2393] [2394] [2395] [2396] [2397] [2398] 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)[] [2399] [2400] 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])[] [2401] [2402] [2403] 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 [2404] 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 [2405] [2406] 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 Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] 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 [2416] [2417] [2418] [2419] 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 [2420] 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])[] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] 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][] [2429] 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 [2430] 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 [2431] [2432] [2433] [2434] 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). [2435] [2436] 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[] [2437] [2438] [2439] 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 [2440] [2441] 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),[] [2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex [2450] Chapter 19. [2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex Chapter 20. [2467] Underfull \hbox (badness 3098) 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- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2468] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2469] 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]))[] [2470] [2471] Underfull \vbox (badness 10000) has occurred while \output is active [2472] [2473] 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, ...)[] [2474] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2475] 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)[] [2476] 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 [2477] [2478] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\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 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2479] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2481] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\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 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2482] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2483] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\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 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2484] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\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 [2485] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \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 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2486] [2487] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\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 1451--1454 [2488] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\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 1492--1492 []\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 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2489] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\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 [2490] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2491] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \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 [2492] [2493] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\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 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2494] [2495] [2496] [2497] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\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. [2498] [2499] [2500] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\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 , [2501] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\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 2403--2405 []\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 2426--2429 [][][]\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 , [2502] [2503] [2504] [2505] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\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 ):[] [2506] [2507] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2509] [2510] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2511] [2512] [2513] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2514] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2515] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] [2517] [2518] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\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 Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2519] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\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 , [2520] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which 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 Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\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 , [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\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 3844--3847 [][][]\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 , [2524] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\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 [2525] [2526] [2527] [2528] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \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 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2529] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2530] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\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 4250--4250 [] \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 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\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 4257--4257 [] \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 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\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 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\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 4653--4653 []\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)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2537] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2538]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2539] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2540] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2541] [2542] [2543]) (./foreign-pkg.tex [2544] Chapter 22. [2545] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2546] [2547] 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 , [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2549] [2550] [2551] 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,[] [2552] 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"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \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 [2553] 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 [2554] 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.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2555] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\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="")[] [2556] [2557] 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])[] [2558] [2559] 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) [2560] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2563] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2564] 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 , [2565] Underfull \hbox (badness 6725) 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 [2566]) (./lattice-pkg.tex Chapter 23. [2567] [2568] [2569] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2570] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2571] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2572] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2573] [2574] 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 [2575] [2576] [2577] [2578] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2579] 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 [2580] [2581] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2582] [2583] [2584] 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 , [2585] 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 , [2586] Underfull \vbox (badness 10000) has occurred while \output is active [2587] 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 [2588] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2589] 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 [2590] [2591] [2592] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2593] 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 [2594] [2595] [2596] 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"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2597] [2598] [2599] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2600] [2601] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2602] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2603] 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 Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \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 [2604] 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- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \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 [2605] [2606] 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),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2607] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x 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 [2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2612] 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"),[] [2613] [2614] [2615] [2616] [2617] 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))) [2618] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2619] [2620] 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) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\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 [2621] 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 [2622] [2623] 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 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\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 [2624] [2625] [2626] [2627] [2628] [2629] 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")[] [2630] [2631] 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 . [2632] [2633] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\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 [2634] [2635] [2636] [2637] [2638] [2639] 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 Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2640] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \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 Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2641] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\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 [2642] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2643] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \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),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2644] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2645] 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 Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \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 [2646] [2647] 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 , [2648] [2649] 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- [2650] [2651] 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 Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \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 [2652] [2653] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2654] 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 [2655] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2656] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2657] [2658] [2659] [2660] [2661] 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- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \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 [2662] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2663] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \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 [2664] 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 [2665] [2666] 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 [2667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2668] [2669] 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 Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2670] 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)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2671] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2672] [2673] [2674] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2675] 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 Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] 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 [2684] [2685] 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, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2686] 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 [2687] 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 [2688] 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 [2689] [2690] 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)[] [2691] [2692] 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)),[] [2693] Overfull \hbox (84.94879pt 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 (104.63074pt 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 [2694] [2695] [2696] [2697] [2698] [2699] [2700] Underfull \hbox (badness 4205) 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 4518) 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 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular 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 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2708]) (./mgcv-pkg.tex Chapter 24. [2709] [2710] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2711] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2712] [2713] [2714] [2715] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\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 , [2716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\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)+[] [2717] [2718] [2719] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\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 [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 697--698 []\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1 /pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then [2722] Underfull \hbox (badness 1158) in paragraph at lines 749--751 []\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 [2723] Underfull \hbox (badness 1259) in paragraph at lines 812--813 []\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). [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] [2726] [2727] [2728] [2729] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1160--1160 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1161--1161 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1167--1167 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2730] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1174--1174 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1176--1176 []\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),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1178--1178 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1209--1209 []\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)[] [2731] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1270--1270 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2732] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1281--1281 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1315--1315 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1818--1818 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2193--2201 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2210--2210 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2222--2225 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2235--2239 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2748] Underfull \hbox (badness 1043) in paragraph at lines 2261--2266 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] Underfull \hbox (badness 1043) in paragraph at lines 2424--2430 \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 [2751] [2752] Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\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 , [2753] Underfull \vbox (badness 10000) has occurred while \output is active [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3216--3216 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2764] [2765] [2766] [2767] [2768] [2769] Underfull \hbox (badness 5189) in paragraph at lines 3580--3584 []\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 [2770] [2771] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3697--3697 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2772] [2773] [2774] Underfull \hbox (badness 1184) in paragraph at lines 3866--3870 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2775] [2776] [2777] [2778] [2779] [2780] [2781] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4312--4312 [] \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)+[] [2782] [2783] [2784] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4462--4462 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2785] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4556--4556 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2786] Underfull \hbox (badness 1142) in paragraph at lines 4587--4591 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2787] Underfull \hbox (badness 10000) in paragraph at lines 4656--4665 []\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 [2788] [2789] Underfull \hbox (badness 5970) in paragraph at lines 4773--4779 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4773--4779 [][]\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 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2790] Underfull \vbox (badness 10000) has occurred while \output is active [2791] [2792] [2793] Underfull \hbox (badness 1577) in paragraph at lines 5053--5056 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5060--5061 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2794] [2795] [2796] [2797] [2798] [2799] [2800] Underfull \hbox (badness 6708) in paragraph at lines 5449--5450 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(..., fit=FALSE) \T1/ptm/m/n/10 or [2801] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5498--5498 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2802] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5523--5523 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5552--5552 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] Underfull \vbox (badness 10000) has occurred while \output is active [2803] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5605--5605 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2804] [2805] [2806] [2807] [2808] [2809] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5929--5929 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5931--5931 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5952--5956 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2810] [2811] [2812] [2813] [2814] [2815] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6267--6267 []\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) [2816] [2817] [2818] [2819] Underfull \vbox (badness 10000) has occurred while \output is active [2820] Underfull \vbox (badness 10000) has occurred while \output is active [2821] [2822] [2823] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6696--6696 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6723--6723 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1242) in paragraph at lines 7266--7267 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2833] [2834] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7353--7353 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2835] [2836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7416--7416 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7435--7435 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] Underfull \vbox (badness 10000) has occurred while \output is active [2855] [2856] Underfull \hbox (badness 10000) in paragraph at lines 8655--8658 []\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 8655--8658 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8655--8658 \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 . [2857] Underfull \hbox (badness 10000) in paragraph at lines 8711--8714 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8711--8714 \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 [2858] [2859] [2860] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8931--8931 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8932--8932 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8935--8935 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2861] [2862] [2863] Underfull \hbox (badness 1629) in paragraph at lines 9093--9098 \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 [2864] [2865] [2866] [2867] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2868] [2869] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9468--9468 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2870] [2871] [2872] [2873] Underfull \vbox (badness 10000) has occurred while \output is active [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9736--9736 [] \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[] [2875] Underfull \hbox (badness 1205) in paragraph at lines 9774--9776 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9774--9776 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9780--9785 []\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 [2876] Underfull \hbox (badness 1205) in paragraph at lines 9864--9866 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9864--9866 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2877] Underfull \hbox (badness 10000) in paragraph at lines 9933--9936 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9933--9936 [][]\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, [2878] [2879] Underfull \hbox (badness 1253) in paragraph at lines 10063--10065 []\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, [2880] [2881] [2882] [2883] Underfull \hbox (badness 1946) in paragraph at lines 10241--10248 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10241--10248 \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 10241--10248 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10249--10252 []\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 10249--10252 \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. [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10315--10315 []\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 10344--10347 []\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 , [2885] [2886] [2887] [2888] [2889] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10631--10631 []\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) [2890] [2891] [2892] [2893] [2894] [2895] Underfull \hbox (badness 3861) in paragraph at lines 10972--10975 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10979--10979 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10992--10996 []\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- [2896] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\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- [2897] [2898] [2899] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11173--11173 [] \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 11184--11189 []\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 [2900] Underfull \hbox (badness 1803) in paragraph at lines 11261--11265 \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 11273--11285 \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 11290--11294 \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 11290--11294 \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 , [2901] [2902] [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] Underfull \hbox (badness 6876) in paragraph at lines 11485--11491 [][][]\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 11526--11527 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2905] [2906] Underfull \hbox (badness 10000) in paragraph at lines 11643--11644 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2907] [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11697--11697 [] \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 11709--11709 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11720--11720 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11721--11721 [] \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 11726--11726 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11732--11732 [] \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 11733--11733 [] \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:[] [2910] Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 \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 [2911] [2912] Underfull \hbox (badness 10000) in paragraph at lines 11930--11931 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12011--12011 []\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 12012--12012 []\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[] [2914] [2915] [2916] Underfull \hbox (badness 10000) in paragraph at lines 12162--12163 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2917] [2918] [2919] [2920] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12401--12401 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2921] Underfull \hbox (badness 10000) in paragraph at lines 12462--12464 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2922] [2923] Underfull \vbox (badness 10000) has occurred while \output is active [2924] Underfull \hbox (badness 10000) in paragraph at lines 12621--12624 []\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 12621--12624 \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 12621--12624 \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" [2925] [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12703--12703 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12748--12754 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12748--12754 \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- [2927] [2928] [2929] Underfull \vbox (badness 10000) has occurred while \output is active [2930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12962--12962 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 13065--13073 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13091--13092 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2933] [2934] [2935] [2936] Underfull \hbox (badness 3396) in paragraph at lines 13352--13355 [][][]\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 [2937] Underfull \hbox (badness 10000) in paragraph at lines 13397--13399 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2938] [2939] [2940] [2941] Underfull \hbox (badness 10000) in paragraph at lines 13621--13624 []\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 13621--13624 \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 [2942] Underfull \hbox (badness 10000) in paragraph at lines 13654--13658 [][][]\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 13654--13658 [][]\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 13654--13658 [][]\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 , [2943] [2944] [2945] [2946] [2947] Underfull \hbox (badness 2158) in paragraph at lines 13944--13944 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2948] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14023--14023 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2949] [2950] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14157--14157 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2951] [2952] [2953] Underfull \hbox (badness 4846) in paragraph at lines 14288--14291 []\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 [2954] [2955] [2956] [2957] [2958] Underfull \vbox (badness 10000) has occurred while \output is active [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2967] [2968] [2969] [2970] [2971] [2972] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15477--15477 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2973] [2974] [2975] [2976] [2977] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15771--15771 []\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 15772--15772 []\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 15784--15784 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2978] [2979] [2980]) (./nlme-pkg.tex Chapter 25. [2981] 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 [2982] 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 [2983] [2984] [2985] [2986] [2987] 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,[] [2988] [2989] 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 --------------------------- ---------------[] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] 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"),[] [2998] 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 [2999] [3000] [3001] [3002] [3003] [3004] [3005] 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 , [3006] 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 [3007] [3008] [3009] [3010] [3011] 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 , [3012] 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")[] [3013] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3014] [3015] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\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 , [3016] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\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 , [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\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 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\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 , [3061] [3062] [3063] [3064] [3065] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3066] [3067] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\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 , [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \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 [3077] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\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 , [3078] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\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 , [3079] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\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 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3080] [3081] [3082] [3083] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\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 , [3084] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\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 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3085] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\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 , [3090] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\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 [3091] [3092] [3093] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\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 , [3094] [3095] [3096] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\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 7407--7415 \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 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\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 , [3097] [3098] [3099] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\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 [3100] [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3106] [3107] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\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 8157--8174 [][]\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 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3108] [3109] [3110] [3111] [3112] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3114] [3115] [3116] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\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 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3126] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\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 [3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3131] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\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 9743--9746 []\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 9743--9746 \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 [3132] [3133] [3134] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3135] [3136] [3137] [3138] [3139] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\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 [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3143] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3144] [3145] [3146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3147] [3148] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\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[][][] [3149] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\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 Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\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 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3150] [3151] [3152] [3153] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\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 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\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 , [3170] [3171] [3172] [3173] [3174] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\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 [3175] [3176] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\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 , [3177] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\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 , [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3192] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\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 Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\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 13728--13735 \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 [3193] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\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 13792--13795 \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 [3194] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3195] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\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 Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \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 , [3196] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\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 , [3197] [3198] [3199] [3200] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3201] [3202] [3203] [3204] [3205] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \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 [3225] [3226] [3227] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3232] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\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 , [3233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3241] [3242] [3243] [3244] [3245] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \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 17147--17156 \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" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3246] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \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 , [3247] [3248] [3249] [3250] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\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 , [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\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 17993--18003 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \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 [3259] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \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 [3260] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \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 [3261] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\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 18221--18226 \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 [3262] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \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 [3263] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\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 18317--18326 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \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 [3264] [3265] [3266] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \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 [3267] [3268] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \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 [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3277] 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,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3278] [3279] [3280] 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,[] [3281] 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)[] [3282] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3283] 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,[] [3284]) (./rpart-pkg.tex Chapter 27. [3285] [3286] [3287] [3288] 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, ...)[] [3289] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3290] [3291] [3292] 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 [3293] [3294] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3295] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3296] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3297] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3298] [3299] [3300] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\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 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3301] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\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 [3302] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\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 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3303] [3304] [3305] [3306] [3307] [3308] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\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 ', [3309] [3310] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3311] [3312] [3313]) (./spatial-pkg.tex [3314] Chapter 28. [3315] [3316] [3317] [3318] [3319] [3320] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333]) (./survival-pkg.tex [3334] Chapter 29. [3335] [3336] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3337] [3338]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \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 \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3339] [3340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3342] [3343] Underfull \vbox (badness 10000) has occurred while \output is active [3344] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3345] [3346] 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,[] [3347] [3348] [3349] 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[] [3350] [3351] 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) [3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3353] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3354] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\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 , [3360] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3367] [3368] [3369] [3370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3371] [3372] [3373] [3374] [3375] Underfull \vbox (badness 2393) has occurred while \output is active [3376] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \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 2862--2864 []\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 [3377] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\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 [3378] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \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 )))[] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3384] [3385] [3386] [3387] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \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 )))[] [3388] Underfull \vbox (badness 10000) has occurred while \output is active [3389] [3390] [3391] [3392] [3393] [3394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3395] [3396] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3397] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\T1/pcr/m/n/9 mresid <- (lung$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[] [3398] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3399] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3400] [3401] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\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 [3402] [3403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3404] [3405] [3406] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3407] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\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 4910--4910 []\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 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3408] [3409] [3410] [3411] [3412] Underfull \vbox (badness 2126) has occurred while \output is active [3413] [3414] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \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 [3415] [3416] [3417] [3418] [3419] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\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 5700--5700 []\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 \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3420] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\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 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3427] [3428] [3429] [3430] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \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 ),[] [3431] [3432] Underfull \vbox (badness 10000) has occurred while \output is active [3433] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\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 [3434] [3435] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3437] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3438] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3439] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3440] [3441] [3442] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\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 , [3443] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3448] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3450] [3451] [3452] [3453] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3454] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3455] [3456] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \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 [3457] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3458] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3459] [3460] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \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 )[] [3461] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \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 )[] [3462] [3463] [3464] [3465] [3466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3467] [3468] [3469] [3470] [3471] [3472]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3473] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3474] [3475] [3476]) (./fullrefman.ind [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2194--2196 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2196--2198 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2198--2200 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2200--2202 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2202--2204 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2204--2206 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2206--2208 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2208--2210 []| \T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method [3572] Overfull \hbox (74.8567pt too wide) in paragraph at lines 13599--13601 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3573] [3574] [3575] Overfull \hbox (50.8567pt too wide) in paragraph at lines 14358--14360 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14364--14366 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 14366--14368 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14368--14370 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14370--14372 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14372--14374 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in 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at lines 14416--14418 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14424--14426 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14426--14428 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14428--14430 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14430--14432 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method [3576] Overfull \hbox (74.8567pt too wide) in paragraph at lines 14432--14434 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3577] [3578] [3579] [3580] Overfull \hbox (52.01662pt too wide) in paragraph at lines 15402--15404 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3581] [3582] Overfull \hbox (8.8567pt too wide) in paragraph at lines 15955--15957 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 15974--15976 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15976--15978 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15982--15984 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method [3583] Overfull \hbox (14.8567pt too wide) in paragraph at lines 16000--16002 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16006--16008 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16008--16010 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3584] Overfull \hbox (26.8567pt too wide) in paragraph at lines 16253--16255 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 16259--16261 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16271--16273 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 16273--16275 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16275--16277 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16277--16279 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 16279--16281 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method [3585] Overfull \hbox (38.8567pt too wide) in paragraph at lines 16299--16301 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16301--16303 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 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)\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 16634--16636 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3588] [3589] [3590] [3591] [3592] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17898--17900 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3593] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17901--17903 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17903--17905 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17905--17907 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17907--17909 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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(\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17923--17925 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17925--17927 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17927--17929 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17929--17931 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17931--17933 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3594] [3595] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18277--18279 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18349--18351 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3596] [3597] [3598] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18812--18814 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18821--18823 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18823--18825 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18825--18827 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18827--18829 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18839--18841 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 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rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19196--19198 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19198--19200 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19200--19202 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19202--19204 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19204--19206 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19206--19208 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19208--19210 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19214--19216 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19218--19220 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19228--19230 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19232--19234 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19234--19236 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method [3601] Overfull \hbox (38.8567pt too wide) in paragraph at lines 19236--19238 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19238--19240 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19240--19242 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19242--19244 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 19244--19246 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19273--19275 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19275--19277 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19277--19279 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19279--19281 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19283--19285 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19287--19289 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19291--19293 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19295--19297 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19299--19301 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19303--19305 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19307--19309 []\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19311--19313 []\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19313--19315 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3602] [3603] [3604] [3605] [3606] Overfull \hbox (20.8567pt too wide) in paragraph at lines 20248--20250 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20250--20252 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(/usr/share/texmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texmf-dist/tex/latex/base/bk10.clo)) (../../share/texmf/tex/latex/Rd.sty (/usr/share/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texmf-dist/tex/latex/url/url.sty) (/usr/share/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texmf-dist/tex/latex/base/ts1enc.def (/usr/share/texmf-dist/tex/latex/base/ts1enc.dfu))) (/usr/share/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 366. 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Underfull \hbox (badness 4595) in paragraph at lines 40--43 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [3] Underfull \hbox (badness 4168) in paragraph at lines 94--99 []\T1/pcr/m/n/10 .Devices \T1/ptm/m/n/10 is a [][]pairlist[][][] of length-one char-ac-ter vec-tors. The first en-try is al-ways [4] Underfull \hbox (badness 10000) in paragraph at lines 135--141 []\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 Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei- Underfull \hbox (badness 6236) in paragraph at lines 135--141 \T1/ptm/m/n/10 ther \T1/pcr/m/n/10 double.base \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, Underfull \hbox (badness 10000) in paragraph at lines 135--141 \T1/ptm/m/n/10 it is \T1/pcr/m/n/10 (double.base ^ double.ulp.digits) / 2\T1/pt m/m/n/10 . Nor-mally Underfull \hbox (badness 10000) in paragraph at lines 141--149 []\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 . Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1 /ptm/m/n/10 if Underfull \hbox (badness 4328) in paragraph at lines 141--149 \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.roundin g \T1/ptm/m/n/10 is 0; oth-er-wise, it is Underfull \hbox (badness 10000) in paragraph at lines 141--149 \T1/pcr/m/n/10 (double.base ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-ma lly Underfull \hbox (badness 10000) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ- Underfull \hbox (badness 10000) in paragraph at lines 152--159 \T1/ptm/m/n/10 i-cally, it is equal to \T1/pcr/m/n/10 (1 - double.neg.eps) * [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] Underfull \hbox (badness 2359) in paragraph at lines 386--389 []\T1/ptm/m/n/10 logical: should \T1/pcr/m/n/10 minlength \T1/ptm/m/n/10 be ob- served strictly? Note that set-ting [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] Overfull \hbox (0.78088pt too wide) in paragraph at lines 860--860 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] Underfull \hbox (badness 1838) in paragraph at lines 1147--1150 []\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 [20] [21] [22] [23] Underfull \hbox (badness 5862) in paragraph at lines 1381--1387 []\T1/pcr/m/n/10 %% \T1/ptm/m/n/10 in-di-cates \T1/pcr/m/n/10 x mod y \T1/ptm/m /n/10 and \T1/pcr/m/n/10 %/% \T1/ptm/m/n/10 in-di-cates in-te-ger di-vi-sion. I t is guar-an-teed that [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1639--1639 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] Underfull \hbox (badness 3168) in paragraph at lines 1656--1663 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , set-ting row n ames and con-vert-ing col-umn names Underfull \hbox (badness 3128) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 (to syn-tac-tic names: see [][]\T1/pcr/m/n/10 make.names[][][]\T 1/ptm/m/n/10 ) is op-tional. Note that all Underfull \hbox (badness 6094) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 of \T1/phv/m/n/10 R\T1/ptm/m/n/10 's \T1/ptm/b/n/10 base \T1/ptm /m/n/10 pack-age \T1/pcr/m/n/10 as.data.frame() \T1/ptm/m/n/10 meth-ods use \T1 /pcr/m/n/10 optional Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 \T1/ptm/m/n/10 only for col-umn names treat-ment, ba-si-cally with the mean-ing of Underfull \hbox (badness 10000) in paragraph at lines 1656--1663 [][]\T1/pcr/m/n/10 data.frame[][][](*, check.names = !optional)\T1/ptm/m/n/10 . See also the [27] Underfull \hbox (badness 1303) in paragraph at lines 1667--1670 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] Underfull \hbox (badness 10000) in paragraph at lines 1785--1787 []\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 [29] [30] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1922--1922 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [31] Overfull \hbox (19.13934pt too wide) in paragraph at lines 1957--1959 []\T1/ptm/m/n/10 If it is a list, the equiv-a-lent of [][]\T1/pcr/m/n/10 list2e nv[][][](x, parent = emptyenv()) Underfull \hbox (badness 10000) in paragraph at lines 1960--1962 []\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] Underfull \hbox (badness 10000) in paragraph at lines 2120--2122 []\T1/ptm/m/n/10 a date-time ob-ject, or some-thing which can be co-erced by [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2233--2233 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 1107) in paragraph at lines 2366--2368 []\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 [38] [39] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2533--2533 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [40] [41] [42] Underfull \hbox (badness 5878) in paragraph at lines 2698--2703 []\T1/ptm/m/n/10 The ex-trac-tion func-tion first looks for an ex-act match to \T1/pcr/m/n/10 which \T1/ptm/m/n/10 amongst the at- Underfull \hbox (badness 10000) in paragraph at lines 2698--2703 \T1/ptm/m/n/10 tributes of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , then (un-less \T1/p cr/m/n/10 exact = TRUE\T1/ptm/m/n/10 ) a unique par-tial match. (Set-ting [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] Underfull \hbox (badness 10000) in paragraph at lines 3656--3658 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [57] [58] [59] Overfull \hbox (102.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [60] [61] [62] [63] Underfull \hbox (badness 4927) in paragraph at lines 4136--4140 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the name of a C func-tion, or an ob-ject Underfull \hbox (badness 2012) in paragraph at lines 4136--4140 \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 [64] [65] Underfull \hbox (badness 4595) in paragraph at lines 4280--4283 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [66] [67] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4435--4435 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] [68] Underfull \hbox (badness 1199) in paragraph at lines 4465--4471 []\T1/ptm/m/n/10 (generalized) vec-tors or ma-tri-ces. These can be given as na med ar-gu- Underfull \hbox (badness 2573) in paragraph at lines 4476--4479 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [69] Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 cbind \T1/ptm/m/n/10 data frame method is j ust a wrap-per for Underfull \hbox (badness 10000) in paragraph at lines 4556--4561 [][]\T1/pcr/m/n/10 data.frame[][][](..., check.names = FALSE)\T1/ptm/m/n/10 . T his means that it will split ma- Underfull \hbox (badness 2181) in paragraph at lines 4556--4561 \T1/ptm/m/n/10 trix columns in data frame ar-gu-ments, and con-vert char-ac-ter columns to fac-tors un-less [70] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4635--4635 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [71] [72] [73] [74] Underfull \hbox (badness 2521) in paragraph at lines 4888--4890 []\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 [75] [76] [77] [78] [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 5285--5293 []\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 [81] [82] [83] [84] [85] [86] [87] [88] Underfull \hbox (badness 1796) in paragraph at lines 5845--5853 []\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 : / / [89] [90] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6039--6039 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6041--6041 []\T1/pcr/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6042--6042 []\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}[] [91] [92] [93] Underfull \hbox (badness 1635) in paragraph at lines 6208--6211 []\T1/ptm/m/n/10 User in-ter-rupts sig-nal a con-di-tion of class \T1/pcr/m/n/1 0 interrupt \T1/ptm/m/n/10 that in-her-its di-rectly from class Underfull \hbox (badness 3009) in paragraph at lines 6212--6215 []\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 Underfull \hbox (badness 1102) in paragraph at lines 6229--6242 []\T1/ptm/m/n/10 New restarts for \T1/pcr/m/n/10 withRestarts \T1/ptm/m/n/10 ca n be spec-i-fied in sev-eral ways. The sim-plest is in Underfull \hbox (badness 1308) in paragraph at lines 6243--6251 []\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 [94] [95] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6396--6396 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [96] Overfull \hbox (107.35893pt too wide) in paragraph at lines 6438--6440 []\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 : [97] [98] Underfull \hbox (badness 10000) in paragraph at lines 6580--6583 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6580--6583 \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 [99] [100] Underfull \hbox (badness 1248) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 Byte Or-der Mark if present (which it of-ten is for files and we b-pages gen-er-ated by Mi- Underfull \hbox (badness 2080) in paragraph at lines 6762--6768 \T1/ptm/m/n/10 crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not rec-o m-mended) when writ-ing it Underfull \hbox (badness 10000) in paragraph at lines 6782--6784 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [101] Underfull \hbox (badness 1067) in paragraph at lines 6824--6831 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [102] [103] Underfull \vbox (badness 10000) has occurred while \output is active [104] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7016--7016 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [105] Underfull \hbox (badness 1231) in paragraph at lines 7141--7147 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [106] [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 7352--7354 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [110] [111] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7497--7497 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] Underfull \hbox (badness 4595) in paragraph at lines 7539--7542 []\T1/ptm/m/n/10 logical, in-di-cat-ing if an `x[i]' equal to the low-est (or h igh-est, for [112] [113] [114] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7735--7735 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [115] [116] Underfull \hbox (badness 8132) in paragraph at lines 7836--7840 []\T1/ptm/m/n/10 logical: should char-ac-ter vec-tors be con-verted to fac-tors ? The Underfull \hbox (badness 4543) in paragraph at lines 7836--7840 \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 Underfull \hbox (badness 10000) in paragraph at lines 7855--7865 []\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 1062) in paragraph at lines 7855--7865 [][]\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 [117] Overfull \hbox (4.63962pt too wide) in paragraph at lines 7887--7891 []\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") Underfull \hbox (badness 7451) in paragraph at lines 7926--7936 [][][]\T1/pcr/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.data.frame [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names[] [][] \T1/ptm/m/n/10 (for the col- Underfull \hbox (badness 3449) in paragraph at lines 7926--7936 \T1/ptm/m/n/10 umn names), [][]\T1/pcr/m/n/10 [.data.frame[][][] \T1/ptm/m/n/10 for sub-set-ting meth-ods and \T1/pcr/m/n/10 I(matrix(..)) \T1/ptm/m/n/10 ex-a m- [118] [119] [120] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/pcr/m/n/10 23:59:59", format = "%Y-%m-%d %H:%M:%S", tz = "UTC") \T1/ptm/m/n /10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8358--8370 \T1/ptm/m/n/10 and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59", tz = "UTC") \T1/ptm/m/n/10 will give [124] [125] [126] Underfull \hbox (badness 5802) in paragraph at lines 8585--8589 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 read.dcf(all = FALSE) \T1/ptm/m/n/10 reads the file byte-by-byte. This al-lows a Underfull \hbox (badness 10000) in paragraph at lines 8620--8621 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 8805--8809 []\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 [130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8893--8893 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8895--8895 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] [131] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8920--8920 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 8921--8921 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [132] [133] Underfull \hbox (badness 5403) in paragraph at lines 9039--9041 []\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 9058--9060 []\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 [134] Underfull \hbox (badness 1132) in paragraph at lines 9130--9137 \T1/ptm/m/n/10 at-tributes as well, but not to use any of the other op-tions to make the re-sult parseable. [135] Underfull \hbox (badness 1603) in paragraph at lines 9266--9269 []\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 [136] [137] [138] [139] [140] [141] [142] [143] [144] Underfull \hbox (badness 1917) in paragraph at lines 9872--9877 []\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 [145] Overfull \hbox (36.7804pt too wide) in paragraph at lines 9927--9927 []\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 9928--9928 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [146] [147] Underfull \hbox (badness 1168) in paragraph at lines 10030--10035 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by Underfull \hbox (badness 10000) in paragraph at lines 10069--10075 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10076--10079 []\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 [148] [149] Underfull \hbox (badness 2828) in paragraph at lines 10235--10239 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10235--10239 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ [150] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10268--10268 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [151] [152] [153] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10483--10483 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [154] Underfull \hbox (badness 1629) in paragraph at lines 10557--10561 []\T1/ptm/m/n/10 Promises will nor-mally only be en-coun-tered by users as a re -sult of lazy-loading (when [155] [156] Underfull \hbox (badness 2150) in paragraph at lines 10658--10661 []\T1/ptm/m/n/10 logical in-di-cat-ing if du-pli-ca-tion should be con-sid-ered from the re-verse Underfull \hbox (badness 3690) in paragraph at lines 10672--10680 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 anyDuplicated\T1/ptm/m/n/10 , \T1/pcr/m/n/10 anyDuplicated(x, ...) \T1/ptm/m/n/10 is a ``gen-er-al-ized'' short-cut for Underfull \hbox (badness 10000) in paragraph at lines 10681--10683 []\T1/pcr/m/n/10 duplicated(x, fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent to but faster than [157] Underfull \hbox (badness 3735) in paragraph at lines 10701--10708 []\T1/ptm/m/n/10 Except for fac-tors, log-i-cal and raw vec-tors the de-fault \ T1/pcr/m/n/10 nmax = NA \T1/ptm/m/n/10 is equiv-a-lent to [158] [159] Underfull \hbox (badness 10000) in paragraph at lines 10897--10900 []\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 [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] Underfull \hbox (badness 5288) in paragraph at lines 11594--11596 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of Underfull \hbox (badness 3039) in paragraph at lines 11604--11609 []\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 [170] Underfull \hbox (badness 10000) in paragraph at lines 11664--11666 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [171] Underfull \hbox (badness 4569) in paragraph at lines 11781--11785 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11781--11785 \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 [172] [173] Underfull \hbox (badness 10000) in paragraph at lines 11896--11898 []\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 [174] Underfull \hbox (badness 2790) in paragraph at lines 11939--11941 []\T1/pcr/m/n/10 get0(): \T1/ptm/m/n/10 The object---as from [][]\T1/pcr/m/n/10 get[][][](x, *)\T1/ptm/m/n/10 --- if \T1/pcr/m/n/10 exists(x, *) \T1/ptm/m/n/1 0 is true, oth-er-wise [175] [176] Underfull \hbox (badness 4048) in paragraph at lines 12110--12120 []\T1/pcr/m/n/10 as.expression \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-me nt into an ex-pres-sion ob-ject. It is Underfull \hbox (badness 3657) in paragraph at lines 12110--12120 \T1/ptm/m/n/10 generic, and only the de-fault method is de-scribed here. (The d e-fault method calls [177] [178] [179] Underfull \hbox (badness 5460) in paragraph at lines 12358--12367 []\T1/ptm/m/n/10 Both \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 and \T1/pcr/m/n/10 [[ \T1 /ptm/m/n/10 can be ap-plied to en-vi-ron-ments. Only char-ac-ter in-dices are a l- Underfull \hbox (badness 2221) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 lowed and no par-tial match-ing is done. The se-man-tics of thes e op-er-a-tions are those Underfull \hbox (badness 2707) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 of \T1/pcr/m/n/10 get(i, env = x, inherits = FALSE)\T1/ptm/m/ n/10 . If no match is found then \T1/pcr/m/n/10 NULL Underfull \hbox (badness 2818) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 is re-turned. The re-place-ment ver-sions, \T1/pcr/m/n/10 $<- \T 1/ptm/m/n/10 and \T1/pcr/m/n/10 [[<-\T1/ptm/m/n/10 , can also be used. Again, Underfull \hbox (badness 6978) in paragraph at lines 12358--12367 \T1/ptm/m/n/10 only char-ac-ter ar-gu-ments are al-lowed. The se-man-tics in th is case are those of [180] [181] [182] [183] [184] [185] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12732--12732 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [186] [187] [188] [189] Underfull \hbox (badness 5119) in paragraph at lines 13017--13020 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 iconv \T1/ptm/m/n/10 this will give the im- ple-men-ta-tion as well as the ver-sion, for ex-am-ple [190] [191] Underfull \hbox (badness 2221) in paragraph at lines 13178--13187 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s [192] [193] [194] [195] Underfull \hbox (badness 2253) in paragraph at lines 13439--13441 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [196] [197] Underfull \hbox (badness 10000) in paragraph at lines 13554--13556 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with [198] [199] Underfull \hbox (badness 10000) in paragraph at lines 13704--13706 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [200] Underfull \hbox (badness 10000) in paragraph at lines 13813--13817 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [201] Underfull \hbox (badness 10000) in paragraph at lines 13824--13827 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 13845--13845 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 13868--13868 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [202] Underfull \hbox (badness 10000) in paragraph at lines 13960--13963 [][][]\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 , [203] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13970--13970 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [204] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14045--14045 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14074--14074 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 7238) in paragraph at lines 14098--14105 []\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 , Underfull \hbox (badness 10000) in paragraph at lines 14098--14105 \T1/ptm/m/n/10 where the lat-ter must be non-decreasing. Where this is triv-ial , equiv-a-lent to Underfull \hbox (badness 2126) in paragraph at lines 14098--14105 \T1/pcr/m/n/10 apply( outer(x, vec, ">="), 1, sum)\T1/ptm/m/n/10 , as a mat-ter of fact, the in-ter-nal al-go- [205] Underfull \hbox (badness 3965) in paragraph at lines 14106--14110 []\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, [206] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14269--14269 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14270--14270 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [208] [209] Underfull \hbox (badness 10000) in paragraph at lines 14349--14353 []\T1/ptm/m/n/10 The C type \T1/pcr/m/n/10 Rcomplex \T1/ptm/m/n/10 is de-fined in `\T1/pcr/m/n/10 Complex.h\T1/ptm/m/n/10 ' as a Underfull \hbox (badness 1389) in paragraph at lines 14349--14353 \T1/pcr/m/n/10 typedef struct {double r; double i;}\T1/ptm/m/n/10 . It may or m ay not be equiv-a-lent to [210] [211] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14497--14497 []\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 14500--14500 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [212] Underfull \hbox (badness 1168) in paragraph at lines 14584--14588 []\T1/ptm/m/n/10 Either a log-i-cal spec-i-fy-ing whether el-e-ments of a real or com-plex vec- Underfull \hbox (badness 2012) in paragraph at lines 14584--14588 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [213] Underfull \hbox (badness 6944) in paragraph at lines 14679--14682 [][][]\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 , [214] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14704--14704 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [215] [216] Underfull \hbox (badness 10000) in paragraph at lines 14838--14840 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 14857--14857 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14859--14859 [] \T1/pcr/m/n/10 zero.print = NULL, drop0trailing = FALSE, is.cmplx = NA,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14862--14862 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)))[] Underfull \hbox (badness 2790) in paragraph at lines 14868--14871 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 4254) in paragraph at lines 14884--14892 []\T1/ptm/m/n/10 the to-tal field width; if both \T1/pcr/m/n/10 digits \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 width \T1/ptm/m/n/10 are un-spec-i-fied, Underfull \hbox (badness 1024) in paragraph at lines 14899--14903 []\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 [217] Underfull \hbox (badness 10000) in paragraph at lines 14968--14970 []\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 [218] Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 []\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, Underfull \hbox (badness 10000) in paragraph at lines 14974--14978 \T1/ptm/m/n/10 so \T1/pcr/m/n/10 formatC(c(6.11, 13.1), digits = 2, format = "f g") \T1/ptm/m/n/10 gives Underfull \hbox (badness 10000) in paragraph at lines 14979--14987 []\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 Underfull \hbox (badness 3601) in paragraph at lines 15013--15017 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 decimal.mark \T1/ptm/m/n/10 in \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt m/m/n/10 3.2.0: for use Underfull \hbox (badness 3302) in paragraph at lines 15013--15017 \T1/ptm/m/n/10 within [][]\T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 meth-ods in pack-ages which might be used with ear-lier ver-sions: use [219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15080--15080 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [220] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15102--15102 []\T1/pcr/m/n/9 doLC <- FALSE # R warns, so change to TRUE manually if you wan t see the effect[] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15920--15920 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [232] [233] Underfull \hbox (badness 2418) in paragraph at lines 16029--16033 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16036--16039 []\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 Underfull \hbox (badness 2326) in paragraph at lines 16064--16071 [][][]\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 , [234] [235] [236] [237] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16310--16310 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, Underfull \hbox (badness 1867) in paragraph at lines 16335--16342 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [238] [239] [240] [241] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16603--16603 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16632--16632 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [242] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16683--16683 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 16689--16693 []\T1/ptm/m/n/10 raw vec-tor con-tain-ing a [][]reg-u-lar ex-pres-sion[][][] (o r fixed pat-tern for Underfull \hbox (badness 1028) in paragraph at lines 16689--16693 \T1/pcr/m/n/10 fixed = TRUE\T1/ptm/m/n/10 ) to be matched in the given raw vec- tor. Co-erced by [243] [244] [245] [246] [247] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17048--17048 []\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))) [248] [249] [250] [251] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17302--17302 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [252] [253] [254] Underfull \hbox (badness 2435) in paragraph at lines 17563--17565 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [255] Underfull \hbox (badness 1867) in paragraph at lines 17605--17612 []\T1/ptm/m/n/10 It is op-tional on Win-dows: if \T1/phv/m/n/10 R \T1/ptm/m/n/1 0 has been built against ICU, it will only be used if Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 en-vi-ron-ment vari-able \T1/pcr/m/n/10 R_ICU_LOCALE \T1/ptm/m/n /10 is set or once \T1/pcr/m/n/10 icuSetCollate \T1/ptm/m/n/10 is called to se- Underfull \hbox (badness 1490) in paragraph at lines 17605--17612 \T1/ptm/m/n/10 lect the lo-cale (as ICU and Win-dows dif-fer in their idea of l o-cale names). Note that Underfull \hbox (badness 2285) in paragraph at lines 17620--17622 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17628--17628 []\T1/pcr/m/n/9 ## As we don\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 t know the current s ettings, we can only reset to the default.[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17638--17638 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] [256] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17658--17658 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [257] [258] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17792--17792 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 17798--17798 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17801--17801 []\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 17807--17807 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [259] [260] Overfull \hbox (4.38043pt too wide) in paragraph at lines 17934--17934 []\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 17942--17942 []\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):[] [261] [262] [263] Underfull \hbox (badness 10000) in paragraph at lines 18147--18149 []\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 [264] Underfull \hbox (badness 4217) in paragraph at lines 18231--18240 [][][]\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 18246--18262 [][][]\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 , [265] [266] [267] [268] [269] [270] Underfull \hbox (badness 4699) in paragraph at lines 18660--18663 []\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 , [271] [272] Overfull \hbox (0.78088pt too wide) in paragraph at lines 18783--18783 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [273] [274] Underfull \hbox (badness 4739) in paragraph at lines 18918--18920 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [275] [276] [277] [278] [279] [280] [281] Underfull \hbox (badness 1430) in paragraph at lines 19331--19336 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an ar-ray i f ap-pro-pri-ate, by ap-ply-ing \T1/pcr/m/n/10 simplify2array()\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 19331--19336 \T1/pcr/m/n/10 sapply(x, f, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is the same as [282] Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 []\T1/ptm/m/n/10 logical; if true, \T1/pcr/m/n/10 simplify2array() \T1/ptm/m/n/ 10 will pro-duce a (``higher Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 rank'') ar-ray when ap-pro-pri-ate, whereas \T1/pcr/m/n/10 highe r = FALSE \T1/ptm/m/n/10 would Underfull \hbox (badness 5008) in paragraph at lines 19392--19397 \T1/ptm/m/n/10 re-turn a ma-trix (or vec-tor) only. These two cases cor-re-spon d to Underfull \hbox (badness 10000) in paragraph at lines 19392--19397 \T1/pcr/m/n/10 sapply(*, simplify = "array") \T1/ptm/m/n/10 or \T1/pcr/m/n/10 s implify = TRUE\T1/ptm/m/n/10 , re- [283] Underfull \hbox (badness 10000) in paragraph at lines 19452--19459 []\T1/pcr/m/n/10 vapply \T1/ptm/m/n/10 re-turns a vec-tor or ar-ray of type mat ch-ing the \T1/pcr/m/n/10 FUN.VALUE\T1/ptm/m/n/10 . If Underfull \hbox (badness 6364) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) == 1 \T1/ptm/m/n/10 a vec-tor of the same leng th as \T1/pcr/m/n/10 X \T1/ptm/m/n/10 is re-turned, oth- Underfull \hbox (badness 5064) in paragraph at lines 19452--19459 \T1/ptm/m/n/10 er-wise an ar-ray. If \T1/pcr/m/n/10 FUN.VALUE \T1/ptm/m/n/10 is not an [][]\T1/pcr/m/n/10 array[][][]\T1/ptm/m/n/10 , the re-sult is a ma-trix with Underfull \hbox (badness 5908) in paragraph at lines 19452--19459 \T1/pcr/m/n/10 length(FUN.VALUE) \T1/ptm/m/n/10 rows and \T1/pcr/m/n/10 length( X) \T1/ptm/m/n/10 columns, oth-er-wise an ar-ray \T1/pcr/m/n/10 a \T1/ptm/m/n/1 0 with Underfull \hbox (badness 10000) in paragraph at lines 19468--19470 []\T1/pcr/m/n/10 sapply(*, simplify = FALSE, USE.NAMES = FALSE) \T1/ptm/m/n/10 is equiv-a-lent to [284] Underfull \hbox (badness 1975) in paragraph at lines 19540--19543 []\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 [285] [286] [287] [288] [289] [290] Underfull \hbox (badness 1077) in paragraph at lines 19935--19940 []\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 [291] Underfull \hbox (badness 10000) in paragraph at lines 19949--19956 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [292] Underfull \hbox (badness 10000) in paragraph at lines 20023--20027 []\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 [293] Underfull \hbox (badness 10000) in paragraph at lines 20153--20157 []\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 20153--20157 [][]\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 [294] [295] Underfull \hbox (badness 10000) in paragraph at lines 20251--20258 [][][]\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 , [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 20372--20376 []\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 [298] Underfull \hbox (badness 5161) in paragraph at lines 20442--20447 []\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 20442--20447 \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 20442--20447 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20442--20447 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [299] [300] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20609--20609 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20613--20613 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [301] Underfull \hbox (badness 3343) in paragraph at lines 20669--20673 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [302] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20755--20755 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20766--20766 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [303] [304] Overfull \hbox (9.78043pt too wide) in paragraph at lines 20877--20877 []\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 20880--20880 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] [305] Underfull \hbox (badness 6380) in paragraph at lines 20925--20930 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- Underfull \hbox (badness 1337) in paragraph at lines 20983--20990 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 category = "LC_ALL" \T1/ptm/m/n/10 the de-t ails of the string are system-specific: it might be Underfull \hbox (badness 1960) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 a sin-gle lo-cale name or a set of lo-cale names sep-a-rated by \T1/pcr/m/n/10 "/" \T1/ptm/m/n/10 (So-laris, ma-cOS) or Underfull \hbox (badness 1043) in paragraph at lines 20983--20990 \T1/ptm/m/n/10 not nec-es-sar-ily the case that the re-sult of \T1/pcr/m/n/10 f oo <- Sys.getlocale() \T1/ptm/m/n/10 can be used in [306] Underfull \hbox (badness 2564) in paragraph at lines 21016--21019 []\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 21046--21046 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [307] Underfull \hbox (badness 1205) in paragraph at lines 21069--21074 \T1/ptm/m/n/10 10) log-a-rithms, and \T1/pcr/m/n/10 log2 \T1/ptm/m/n/10 com-put es bi-nary (i.e., base 2) log-a-rithms. The gen-eral form [308] [309] Underfull \hbox (badness 1400) in paragraph at lines 21214--21218 [][][]\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 Overfull \hbox (36.83002pt too wide) in paragraph at lines 21234--21241 []\T1/pcr/m/n/10 isTRUE(x) \T1/ptm/m/n/10 is the same as \T1/pcr/m/n/10 { is.lo gical(x) && length(x) == 1 && !is.na(x) && x }\T1/ptm/m/n/10 ; Underfull \hbox (badness 4886) in paragraph at lines 21234--21241 \T1/ptm/m/n/10 In ear-lier \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions, \T1/pcr/m /n/10 isTRUE <- function(x) identical(x, TRUE)\T1/ptm/m/n/10 , had the [310] [311] Underfull \hbox (badness 2469) in paragraph at lines 21384--21390 []\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 1939) in paragraph at lines 21384--21390 \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 names. Underfull \hbox (badness 10000) in paragraph at lines 21384--21390 \T1/ptm/m/n/10 Char-ac-ter strings \T1/pcr/m/n/10 c("T", "TRUE", "True", "true" ) \T1/ptm/m/n/10 are re-garded as true, [312] [313] [314] [315] [316] Underfull \hbox (badness 10000) in paragraph at lines 21701--21703 []\T1/ptm/m/n/10 The al-go-rithm used by \T1/pcr/m/n/10 make.unique \T1/ptm/m/n /10 has the prop-erty that [317] [318] [319] [320] [321] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22005--22005 []\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 22006--22006 [] \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 22009--22009 []\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)[] [322] [323] Underfull \hbox (badness 1655) in paragraph at lines 22133--22137 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [324] [325] [326] Underfull \hbox (badness 2277) in paragraph at lines 22382--22385 []\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. [327] [328] [329] [330] [331] [332] [333] [334] Underfull \hbox (badness 10000) in paragraph at lines 22867--22873 []\T1/ptm/m/n/10 There are also lim-its on in-di-vid-ual ob-jects. The stor-age space can-not ex-ceed Underfull \hbox (badness 6316) in paragraph at lines 22867--22873 \T1/ptm/m/n/10 the ad-dress limit, and if you try to ex-ceed that limit, the er -ror mes-sage be-gins Underfull \hbox (badness 1484) in paragraph at lines 22899--22907 []\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 2951) in paragraph at lines 22899--22907 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / www . microsoft . com / whdc / Underfull \hbox (badness 3460) in paragraph at lines 22899--22907 \T1/pcr/m/n/10 system / platform / server / PAE / PAEmem . mspx$[][] \T1/ptm/m/ n/10 and [][]$\T1/pcr/m/n/10 https : / / msdn . microsoft . [335] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22976--22976 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [336] Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 by \T1/ptm/m/n/10 or both \T1/pcr/m/n/10 by. x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 by.y \T1/ptm/m/n/10 are of length 0 (a leng th zero vec- Underfull \hbox (badness 10000) in paragraph at lines 23030--23034 \T1/ptm/m/n/10 tor or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ), the re-sult, \T1/pcr /m/n/10 r\T1/ptm/m/n/10 , is the \T1/ptm/m/it/10 Carte-sian prod-uct \T1/ptm/m/ n/10 of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , i. e., [337] [338] [339] [340] [341] [342] Underfull \hbox (badness 10000) in paragraph at lines 23481--23489 \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 ; [343] [344] Underfull \hbox (badness 3849) in paragraph at lines 23595--23600 []\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 [345] Underfull \hbox (badness 7308) in paragraph at lines 23672--23678 []\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 5077) in paragraph at lines 23672--23678 \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 10000) in paragraph at lines 23682--23685 []\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 23682--23685 \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 [346] [347] Underfull \hbox (badness 10000) in paragraph at lines 23834--23836 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [348] [349] [350] [351] Underfull \hbox (badness 6188) in paragraph at lines 24053--24056 []\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 [352] [353] [354] [355] [356] [357] [358] Underfull \hbox (badness 2197) in paragraph at lines 24535--24539 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24535--24539 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use Underfull \hbox (badness 2846) in paragraph at lines 24549--24553 []\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 24549--24553 \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 [359] Underfull \hbox (badness 10000) in paragraph at lines 24642--24648 []\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 24642--24648 \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 [360] Underfull \hbox (badness 10000) in paragraph at lines 24655--24657 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than Overfull \hbox (4.38043pt too wide) in paragraph at lines 24706--24706 [] \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:[] [361] [362] [363] Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 []\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 Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 [][]\T1/ptm/m/n/10 mode[][][] \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 ([][]type [][][] \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 or type \T1/pcr/m/n/10 "integer"\ T1/ptm/m/n/10 ) and not a fac-tor, Underfull \hbox (badness 10000) in paragraph at lines 24899--24905 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 oth-er-wise. That is, \T 1/pcr/m/n/10 is.integer(x) || is.double(x)\T1/ptm/m/n/10 , or [364] Underfull \hbox (badness 4120) in paragraph at lines 24985--24992 []\T1/ptm/m/n/10 Hexadecimal con-stants start with \T1/pcr/m/n/10 0x \T1/ptm/m/ n/10 or \T1/pcr/m/n/10 0X \T1/ptm/m/n/10 fol-lowed by a nonempty se-quence from [365] [366] Underfull \hbox (badness 1694) in paragraph at lines 25121--25124 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [367] [368] [369] [370] Underfull \hbox (badness 1603) in paragraph at lines 25368--25370 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [371] Overfull \hbox (73.28088pt too wide) in paragraph at lines 25491--25499 \T1/pcr/m/n/10 c("datasets", "utils", "grDevices", "graphics", "stats", "methods")\T1/ptm/m/n/10 . [372] [373] Underfull \hbox (badness 5475) in paragraph at lines 25628--25638 []\T1/ptm/m/n/10 the com-mand used for dis-play-ing text files by [][]\T1/pcr/m /n/10 file.show[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 3271) in paragraph at lines 25670--25673 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able Underfull \hbox (badness 10000) in paragraph at lines 25685--25687 []\T1/ptm/m/n/10 Used for the readline-based ter-mi-nal in-ter-face. De-fault v alue [374] [375] [376] Underfull \hbox (badness 3138) in paragraph at lines 25948--25954 []\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 25948--25954 \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 25948--25954 \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 [377] Underfull \hbox (badness 1194) in paragraph at lines 25961--25964 []\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 25987--25989 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 25999--26003 []\T1/ptm/m/n/10 string used as the user agent in HTTP(S) re-quests. If Underfull \hbox (badness 6592) in paragraph at lines 25999--26003 \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 , re-quests will be made with-out a user agen t header. The de-fault is Underfull \hbox (badness 10000) in paragraph at lines 26004--26010 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26019--26024 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Overfull \hbox (49.4607pt too wide) in paragraph at lines 26025--26036 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][](type = "both ") Underfull \hbox (badness 1009) in paragraph at lines 26037--26040 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and Underfull \hbox (badness 10000) in paragraph at lines 26047--26059 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 1072) in paragraph at lines 26047--26059 [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 . Pos-si-ble val-ues ar e \T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a [378] Underfull \hbox (badness 10000) in paragraph at lines 26061--26068 []\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 10000) in paragraph at lines 26061--26068 \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 Underfull \hbox (badness 6380) in paragraph at lines 26061--26068 \T1/ptm/m/n/10 CRAN mir-ror. To avoid this do set the CRAN mir-ror, by some-thi ng like Overfull \hbox (34.78088pt too wide) in paragraph at lines 26061--26068 \T1/pcr/m/n/10 local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cr an"; [379] [380] [381] [382] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26392--26392 []\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 26405--26409 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26405--26409 \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)] [383] [384] [385] [386] [387] Underfull \hbox (badness 4341) in paragraph at lines 26729--26731 []\T1/pcr/m/n/10 paste0(..., collapse) \T1/ptm/m/n/10 is equiv-a-lent to \T1/pc r/m/n/10 paste(..., sep = "", collapse)\T1/ptm/m/n/10 , Underfull \hbox (badness 4518) in paragraph at lines 26765--26771 [][][]\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 [388] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26787--26787 []\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 26799--26799 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [389] [390] [391] [392] [393] [394] [395] Underfull \hbox (badness 10000) in paragraph at lines 27233--27237 []\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, [396] Underfull \hbox (badness 1796) in paragraph at lines 27299--27302 []\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 [397] [398] [399] Underfull \hbox (badness 10000) in paragraph at lines 27499--27502 []\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 [400] [401] [402] [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 1226) in paragraph at lines 28131--28136 \T1/pcr/m/n/10 ncol(X) <= nrow(X)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 complete \T 1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 or the ar-gu-ment \T1/pcr/m/ n/10 ncol \T1/ptm/m/n/10 is greater than [409] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28176--28176 [] \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))[] [410] [411] [412] [413] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28442--28442 []\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 28453--28453 []\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 28459--28459 []\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 28460--28460 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 28463--28463 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [414] Underfull \hbox (badness 7415) in paragraph at lines 28538--28542 []\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 [415] Overfull \hbox (42.18039pt too wide) in paragraph at lines 28559--28559 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] [416] Underfull \hbox (badness 2418) in paragraph at lines 28718--28729 []\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 [417] [418] Underfull \hbox (badness 1248) in paragraph at lines 28852--28859 \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 28852--28859 \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 / [419] [420] Underfull \hbox (badness 1533) in paragraph at lines 28968--28971 []\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 [421] Underfull \hbox (badness 1337) in paragraph at lines 29065--29068 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 finite \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the min-i-mum and max-i-mum of all fi-nite val-ues is com-pute d, i.e., [422] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29113--29113 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] Underfull \hbox (badness 1038) in paragraph at lines 29131--29142 []\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 Underfull \hbox (badness 10000) in paragraph at lines 29143--29146 []\T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are never con-sid-ered to be equal: for \T1/pcr/m/n/10 na.last = TRUE \T1/ptm/m/n/10 and [423] [424] Underfull \hbox (badness 1117) in paragraph at lines 29238--29244 \T1/ptm/m/n/10 e-ments which have a class in-cluded in \T1/pcr/m/n/10 classes \ T1/ptm/m/n/10 are re-placed by the re-sult of ap-ply-ing [425] [426] [427] [428] [429] [430] Underfull \hbox (badness 4048) in paragraph at lines 29616--29621 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 29616--29621 \T1/ptm/m/n/10 be read, or a char-ac-ter vec-tor of length one de-scrib-ing the mode: Underfull \hbox (badness 1824) in paragraph at lines 29616--29621 \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 , [431] [432] [433] [434] [435] [436] [437] [438] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30162--30162 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [439] [440] [441] [442] Overfull \hbox (13.9408pt too wide) in paragraph at lines 30448--30450 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 ! " # $ % & \TS1/pcr/m/n/10 ' \T1/pcr/m/n/10 ( ) * + , - . / : ; < = > ? @ [ \ ] ^ _ \TS1/pcr/m/n/10 ` \T1/pcr/m/n/10 { | } ~\T 1/ptm/m/n/10 '. [443] [444] [445] Underfull \hbox (badness 7558) in paragraph at lines 30664--30668 []\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 30674--30676 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 30679--30682 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 30683--30685 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 30686--30688 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [446] [447] [448] [449] [450] [451] Underfull \hbox (badness 10000) in paragraph at lines 31091--31095 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [452] [453] [454] [455] [456] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31422--31422 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 31425--31425 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [457] [458] [459] Underfull \hbox (badness 3375) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pen if the spec-i-fied row names, i.e., \T1/pcr/m/n/10 value\T1/ ptm/m/n/10 , are in-valid, e.g., du- Underfull \hbox (badness 2359) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 pli-cated or \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 . The de-fault (is back com-pat-i-ble), \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , will sig-nal Underfull \hbox (badness 2582) in paragraph at lines 31653--31660 \T1/ptm/m/n/10 an er-ror, where \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 will ``au-to-m atic'' row names and \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 will call [460] [461] [462] Overfull \hbox (54.78088pt too wide) in paragraph at lines 31806--31806 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [463] [464] Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 []\T1/pcr/m/n/10 save.image() \T1/ptm/m/n/10 is just a short-cut for `save my c ur-rent Underfull \hbox (badness 10000) in paragraph at lines 31937--31941 \T1/ptm/m/n/10 workspace', i.e., \T1/pcr/m/n/10 save(list = ls(all.names = TRUE ), file = [465] [466] [467] Underfull \hbox (badness 2302) in paragraph at lines 32188--32195 []\T1/ptm/m/n/10 The root-mean-square for a (pos-si-bly cen-tered) col-umn is d e-fined as $[]$, Underfull \hbox (badness 2837) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 x$ \T1/ptm/m/n/10 is a vec-tor of the no n-missing val-ues and $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 is the num-ber of non -missing Underfull \hbox (badness 3815) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 val-ues. In the case \T1/pcr/m/n/10 center = TRUE\T1/ptm/m/n/10 , this is the same as the stan-dard de-vi-a-tion, Underfull \hbox (badness 2181) in paragraph at lines 32188--32195 \T1/ptm/m/n/10 but in gen-eral it is not. (To scale by the stan-dard de-vi-a-ti ons with-out cen-ter-ing, use [468] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32240--32240 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [469] Underfull \hbox (badness 1158) in paragraph at lines 32344--32349 []\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 [470] Underfull \hbox (badness 10000) in paragraph at lines 32371--32377 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1953) in paragraph at lines 32371--32377 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a, \b, \f, \n, \r, \t, \v\T1/ptm/m/n/10 ' and o c-tal and hex-adec-i-mal rep-re- [471] Underfull \hbox (badness 10000) in paragraph at lines 32447--32452 []\T1/ptm/m/n/10 Note that since \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 is a sep-a-r a-tor and not a ter-mi-na-tor, read-ing a file by Underfull \hbox (badness 6725) in paragraph at lines 32447--32452 \T1/pcr/m/n/10 scan("foo", sep = "\n", blank.lines.skip = FALSE) \T1/ptm/m/n/10 will give an empty [472] Overfull \hbox (15.18042pt too wide) in paragraph at lines 32529--32529 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [473] [474] [475] Underfull \hbox (badness 2809) in paragraph at lines 32793--32799 []\T1/ptm/m/n/10 The fifth form gen-er-ates the se-quence \T1/pcr/m/n/10 1, 2, ..., length(from) \T1/ptm/m/n/10 (as if ar-gu-ment Underfull \hbox (badness 7759) in paragraph at lines 32800--32803 []\T1/ptm/m/n/10 The fi-nal form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1, 2, ..., length.out \T1/ptm/m/n/10 un-less [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486] [487] Underfull \hbox (badness 1735) in paragraph at lines 33605--33611 \T1/ptm/m/n/10 Only prompts and (most) mes-sages con-tinue to ap-pear on the co n-sole. Mes-sages sent [488] Underfull \hbox (badness 4303) in paragraph at lines 33621--33624 []\T1/pcr/m/n/10 split = TRUE \T1/ptm/m/n/10 only splits \T1/phv/m/n/10 R \T1/p tm/m/n/10 out-put (via \T1/pcr/m/n/10 Rvprintf\T1/ptm/m/n/10 ) and the de-fault out-put from [489] [490] [491] [492] Overfull \hbox (66.78088pt too wide) in paragraph at lines 33939--33939 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [493] [494] [495] [496] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34191--34191 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34193--34193 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [497] Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 [][][]\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 Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 also [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T 1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion <= 3.3.x, this was hard- Underfull \hbox (badness 10000) in paragraph at lines 34236--34242 \T1/ptm/m/n/10 coded to \T1/pcr/m/n/10 "showAttributes"\T1/ptm/m/n/10 , which i s the de-fault cur-rently; Underfull \hbox (badness 2512) in paragraph at lines 34251--34253 []\T1/ptm/m/n/10 integer; how many com-ment lines at the start of the file to s kip if [498] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34347--34347 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [499] [500] [501] [502] [503] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34675--34675 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 34690--34690 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [504] [505] [506] [507] [508] [509] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35129--35129 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35130--35130 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [510] [511] [512] [513] Overfull \hbox (63.78036pt too wide) in paragraph at lines 35394--35394 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [514] Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 []\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 ' Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have b een saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want Underfull \hbox (badness 8113) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 a dif-fer-ent set of pack-ages than the de-fault ones when you s tart, in-sert a call Underfull \hbox (badness 10000) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n /10 ' file. For ex-am-ple, Underfull \hbox (badness 6542) in paragraph at lines 35478--35488 \T1/pcr/m/n/10 options(defaultPackages = character()) \T1/ptm/m/n/10 will at-ta ch no ex-tra pack-ages on Underfull \hbox (badness 5189) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) ( or set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi- Underfull \hbox (badness 4193) in paragraph at lines 35478--35488 \T1/ptm/m/n/10 ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/ 10 ). Us-ing \T1/pcr/m/n/10 options(defaultPackages = "") \T1/ptm/m/n/10 or [515] Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 35522--35528 \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 35522--35528 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1728) in paragraph at lines 35534--35541 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 here is a lso a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/ptm /m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 35534--35541 \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 35534--35541 \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 [516] [517] [518] [519] [520] Underfull \hbox (badness 10000) in paragraph at lines 35875--35881 []\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/pcr/m/n/10 form at \T1/ptm/m/n/10 meth-ods is [521] [522] [523] Underfull \hbox (badness 1163) in paragraph at lines 36064--36071 []\T1/ptm/m/n/10 Specific to \T1/phv/m/n/10 R \T1/ptm/m/n/10 is \T1/pcr/m/n/10 %OSn\T1/ptm/m/n/10 , which for out-put gives the sec-onds trun-cated to \T1/pcr /m/n/10 0 <= n <= 6 Underfull \hbox (badness 8132) in paragraph at lines 36064--36071 \T1/ptm/m/n/10 dec-i-mal places (and if \T1/pcr/m/n/10 %OS \T1/ptm/m/n/10 is no t fol-lowed by a digit, it uses the set-ting of [524] [525] [526] [527] Underfull \hbox (badness 1142) in paragraph at lines 36346--36352 []\T1/ptm/m/n/10 Note that split-ting into sin-gle char-ac-ters can be done \T1 /ptm/m/it/10 via \T1/pcr/m/n/10 split = character(0) \T1/ptm/m/n/10 or Overfull \hbox (0.78088pt too wide) in paragraph at lines 36361--36361 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [528] [529] [530] [531] Overfull \hbox (6.78088pt too wide) in paragraph at lines 36609--36609 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 36653--36653 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [532] [533] [534] [535] [536] [537] [538] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37087--37087 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37090--37090 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [539] Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 []\T1/ptm/m/n/10 integer, used for num-ber for-mat-ting with [][]\T1/pcr/m/n/10 signif[][][]() \T1/ptm/m/n/10 (for Underfull \hbox (badness 10000) in paragraph at lines 37141--37148 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). Overfull \hbox (4.38043pt too wide) in paragraph at lines 37192--37192 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [540] [541] [542] [543] Underfull \hbox (badness 2762) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 of the el-e-ments in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . If there is a match then that el-e-ment is eval-u-ated un-less Underfull \hbox (badness 1466) in paragraph at lines 37431--37440 \T1/ptm/m/n/10 it is miss-ing, in which case the next non-missing el-e-ment is eval-u-ated, so for ex-am-ple [544] Overfull \hbox (31.3804pt too wide) in paragraph at lines 37493--37493 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [545] [546] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37658--37658 []\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. [547] Overfull \hbox (20.58041pt too wide) in paragraph at lines 37696--37696 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] [548] Underfull \hbox (badness 3219) in paragraph at lines 37745--37750 []\T1/ptm/m/n/10 If a file-name starts with \T1/pcr/m/n/10 . \T1/ptm/m/n/10 thi s may need to be matched ex-plic-itly: for ex-am-ple Underfull \hbox (badness 1107) in paragraph at lines 37745--37750 \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 [549] Underfull \hbox (badness 2452) in paragraph at lines 37835--37838 \T1/ptm/m/n/10 The first five fields come from the \T1/pcr/m/n/10 uname(2) \T1/ ptm/m/n/10 sys-tem call. The lo-gin name comes Underfull \hbox (badness 10000) in paragraph at lines 37835--37838 \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 [550] [551] [552] Underfull \hbox (badness 10000) in paragraph at lines 38022--38026 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38037--38040 []\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 [553] [554] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38169--38169 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [555] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38239--38239 []\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 [556] [557] [558] Underfull \hbox (badness 1082) in paragraph at lines 38377--38380 []\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 [559] [560] Underfull \hbox (badness 1038) in paragraph at lines 38564--38567 []\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 [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 1515) in paragraph at lines 38928--38931 []\T1/ptm/m/n/10 Because of the way it is im-ple-mented, on a Unix-alike \T1/pc r/m/n/10 stderr = TRUE \T1/ptm/m/n/10 im-plies [567] [568] [569] Underfull \hbox (badness 4096) in paragraph at lines 39169--39172 []\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 , [570] [571] Underfull \hbox (badness 10000) in paragraph at lines 39283--39287 []\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., [572] [573] Overfull \hbox (63.78036pt too wide) in paragraph at lines 39437--39437 [] \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 39439--39439 [] \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),[] [574] Overfull \hbox (58.38037pt too wide) in paragraph at lines 39441--39441 [] \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 39454--39456 []\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 [575] Underfull \hbox (badness 10000) in paragraph at lines 39534--39537 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [576] [577] Underfull \hbox (badness 1867) in paragraph at lines 39652--39656 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getTaskCallbackNames [][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 5475) in paragraph at lines 39714--39718 [][][]\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 \ [][]$\T1/pcr/m/n/10 https : / / [578] [579] [580] [581] [582] [583] [584] Underfull \hbox (badness 10000) in paragraph at lines 40132--40139 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40188--40197 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40188--40197 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40198--40206 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40198--40206 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 1303) in paragraph at lines 40198--40206 \T1/pcr/m/n/10 file.path(R.home("share"), "zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [585] Underfull \hbox (badness 1337) in paragraph at lines 40264--40272 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40273--40276 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [586] Underfull \hbox (badness 4429) in paragraph at lines 40330--40332 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 40339--40339 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [587] [588] [589] Underfull \hbox (badness 10000) in paragraph at lines 40556--40558 []\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 [590] [591] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40678--40678 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 40680--40680 []\T1/pcr/m/n/9 power.t.test(20, 1, power=0.8, sd=NULL) ##--> showing the ncp root finding:[] Underfull \vbox (badness 10000) has occurred while \output is active [592] [593] [594] [595] [596] Underfull \hbox (badness 6542) in paragraph at lines 41042--41044 []\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 [597] [598] [599] Underfull \hbox (badness 3460) in paragraph at lines 41208--41211 []\T1/ptm/m/n/10 a [][]con-nec-tion[][][], or a char-ac-ter string nam-ing the file to print to (via Underfull \hbox (badness 1708) in paragraph at lines 41215--41223 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e r-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 3713) in paragraph at lines 41215--41223 \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 Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 []\T1/pcr/m/n/10 try \T1/ptm/m/n/10 is im-ple-mented us-ing [][]\T1/pcr/m/n/10 tryCatch[][][]\T1/ptm/m/n/10 ; for pro-gram-ming, in- Underfull \hbox (badness 10000) in paragraph at lines 41224--41228 \T1/ptm/m/n/10 stead of \T1/pcr/m/n/10 try(expr, silent = TRUE)\T1/ptm/m/n/10 , some-thing like Underfull \hbox (badness 3281) in paragraph at lines 41224--41228 \T1/pcr/m/n/10 tryCatch(expr, error = function(e) e) \T1/ptm/m/n/10 (or other s im-ple er-ror han-dler func- Underfull \hbox (badness 4859) in paragraph at lines 41245--41250 [][][]\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; [600] Underfull \hbox (badness 3895) in paragraph at lines 41307--41319 []\T1/ptm/m/n/10 A char-ac-ter string. The pos-si-ble val-ues are listed in the struc-ture \T1/pcr/m/n/10 TypeTable \T1/ptm/m/n/10 in Underfull \hbox (badness 1303) in paragraph at lines 41307--41319 \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 , [601] [602] [603] Underfull \hbox (badness 10000) in paragraph at lines 41492--41495 []\T1/ptm/m/n/10 On most plat-forms `file' in-cludes sym-bolic links, fi-fos an d sock-ets. [604] [605] Overfull \hbox (9.78043pt too wide) in paragraph at lines 41629--41629 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [606] [607] [608] [609] [610] [611] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42096--42096 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42105--42105 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [613] Underfull \hbox (badness 1803) in paragraph at lines 42222--42225 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2334) in paragraph at lines 42226--42233 []\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 [614] Underfull \hbox (badness 4726) in paragraph at lines 42252--42256 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 is.vector\T1/ptm/m/n/10 , \T1/pcr/m/n/10 TR UE \T1/ptm/m/n/10 or \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 . \T1/pcr/m/n/10 is.vec tor(x, mode = "numeric") \T1/ptm/m/n/10 can be Underfull \hbox (badness 1122) in paragraph at lines 42252--42256 \T1/ptm/m/n/10 true for vec-tors of types \T1/pcr/m/n/10 "integer" \T1/ptm/m/n/ 10 or \T1/pcr/m/n/10 "double" \T1/ptm/m/n/10 whereas \T1/pcr/m/n/10 is.vector(x , mode = [615] [616] Underfull \hbox (badness 3668) in paragraph at lines 42441--42443 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [617] [618] Overfull \hbox (36.78088pt too wide) in paragraph at lines 42545--42545 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42620--42620 []\T1/pcr/m/n/9 ## at the end prints all three warnings, from the \TS1/pcr/m/n /9 '\T1/pcr/m/n/9 option(warn = 0)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 above[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 42628--42628 []\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 ...[] [620] [621] Underfull \hbox (badness 6220) in paragraph at lines 42758--42763 []\T1/ptm/m/n/10 optional list of char-ac-ter [][]\T1/pcr/m/n/10 dimnames[][][] (.)\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 useNames \T1/ptm/m/n/10 is true, Underfull \hbox (badness 3098) in paragraph at lines 42758--42763 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, Underfull \hbox (badness 1533) in paragraph at lines 42758--42763 \T1/pcr/m/n/10 which(*, arr.ind=TRUE)\T1/ptm/m/n/10 ). If [][]\T1/pcr/m/n/10 na mes[][][](.dimnames) \T1/ptm/m/n/10 is not empty, Underfull \hbox (badness 6592) in paragraph at lines 42774--42779 []\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 [622] Underfull \hbox (badness 1603) in paragraph at lines 42793--42797 [][][]\T1/pcr/m/n/10 Logic[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 which.min[] [][] \T1/ptm/m/n/10 for the in-dex of the min-i-mum or max-i-mum, and [][]\T1/p cr/m/n/10 match[][][] \T1/ptm/m/n/10 for the [623] Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 []\T1/ptm/m/n/10 If this ex-tremum is unique (or empty), the re-sults are the s ame as Underfull \hbox (badness 10000) in paragraph at lines 42858--42861 \T1/ptm/m/n/10 (but more ef-fi-cient than) \T1/pcr/m/n/10 which(x == min(x, na. rm = TRUE)) \T1/ptm/m/n/10 or Underfull \hbox (badness 2818) in paragraph at lines 42864--42870 []\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 Overfull \hbox (15.18042pt too wide) in paragraph at lines 42899--42899 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [624] [625] Underfull \hbox (badness 1622) in paragraph at lines 42993--42995 []\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 . [626] [627] [628] [629] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 []\T1/ptm/m/n/10 This is a spe-cial case of rank-ing, but as a less gen-eral fu nc-tion than [][]\T1/pcr/m/n/10 rank[][][] Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/ptm/m/n/10 is more suit-able to be made generic. The de-fault method is sim -i-lar to Underfull \hbox (badness 10000) in paragraph at lines 43261--43266 \T1/pcr/m/n/10 rank(x, ties.method = "min", na.last = "keep")\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 val-ues are [630] Underfull \hbox (badness 2846) in paragraph at lines 43355--43359 []\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 [631] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43395--43395 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 43416--43420 []\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 [632]) (./compiler-pkg.tex Chapter 2. [633] Underfull \hbox (badness 2884) in paragraph at lines 101--115 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 options \T1/ptm/m/n/10 ar-gu-ment can be us ed to con-trol com-piler op-er-a-tion. There are cur- Underfull \hbox (badness 10000) in paragraph at lines 101--115 \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 [634] [635] [636]) (./datasets-pkg.tex Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 This pack-age con-tains a va-ri-ety of datasets. For a com-ple te list, use [637] [638] [639] [640] [641] Overfull \hbox (15.18042pt too wide) in paragraph at lines 301--301 [] \T1/pcr/m/n/9 plot(ff, data = anscombe, col = "red", pch = 21, bg = "orang e", cex = 1.2,[] [642] Overfull \hbox (4.38043pt too wide) in paragraph at lines 379--379 []\T1/pcr/m/n/9 coplot(accel ~ dist | as.factor(event), data = attenu, show.gi ven = FALSE)[] Underfull \vbox (badness 1472) has occurred while \output is active [643] [644] [645] [646] [647] Overfull \hbox (66.81013pt too wide) in paragraph at lines 702--705 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [648] [649] Overfull \hbox (66.81013pt too wide) in paragraph at lines 835--838 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [650] [651] Underfull \hbox (badness 1097) in paragraph at lines 1031--1035 []\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. [652] [653] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1146--1149 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [654] [655] [656] [657] [658] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1456--1456 []\T1/pcr/m/n/9 plot(names(te), te, type = "h", main = f.tit, xlab = "Eruption time (sec)")[] [659] [660] Underfull \hbox (badness 10000) in paragraph at lines 1541--1544 []\T1/ptm/m/n/10 Finally, \T1/pcr/m/n/10 freeny \T1/ptm/m/n/10 is a data frame with vari-ables \T1/pcr/m/n/10 y\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lag.quarterly.r evenue\T1/ptm/m/n/10 , Underfull \hbox (badness 2903) in paragraph at lines 1541--1544 \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 [661] [662] [663] Overfull \hbox (66.81013pt too wide) in paragraph at lines 1730--1733 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [664] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 model1 <- glm(case ~ spontaneous+induced, data = infert, famil y = binomial())[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1832--1832 [] \T1/pcr/m/n/9 model3 <- clogit(case ~ spontaneous+induced+strata(stratum), data = infert)[] [665] [666] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1948--1948 [] \T1/pcr/m/n/9 sub(" W.",".Width", dn i3[[2]])))),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1949--1949 [] \T1/pcr/m/n/9 Species = gl(3, 50, labels = sub("S", "s", sub("V", "v", d ni3[[3]]))))[] [667] [668] [669] [670] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2152--2155 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [671] [672] [673] Overfull \vbox (4.29591pt too high) has occurred while \output is active [674] [675] [676] [677] [678] Overfull \hbox (66.81013pt too wide) in paragraph at lines 2708--2711 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [679] Overfull \vbox (13.87083pt too high) has occurred while \output is active [680] Underfull \vbox (badness 2376) has occurred while \output is active [681] [682] Overfull \vbox (12.25539pt too high) has occurred while \output is active [683] [684] Overfull \vbox (17.12102pt too high) has occurred while \output is active [685] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3137--3137 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [686] [687] [688] [689] [690] [691] [692] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3594--3594 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [693] [694] Overfull \hbox (66.81013pt too wide) in paragraph at lines 3742--3745 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData", "nfGrou pedData", "groupedData", "data.frame") [695] Overfull \vbox (10.49593pt too high) has occurred while \output is active [696] Underfull \hbox (badness 1173) in paragraph at lines 3876--3880 \T1/ptm/m/it/10 Ed-u-ca-tion\T1/ptm/m/n/10 , \T1/ptm/b/n/10 3\T1/ptm/m/n/10 . [ ][]$\T1/pcr/m/n/10 https : / / www . amstat . org / publications / jse / v3n3 / datasets . Overfull \vbox (27.49593pt too high) has occurred while \output is active [697] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3951--3951 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3980--3983 []\T1/ptm/m/n/10 Time Se-ries Data Li-brary: [][]$\T1/pcr/m/n/10 http : / / www -[]personal . buseco . monash . edu . au / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 []\T1/ptm/m/n/10 For some pho-tos of Methuse-lah Walk see [][]$\T1/pcr/m/n/10 h ttps : / / web . archive . org / web / Underfull \hbox (badness 10000) in paragraph at lines 3989--3991 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [698] [699] [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711]) (./grDevices-pkg.tex [712] Chapter 4. [713] [714] [715] [716] [717] [718] Underfull \hbox (badness 10000) in paragraph at lines 374--382 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 10000) in paragraph at lines 374--382 [][]\T1/pcr/m/n/10 quantile[][][](x, c(1,3)/4)\T1/ptm/m/n/10 . The hinges equal the quar-tiles for odd $\OML/cmm/m/it/10 n$ \T1/ptm/m/n/10 (where [719] Overfull \hbox (6.78088pt too wide) in paragraph at lines 479--479 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [720] [721] [722] [723] [724] [725] [726] [727] [728] Underfull \hbox (badness 5175) in paragraph at lines 1082--1084 []\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 [729] Underfull \hbox (badness 1325) in paragraph at lines 1144--1150 \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 make.rgb[][][]\T1/ptm/m/n/10 . Built-in co lor spaces may be ref-er-enced by strings: \T1/pcr/m/n/10 "XYZ"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sRGB"\T1/ptm/m/n/10 , [730] Underfull \hbox (badness 10000) in paragraph at lines 1185--1187 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / [731] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1237--1237 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [732] Underfull \hbox (badness 1173) in paragraph at lines 1279--1282 []\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 [733] [734] [735] Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 []\T1/ptm/m/n/10 character: Which events can be gen-er-ated on Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/ptm/m/n/10 this de-vice? Cur-rently this will be a sub-set of Underfull \hbox (badness 10000) in paragraph at lines 1494--1498 \T1/pcr/m/n/10 c("MouseDown", "MouseMove", "MouseUp", "Keybd")\T1/ptm/m/n/10 , Underfull \hbox (badness 2221) in paragraph at lines 1539--1542 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 if the de-vice does not sup-port cap-ture, oth-er-wise a ma-trix of color names (for [736] Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the func-tion also re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 when Underfull \hbox (badness 10000) in paragraph at lines 1608--1612 [][]\T1/pcr/m/n/10 .Device[][][] == "null device" \T1/ptm/m/n/10 and [][]\T1/pc r/m/n/10 getOption[][][]("device") \T1/ptm/m/n/10 is [737] [738] [739] Underfull \hbox (badness 1565) in paragraph at lines 1767--1772 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 dev.print \T1/ptm/m/n/10 is to pro-duce and print a postscript copy. This will not Underfull \hbox (badness 1354) in paragraph at lines 1767--1772 \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 [740] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1850--1850 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] [741] Underfull \hbox (badness 1184) in paragraph at lines 1891--1901 []\T1/ptm/m/n/10 The types avail-able will de-pend on the ver-sion of \T1/pcr/m /n/10 ghostscript\T1/ptm/m/n/10 , but are likely to in- Underfull \hbox (badness 2057) in paragraph at lines 1891--1901 \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 , [742] Underfull \hbox (badness 10000) in paragraph at lines 1996--1998 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [743] [744] Underfull \hbox (badness 6758) in paragraph at lines 2157--2160 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [745] [746] Underfull \hbox (badness 2326) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 are given, then it uses those in a call to \T1/pcr/m/n/10 setGra phicsEventHandlers \T1/ptm/m/n/10 to re-place Underfull \hbox (badness 2318) in paragraph at lines 2267--2277 \T1/ptm/m/n/10 any ex-ist-ing han-dlers in the cur-rent de-vice. This is for co m-pat-i-bil-ity with pre-2.12.0 Underfull \hbox (badness 2460) in paragraph at lines 2267--2277 \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions. The cur-rent nor-mal way to set up e vent han-dlers is to set them us-ing Underfull \hbox (badness 1221) in paragraph at lines 2267--2277 \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 [747] [748] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2370--2370 []\T1/pcr/m/n/9 dragplot <- function(..., xlim = NULL, ylim = NULL, xaxs = "r" , yaxs = "r") {[] Underfull \vbox (badness 10000) has occurred while \output is active [749] [750] [751] [752] [753] [754] Underfull \hbox (badness 10000) in paragraph at lines 2750--2751 Underfull \vbox (badness 10000) has occurred while \output is active [755] [756] [757] [758] [759] [760] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3156--3156 []\T1/pcr/m/n/9 zapsmall(luv <- convertColor(cols, from = "sRGB", to = "Luv", scale.in = 255))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3157--3157 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] Underfull \hbox (badness 1210) in paragraph at lines 3188--3190 []\T1/ptm/m/n/10 A length two in-te-ger vec-tor \T1/pcr/m/n/10 nr, nc \T1/ptm/m /n/10 giv-ing the num-ber of rows and columns, ful-fill-ing [761] Underfull \hbox (badness 10000) in paragraph at lines 3248--3253 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range [762] [763] [764] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3407--3407 []\T1/pcr/m/n/10 rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, al pha = 1) [765] Underfull \hbox (badness 3525) in paragraph at lines 3514--3517 []\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 [766] Underfull \hbox (badness 1968) in paragraph at lines 3528--3530 []\T1/ptm/m/n/10 title string to em-bed as the `\T1/pcr/m/n/10 /Title\T1/ptm/m/ n/10 ' field in the file. De-faults to [767] [768] [769] [770] Underfull \hbox (badness 5939) in paragraph at lines 3822--3827 []\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 , [771] [772] [773] [774] [775] Underfull \hbox (badness 7576) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 / / www . adobe . com / products / postscript / pdfs / PLRM . pd f$[][] \T1/ptm/m/n/10 or PDF [][]$\T1/pcr/m/n/10 https : / / Underfull \hbox (badness 3701) in paragraph at lines 4199--4206 \T1/pcr/m/n/10 www . adobe . com / devnet / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i- [776] Underfull \vbox (badness 10000) has occurred while \output is active [777] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [778] Underfull \hbox (badness 1502) in paragraph at lines 4363--4368 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 type = "cairo"\T1/ptm/m/n/10 , giv-ing the type of anti-aliasing (if any) to be [779] [780] Underfull \hbox (badness 1348) in paragraph at lines 4515--4518 []\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 Underfull \hbox (badness 4765) in paragraph at lines 4525--4527 [][][]\T1/pcr/m/n/10 capabilities[][][] \T1/ptm/m/n/10 to see if these de-vices are sup-ported by this build of \T1/phv/m/n/10 R\T1/ptm/m/n/10 , and if Overfull \hbox (9.78043pt too wide) in paragraph at lines 4539--4539 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] [781] Underfull \hbox (badness 5077) in paragraph at lines 4579--4585 []\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 Underfull \hbox (badness 1342) in paragraph at lines 4595--4597 []\T1/ptm/m/n/10 title string to em-bed as the \T1/pcr/m/n/10 Title \T1/ptm/m/n /10 com-ment in the file. De-faults to [782] Underfull \hbox (badness 1874) in paragraph at lines 4672--4680 \T1/ptm/m/n/10 For use in this way you will prob-a-bly want to use [][]\T1/pcr/ m/n/10 setEPS[][][]() \T1/ptm/m/n/10 to set the de-faults as [783] Underfull \hbox (badness 1755) in paragraph at lines 4739--4741 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [784] [785] Underfull \hbox (badness 7344) in paragraph at lines 4910--4912 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso Underfull \hbox (badness 7397) in paragraph at lines 4921--4925 [][][]\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 [786] [787] Underfull \hbox (badness 1552) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Bookman"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica"\T1/pt m/m/n/10 , \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Palatino" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 "URWG othic"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5034--5043 \T1/pcr/m/n/10 "URWBookman"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "NimbusMon"\T1/ptm/m /n/10 , \T1/pcr/m/n/10 "NimbusSan" \T1/ptm/m/n/10 (syn-onym \T1/pcr/m/n/10 "URW Helvetica"\T1/ptm/m/n/10 ), Underfull \hbox (badness 2221) in paragraph at lines 5044--5046 []\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 [788] Underfull \hbox (badness 4686) in paragraph at lines 5076--5082 \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 Underfull \hbox (badness 10000) in paragraph at lines 5102--5109 []\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 / [789] [790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5203--5203 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [791] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5315--5315 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] Underfull \hbox (badness 1648) in paragraph at lines 5321--5325 []\T1/ptm/m/n/10 title for the Quartz win-dow (ap-plies to on-screen out-put on ly), de-fault [792] [793] Underfull \hbox (badness 10000) in paragraph at lines 5401--5403 []\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 Underfull \hbox (badness 1072) in paragraph at lines 5437--5443 []\T1/ptm/m/n/10 A fairly com-mon Mac prob-lem is no text ap-pear-ing on plots due to cor-rupted or du-pli- [794] [795] [796] [797] [798] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5759--5759 []\T1/pcr/m/n/9 rgb((0:15)/15, green = 0, blue = 0, names = paste("red", 0:15, sep = "."))[] Underfull \hbox (badness 10000) in paragraph at lines 5772--5775 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [799] [800] [801] [802] [803] [804] [805] Underfull \hbox (badness 1189) in paragraph at lines 6169--6171 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [806] Underfull \hbox (badness 10000) in paragraph at lines 6267--6269 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and Underfull \hbox (badness 10000) in paragraph at lines 6306--6313 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 6306--6313 \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 [807] Underfull \hbox (badness 3088) in paragraph at lines 6390--6394 []\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 [808] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6435--6435 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [809] Underfull \hbox (badness 10000) in paragraph at lines 6467--6470 []\T1/ptm/m/n/10 These func-tions ap-ply only to an [][]\T1/pcr/m/n/10 X11[][][ ] \T1/ptm/m/n/10 de-vice with \T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 -- [810] Underfull \hbox (badness 5637) in paragraph at lines 6558--6564 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , Underfull \hbox (badness 1721) in paragraph at lines 6591--6594 []\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 / [811] [812] [813] Underfull \hbox (badness 6157) in paragraph at lines 6748--6751 \T1/ptm/m/n/10 ity of co-or-di-nates. These are com-pared af-ter round-ing them via Underfull \hbox (badness 1231) in paragraph at lines 6759--6761 []\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 [814] [815] [816]) (./graphics-pkg.tex Chapter 5. Underfull \hbox (badness 10000) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use [817] [818] [819] [820] Underfull \hbox (badness 1412) in paragraph at lines 287--292 []\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- [821] [822] [823] Underfull \hbox (badness 2726) in paragraph at lines 466--472 []\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 [824] [825] [826] Underfull \hbox (badness 10000) in paragraph at lines 659--663 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 659--663 [][]\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 Underfull \hbox (badness 2735) in paragraph at lines 687--694 []\T1/pcr/m/n/10 axTicks() \T1/ptm/m/n/10 can be used an \T1/phv/m/n/10 R \T1/p tm/m/n/10 in-ter-face to the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/pt m/m/n/10 in [827] Overfull \hbox (4.38043pt too wide) in paragraph at lines 744--744 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] [828] [829] Underfull \hbox (badness 1062) in paragraph at lines 853--856 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , the lines whic h di-vide ad-ja-cent (non-stacked!) bars [830] [831] [832] [833] [834] [835] [836] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1290--1290 [] \T1/pcr/m/n/10 horizontal = FALSE, add = FALSE, at = NULL, show.names = NULL,[] [837] Underfull \hbox (badness 1024) in paragraph at lines 1335--1343 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 1248) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 width, point char-ac-ter, point size ex-pan-sion, color, and bac k-ground Underfull \hbox (badness 6893) in paragraph at lines 1363--1369 \T1/ptm/m/n/10 color. The de-fault \T1/pcr/m/n/10 medpch = NA \T1/ptm/m/n/10 su p-presses the point, and Underfull \hbox (badness 3375) in paragraph at lines 1369--1371 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), Overfull \hbox (19.3703pt too wide) in paragraph at lines 1391--1395 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 add = FALSE\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xlim \T1/ptm/m/n/10 now de-faults to \T1/pcr/m/n/10 xlim = range(at, *) + c(-0.5, 0.5)\T1/ptm/m/n/10 . [838] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1439--1439 []\T1/pcr/m/n/9 boxplot(z, col.axis = "skyblue3", main = "boxplot(*, col.axi s=..,main=..)")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1440--1440 []\T1/pcr/m/n/9 plot(z[[1]], col.axis = "skyblue3", main = "plot(*, col.axi s=..,main=..)")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1446--1446 []\T1/pcr/m/n/9 splus <- list(boxwex = 0.4, staplewex = 1, outwex = 1, boxfill = "grey40",[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1447--1447 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [839] [840] [841] [842] [843] Underfull \hbox (badness 10000) in paragraph at lines 1747--1753 [][][]\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 [844] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1784--1784 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1793--1793 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [846] [847] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2005--2005 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [848] [849] [850] [851] Underfull \hbox (badness 1009) in paragraph at lines 2296--2303 \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 [852] [853] [854] [855] [856] [857] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2624--2624 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [858] [859] Underfull \hbox (badness 5878) in paragraph at lines 2785--2789 \T1/ptm/m/n/10 they are the rel-a-tive fre-quen-cies \T1/pcr/m/n/10 counts/n \T 1/ptm/m/n/10 and in gen-eral sat-isfy Underfull \hbox (badness 10000) in paragraph at lines 2810--2813 []\T1/ptm/m/n/10 Typical plots with ver-ti-cal bars are \T1/ptm/m/it/10 not \T1 /ptm/m/n/10 his-tograms. Con-sider [][]\T1/pcr/m/n/10 barplot[][][] \T1/ptm/m/n /10 or [860] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2838--2838 []\T1/pcr/m/n/9 ## Extreme outliers; the "FD" rule would take very large numbe r of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 breaks\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2842--2842 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [861] Underfull \hbox (badness 10000) in paragraph at lines 2894--2897 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [862] [863] [864] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3091--3091 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3096--3096 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [865] Underfull \hbox (badness 1755) in paragraph at lines 3161--3165 []\T1/ptm/m/n/10 a list of col-ors such as that gen-er-ated by [][]\T1/pcr/m/n/ 10 rainbow[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 heat.colors[][][]\T1/ptm/m/ n/10 , [866] Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3236--3241 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [867] [868] [869] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3423--3423 []\T1/pcr/m/n/9 barplot(yhist$counts, axes = FALSE, xlim = c(0, top), space = 0, horiz = TRUE)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 3442--3442 [] \T1/pcr/m/n/10 box.lwd = par("lwd"), box.lty = par("lty"), box.col = par("fg"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3446--3446 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [870] [871] [872] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3623--3623 [] \T1/pcr/m/n/9 text (1, y.leg[i] - 0.1, paste("cex=", formatC(cexv[i])), c ex = 0.8, adj = 0)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3624--3624 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3663--3663 [] \T1/pcr/m/n/9 "text(c(3,3),2:3,\"c(rect(...)\")"), adj = c(0, 0.3))[] Underfull \vbox (badness 10000) has occurred while \output is active [873] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3715--3715 []\T1/pcr/m/n/9 legend(.4,1, "sin(c x)", pch = 21, pt.bg = "white", lty = 1, c ol = "blue")[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3723--3723 []\T1/pcr/m/n/9 legend("topleft", "(x,y)", pch=1, title= "topleft, inset = .05", inset = .05)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 3725--3725 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Underfull \vbox (badness 10000) has occurred while \output is active [874] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3733--3733 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] Underfull \hbox (badness 10000) in paragraph at lines 3796--3800 [][][]\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 [875] [876] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3907--3907 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [877] Underfull \hbox (badness 1867) in paragraph at lines 3950--3954 []\T1/ptm/m/n/10 vector of back-ground (fill) col-ors for the open plot sym-bol s given by [878] [879] Underfull \hbox (badness 3930) in paragraph at lines 4114--4116 []\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 [880] [881] [882] [883] Underfull \hbox (badness 1924) in paragraph at lines 4400--4405 []\T1/ptm/m/n/10 a func-tion which in-di-cates what should hap-pen when the dat a con-tain [884] Underfull \hbox (badness 1286) in paragraph at lines 4424--4427 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing Underfull \hbox (badness 3229) in paragraph at lines 4432--4437 []\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 [885] [886] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4525--4525 []\T1/pcr/m/n/9 pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4574--4574 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [887] Underfull \hbox (badness 1264) in paragraph at lines 4648--4661 \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 , [888] [889] Underfull \hbox (badness 7925) in paragraph at lines 4785--4791 []\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. [890] [891] Underfull \hbox (badness 10000) in paragraph at lines 4916--4919 [892 ] Underfull \hbox (badness 10000) in paragraph at lines 4977--4979 [893 ] [894] Underfull \hbox (badness 10000) in paragraph at lines 5167--5169 []\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 [895] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5224--5224 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] Underfull \vbox (badness 10000) has occurred while \output is active [896] [897] Underfull \hbox (badness 3954) in paragraph at lines 5325--5328 []\T1/ptm/m/n/10 a ex-pan-sion fac-tor ap-plied to the \T1/pcr/m/n/10 z \T1/ptm /m/n/10 co-or-di-nates. Of-ten used with Underfull \hbox (badness 10000) in paragraph at lines 5381--5385 \T1/ptm/m/n/10 are con-trolled by graph-ics pa-ram-e-ters \T1/pcr/m/n/10 "cex.l ab"\T1/ptm/m/n/10 /\T1/pcr/m/n/10 "font.lab" \T1/ptm/m/n/10 and [898] [899] [900] [901] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5589--5589 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5590--5590 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 10000) in paragraph at lines 5641--5645 []\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., Underfull \hbox (badness 1024) in paragraph at lines 5641--5645 \T1/pcr/m/n/10 type = "punkte" \T1/ptm/m/n/10 be-ing equiv-a-lent to \T1/pcr/m/ n/10 type = "p" \T1/ptm/m/n/10 for S com- [902] [903] [904] [905] [906] [907] [908] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6068--6068 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6074--6074 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [909] [910] [911] [912] [913] [914] Underfull \hbox (badness 10000) in paragraph at lines 6501--6503 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [915] [916] Underfull \hbox (badness 1028) in paragraph at lines 6595--6597 []\T1/ptm/m/n/10 character (or sym-bol) ex-pan-sion: a nu-mer-i-cal vec-tor. Th is works as a mul-ti-ple of Overfull \hbox (31.57222pt too wide) in paragraph at lines 6638--6639 [][] [917 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6732--6732 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [918] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6763--6763 [] \T1/pcr/m/n/9 plot(rx, ry, type = "n", axes = FALSE, xlab = "", ylab = "", main = main)[] Underfull \vbox (badness 10000) has occurred while \output is active [919] [920] Underfull \hbox (badness 10000) in paragraph at lines 6885--6887 []\T1/ptm/m/n/10 The code im-ple-ment-ing poly-gon shad-ing was do-nated by Kev in Buhr Overfull \hbox (15.18042pt too wide) in paragraph at lines 6912--6912 [] \T1/pcr/m/n/9 polygon(x, y, xpd = xpd, col = "orange", lty = 2, lwd = 2, b order = "red")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6918--6918 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [921] Underfull \hbox (badness 2600) in paragraph at lines 6978--6980 []\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 [922] [923] [924] Underfull \hbox (badness 1881) in paragraph at lines 7167--7172 []\T1/ptm/m/n/10 color for rect-an-gle bor-der(s). The de-fault means \T1/pcr/m /n/10 par("fg")\T1/ptm/m/n/10 . Use [925] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7210--7210 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [926] [927] [928] [929] [930] [931] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7597--7597 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7601--7601 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [932] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7613--7613 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [933] [934] [935] [936] [937] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7962--7962 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7965--7965 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] [938] Overfull \hbox (31.3804pt too wide) in paragraph at lines 7969--7969 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [939] [940] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8140--8140 []\T1/pcr/m/n/10 strwidth(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...) Overfull \hbox (36.78088pt too wide) in paragraph at lines 8141--8141 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [941] [942] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8245--8245 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8256--8261 []\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 [943] [944] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8364--8364 []\T1/pcr/m/n/9 sunflowerplot(iris[, 3:4], cex = .2, cex.fact = 1, size = .035 , seg.lwd = .8)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8379--8379 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [945] [946] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8510--8510 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [947] [948] [949] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8695--8695 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] Underfull \hbox (badness 10000) in paragraph at lines 8723--8725 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8725--8727 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8757--8763 []\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 [950]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8805 \HeaderA{units}{Graphical Units}{units} [951] Underfull \hbox (badness 1205) in paragraph at lines 8870--8872 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [952] [953] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8989--8989 []\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)[] [954]) (./grid-pkg.tex Chapter 6. [955] [956] [957] [958] [959] [960] Underfull \hbox (badness 10000) in paragraph at lines 385--391 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 385--391 \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 [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1025--1025 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1027--1027 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1029--1029 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1074--1079 []\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- [971] [972] [973] [974] Underfull \hbox (badness 3219) in paragraph at lines 1288--1291 []\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 [975] [976] [977] [978] [979] [980] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1675--1675 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [981] [982] [983] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1889--1889 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.25, y=.75, gp=gpar(fill="bla ck"), name="r1")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1890--1890 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.5, y=.5, gp=gpar(fill="grey" ), name="r2")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1891--1891 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [984] Underfull \hbox (badness 2961) in paragraph at lines 1926--1931 []\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 , [985] Underfull \hbox (badness 1430) in paragraph at lines 1985--1990 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- Underfull \hbox (badness 4479) in paragraph at lines 2014--2017 []\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 [986] [987] [988] Underfull \hbox (badness 2894) in paragraph at lines 2221--2228 []\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 [989] [990] [991] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2377--2377 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2389--2394 []\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- [992] [993] [994] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2590--2590 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2622--2622 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [995] [996] [997] [998] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2864--2864 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [999] [1000] [1001] [1002] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3179--3179 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1003] [1004] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3275--3275 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1005] Underfull \hbox (badness 2799) in paragraph at lines 3309--3315 []\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 [1006] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3401--3401 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3408--3408 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1007] [1008] [1009] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3602--3602 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] [1010] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3617--3617 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] Underfull \hbox (badness 1067) in paragraph at lines 4355--4358 []\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 [1023] Underfull \hbox (badness 1430) in paragraph at lines 4401--4406 []\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- [1024] [1025] [1026] Underfull \hbox (badness 7256) in paragraph at lines 4600--4602 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] Underfull \hbox (badness 10000) in paragraph at lines 5189--5191 []\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 [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] Underfull \hbox (badness 3449) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 to add and sub-tract unit ob-jects (e.g., \T1/pcr/m/n/10 unit(1, "npc") - unit(1, "inches")\T1/ptm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 5877--5883 \T1/ptm/m/n/10 and to spec-ify the min-i-mum or max-i-mum of a list of unit ob- jects (e.g., [1046] [1047] [1048] [1049] [1050] Underfull \hbox (badness 1867) in paragraph at lines 6187--6189 []\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 [1051] Underfull \hbox (badness 10000) in paragraph at lines 6224--6230 [][][]\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 , [1052] [1053] Underfull \hbox (badness 7649) in paragraph at lines 6356--6359 []\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 [1054] [1055] [1056] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6560--6560 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1057]) (./methods-pkg.tex [1058] Chapter 7. [1059] [1060] Underfull \hbox (badness 1688) in paragraph at lines 166--171 \T1/ptm/m/n/10 func-tion. See that doc-u-men-ta-tion also for de-tails of how c o-erce meth-ods work. Use [1061] [1062] [1063] 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- [1064] [1065] Overfull \hbox (15.18042pt too wide) in paragraph at lines 558--558 []\T1/pcr/m/n/9 ## vector. The next method will always be the default, usuall y a primitive.[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 568--568 []\T1/pcr/m/n/9 ## For arithmetic and one rnum with anything, callNextMethod w ith no arguments[] [1066] Overfull \hbox (4.38043pt too wide) in paragraph at lines 619--619 []\T1/pcr/m/n/9 ## Simple examples to illustrate callNextMethod with and witho ut arguments[] Underfull \vbox (badness 10000) has occurred while \output is active [1067] Overfull \hbox (25.98041pt too wide) in paragraph at lines 637--637 []\T1/pcr/m/n/9 ## call f() with 2 arguments: callNextMethod passes both to th e default method[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 640--640 []\T1/pcr/m/n/9 ## call f() with 1 argument: the default "B0" is not passed b y callNextMethod[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 657--657 []\T1/pcr/m/n/9 ## uses the class of the *argument* to consistently select the "B0" method[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 672--672 []\T1/pcr/m/n/9 ## Although the argument here is numeric, it\TS1/pcr/m/n/9 '\T 1/pcr/m/n/9 s still the "B0" method that\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s called[ ] Underfull \vbox (badness 10000) has occurred while \output is active [1068] [1069] Underfull \hbox (badness 1546) in paragraph at lines 791--797 []\T1/ptm/m/n/10 A ma-trix (or ma-trix like ob-ject) com-bin-ing the columns (o r rows) of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y\T1/ptm/m/n/10 . Note Underfull \hbox (badness 3780) in paragraph at lines 791--797 \T1/ptm/m/n/10 that meth-ods must con-struct [][]\T1/pcr/m/n/10 colnames[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 rownames[][][] \T1/ptm/m/n/10 from the co r-re-spond-ing col- Underfull \hbox (badness 1789) in paragraph at lines 791--797 \T1/ptm/m/n/10 umn and row names of \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr /m/n/10 y \T1/ptm/m/n/10 (but not from de-pars-ing ar-gu-ment names such as in [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1794--1794 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i), sum(1:10, 1+1i))) # the "N umber" method[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1796--1796 []\T1/pcr/m/n/9 stopifnot(identical(cc(1:10, 1+1i, TRUE), c(1:10, 1+1i, TRUE)) ) # the default[] Underfull \hbox (badness 10000) in paragraph at lines 1838--1840 []\T1/pcr/m/n/10 signature(from = "ANY", to = "environment")\T1/ptm/m/n/10 : ca lls [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 1981--1986 []\T1/ptm/m/n/10 The ar-gu-ment to \T1/pcr/m/n/10 insertSource \T1/ptm/m/n/10 c an be an ob-ject of class [1085] [1086] [1087] Underfull \hbox (badness 1132) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1088] [1089] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an en-vi-ron-ment) used for meth-od s dis-patch, call Overfull \hbox (6.78088pt too wide) in paragraph at lines 2360--2360 []\T1/pcr/m/n/10 ## Deprecated in 2010 and defunct in 2015 for \code{table = F ALSE}:[] [1090] [1091] [1092] Underfull \hbox (badness 3792) in paragraph at lines 2574--2577 []\T1/ptm/m/n/10 As you might ex-pect [][]\T1/pcr/m/n/10 setGeneric[][][] \T1/p tm/m/n/10 and [][]\T1/pcr/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o b-jects of class Underfull \hbox (badness 1194) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Object of class \T1/pcr/m/n/10 "optionalMethod" \T1/ptm/m/n/10 (a union of classes \T1/pcr/m/n/10 "function" \T1/ptm/m/n/10 and [1093] Overfull \hbox (24.78088pt too wide) in paragraph at lines 2661--2661 []\T1/pcr/m/n/10 removeMethods(f, where = topenv(parent.frame()), all = missin g(where))[] [1094] [1095] [1096] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2880--2880 []\T1/pcr/m/n/9 ## get the function "myFun" -- throw an error if 0 or > 1 vers ions visible:[] [1097] [1098] [1099] [1100] [1101] [1102] [1103] Underfull \hbox (badness 10000) in paragraph at lines 3403--3408 []\T1/ptm/m/n/10 Function \T1/pcr/m/n/10 implicitGeneric() \T1/ptm/m/n/10 re-tu rns the im-plicit generic ver-sion, Underfull \hbox (badness 6268) in paragraph at lines 3403--3408 \T1/pcr/m/n/10 setGenericImplicit() \T1/ptm/m/n/10 turns a generic im-plicit, \ T1/pcr/m/n/10 prohibitGeneric() \T1/ptm/m/n/10 pre-vents [1104] [1105] Underfull \hbox (badness 10000) in paragraph at lines 3531--3535 []\T1/ptm/m/n/10 For a class (or class def-i-ni-tion, see [][]\T1/pcr/m/n/10 ge tClass[][][] \T1/ptm/m/n/10 and the de-scrip-tion of class [1106] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (28.78088pt too wide) in paragraph at lines 3642--3651 [] [1107] [1108] Overfull \hbox (276.78088pt too wide) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longitude = "numeric", altitude = "numeric")) Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot", c("Pos", "missing"), function(x, y, ...) { Overfull \hbox (12.78088pt too wide) in paragraph at lines 3828--3829 []\T1/pcr/m/n/10 GPS <- setClass("GPS", slots = c(time = "POSIXt"), contains = "Pos") [1109] Overfull \hbox (120.78088pt too wide) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <- setClass("Currency", slots = c(unit = "character") , contains = "numeric") Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1110] [1111] [1112] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY", to = "call")\T1/ptm/m/n/10 . A method ex-ists for [1113] [1114] Underfull \hbox (badness 1629) in paragraph at lines 4247--4256 \T1/pcr/m/n/10 x$ensureLocal() \T1/ptm/m/n/10 on the ob-ject. The other way is to mod-ify a field ex-plic-itly by [1115] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4308--4308 []\T1/pcr/m/n/10 makeClassRepresentation(name, slots=list(), superClasses=char acter(), Overfull \hbox (0.78088pt too wide) in paragraph at lines 4309--4309 [] \T1/pcr/m/n/10 prototype=NULL, package, validity, ac cess,[] [1116] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4366--4366 []\T1/pcr/m/n/10 method.skeleton(generic, signature, file, external = FALSE, w here) [1117] [1118] Underfull \hbox (badness 1033) in paragraph at lines 4531--4538 \T1/ptm/m/n/10 se-lect-ing class \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/10 for \T 1/pcr/m/n/10 y \T1/ptm/m/n/10 would pro-duce a method as-so-ci-ated with the si g-na-ture [1119] 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 , [1120] [1121] [1122] 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 [1123] [1124] [1125] [1126] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5195--5195 []\T1/pcr/m/n/9 f3 <- function(x)UseMethod("f3") # an S3 generic to illustrate inheritance[] [1127] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5223--5223 []\T1/pcr/m/n/9 stopifnot(identical(abs(y), abs(x))) # (version 2.9.0 or earli er fails here)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5237--5237 []\T1/pcr/m/n/9 ## The S3 method for classA and the closest inherited S3 metho d for classB[] Underfull \vbox (badness 10000) has occurred while \output is active [1128] [1129] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <- function(x, incomparables = FALSE, ...) [1130] Underfull \hbox (badness 10000) in paragraph at lines 5463--5465 []\T1/pcr/m/n/10 signature(method = "MethodWithNext")\T1/ptm/m/n/10 : used in-t er-nally by [1131] Underfull \hbox (badness 3803) in paragraph at lines 5512--5514 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1132] [1133] [1134] Underfull \hbox (badness 1087) in paragraph at lines 5744--5749 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1135] Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5757--5761 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1136] Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 5848--5852 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1137] [1138] [1139] [1140] Underfull \hbox (badness 10000) in paragraph at lines 6210--6226 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 $initialize() \T1/ptm/m /n/10 is equiv-a-lent to in-vok-ing the method [1141] [1142] Underfull \hbox (badness 1248) in paragraph at lines 6343--6347 []\T1/ptm/m/n/10 Typically, a spe-cial-ized \T1/pcr/m/n/10 $initialize() \T1/pt m/m/n/10 method car-ries out its own com-pu-ta-tions, Underfull \hbox (badness 1960) in paragraph at lines 6343--6347 \T1/ptm/m/n/10 then in-vokes \T1/pcr/m/n/10 $initFields() \T1/ptm/m/n/10 to per -form stan-dard ini-tial-iza-tion, as shown in the [1143] Underfull \hbox (badness 4647) in paragraph at lines 6498--6500 []\T1/ptm/m/n/10 This method is equiv-a-lent to call-ing the gen-er-a-tor func- tion re-turned by [1144] Underfull \hbox (badness 1072) in paragraph at lines 6575--6582 []\T1/ptm/m/n/10 Establish a traced ver-sion of method [1145] 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 [1146] Underfull \vbox (badness 10000) has occurred while \output is active [1147] [1148] [1149]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1150] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7009--7009 []\T1/pcr/m/n/10 ## Create a new object from the class or use the replacement version of as().[] Underfull \hbox (badness 2042) in paragraph at lines 7065--7072 \T1/ptm/m/n/10 i-nat-ing all the for-mally de-fined slots and turn-ing off the S4 bit of the ob-ject. With [1151] [1152] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7200--7200 []\T1/pcr/m/n/9 fit <- lm(sepal ~ Petal.Length + Petal.Width + Species, data = datasets::iris)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7204--7204 []\T1/pcr/m/n/9 myReg <- setClass("myReg", slots = c(title = "character"), con tains = "mlm")[] [1153]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Com plex}) has been already used, duplicate ignored \relax l.7229 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destinat ion with the same identifier (name{Rfn.Logic}) has been already used, duplicate ignored \relax l.7231 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) has been already used, duplicate igno red \relax l.7232 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination wi th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7234 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor ed \relax l.7235 \aliasA{Summary}{S4groupGeneric}{Summary} Underfull \hbox (badness 2050) in paragraph at lines 7296--7300 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1154] Underfull \hbox (badness 6708) in paragraph at lines 7309--7321 []\T1/pcr/m/n/10 "abs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sign"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sqrt"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ceiling"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "floor"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "trunc"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cummax"\T1/ptm/m/n/10 , Underfull \hbox (badness 2012) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "acosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "asin"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "asinh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "atan"\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 "atanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "exp"\T1/ptm/m/n/10 , \T1/pcr /m/n/10 "expm1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cos"\T1/ptm/m/n/10 , Underfull \hbox (badness 3209) in paragraph at lines 7309--7321 \T1/pcr/m/n/10 "cosh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cospi"\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 "sin"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "sinh"\T1/ptm/m/n/10 , \T1/pc r/m/n/10 "sinpi"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tan"\T1/ptm/m/n/10 , \T1/pcr/m /n/10 "tanh"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tanpi"\T1/ptm/m/n/10 , [1155] [1156] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see Underfull \hbox (badness 10000) in paragraph at lines 7496--7499 []\T1/ptm/m/n/10 The typ-i-cal user level func-tion is \T1/pcr/m/n/10 selectSup erClasses() \T1/ptm/m/n/10 which calls [1157] [1158] Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 []\T1/ptm/m/n/10 If no sub-class/superclass re-la-tion-ship pro-vides a method, \T1/pcr/m/n/10 as \T1/ptm/m/n/10 looks for an in-her- Underfull \hbox (badness 7704) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ited method, but ap-ply-ing, in-her-i-tance for the ar-gu-ment \ T1/pcr/m/n/10 from \T1/ptm/m/n/10 only, not for the Underfull \hbox (badness 10000) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 ar-gu-ment \T1/pcr/m/n/10 to \T1/ptm/m/n/10 (if you think about it, you'll prob-a-bly agree that you wouldn't Underfull \hbox (badness 5817) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 want the re-sult to be from some class other than the \T1/pcr/m/ n/10 Class \T1/ptm/m/n/10 spec-i-fied). Thus, Overfull \hbox (0.78088pt too wide) in paragraph at lines 7663--7670 \T1/pcr/m/n/10 selectMethod("coerce", sig, useInherited= c(from=TRUE, to= FALSE )) [1159] [1160] [1161] [1162] [1163] [1164] [1165] [1166] [1167] [1168] [1169] Underfull \hbox (badness 1052) in paragraph at lines 8489--8496 []\T1/ptm/m/n/10 By de-fault, the generic func-tion can re-turn any ob-ject. If \T1/pcr/m/n/10 valueClass \T1/ptm/m/n/10 is sup-plied, it [1170] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8622--8622 []\T1/pcr/m/n/10 setGroupGeneric(name, def= , group=list(), valueClass=charact er(), [1171] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8697--8697 [] \T1/pcr/m/n/10 by = character(), where = topenv(parent.frame()), class Def =,[] [1172] [1173] [1174] [1175] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8959--8959 []\T1/pcr/m/n/9 ## "trackMultiCurve", by making the y, smooth slots into 1-col umn matrices[] [1176] [1177] [1178] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9167--9167 [] \T1/pcr/m/n/9 setLoadAction(function(ns) assign("myCount", 0, envir = ns), "setCount")[] [1179] [1180] Underfull \vbox (badness 2302) has occurred while \output is active [1181] 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[] [1182] [1183] [1184] [1185] 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[] [1186] 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][] [1187] 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][] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class Underfull \hbox (badness 1852) in paragraph at lines 10564--10568 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., Underfull \hbox (badness 1681) in paragraph at lines 10564--10568 \T1/pcr/m/n/10 "functionWithTrace" \T1/ptm/m/n/10 ex-tends \T1/pcr/m/n/10 "func tion"\T1/ptm/m/n/10 . Each of the spe-cific classes ex-tends [1197] [1198] [1199] [1200]) (./parallel-pkg.tex 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 [1201] 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 [1202] [1203] Underfull \hbox (badness 1024) in paragraph at lines 213--216 []\T1/ptm/m/n/10 Two ex-cep-tions: \T1/pcr/m/n/10 parLapply \T1/ptm/m/n/10 has ar-gu-ment \T1/pcr/m/n/10 X \T1/ptm/m/n/10 not \T1/pcr/m/n/10 x \T1/ptm/m/n/10 for con-sis-tency with [][]\T1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , and [1204] Underfull \hbox (badness 10000) in paragraph at lines 318--326 []\T1/ptm/m/n/10 On Sparc So-laris \T1/pcr/m/n/10 logical = FALSE \T1/ptm/m/n/1 0 re-turns the num-ber of phys-i-cal cores and [1205] [1206] 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 [1207] [1208] [1209] [1210] Underfull \hbox (badness 1917) in paragraph at lines 742--751 []\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 742--751 \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 [1211] [1212] Overfull \hbox (60.78088pt too wide) in paragraph at lines 824--824 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1213] Underfull \hbox (badness 10000) in paragraph at lines 884--887 []\T1/pcr/m/n/10 mclapply \T1/ptm/m/n/10 is a par-al-lelized ver-sion of [][]\T 1/pcr/m/n/10 lapply[][][]\T1/ptm/m/n/10 , pro-vided \T1/pcr/m/n/10 mc.cores > 1 \T1/ptm/m/n/10 : for [1214] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1005--1005 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] [1215] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1009--1009 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1216] Underfull \hbox (badness 5388) in paragraph at lines 1119--1124 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1143--1151 []\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 [1217] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1180--1180 []\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)[] [1218] [1219] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1296--1296 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1310--1310 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] Underfull \hbox (badness 1577) in paragraph at lines 1339--1342 []\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 [1220] Underfull \hbox (badness 3375) in paragraph at lines 1385--1387 []\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 [1221] [1222]) (./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 \T1/ptm/ m/n/10 and William N. Ven-ables [1223] [1224] [1225] [1226] [1227] [1228] [1229] Overfull \hbox (4.38043pt too wide) in paragraph at lines 492--492 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1230] [1231] [1232] [1233] Overfull \hbox (25.98041pt too wide) in paragraph at lines 706--706 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1234] [1235] [1236]) (./stats-pkg.tex Chapter 10. [1237] Underfull \hbox (badness 2781) in paragraph at lines 65--68 []\T1/pcr/m/n/10 .MFclass \T1/ptm/m/n/10 re-turns a char-ac-ter string, one of \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , [1238] [1239] [1240] [1241] [1242] Overfull \hbox (20.58041pt too wide) in paragraph at lines 417--417 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 438--438 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1243] [1244] [1245] [1246] [1247] [1248] [1249] Underfull \hbox (badness 1024) in paragraph at lines 847--849 []\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 [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] Underfull \hbox (badness 10000) in paragraph at lines 1391--1393 []\T1/ptm/m/n/10 an es-ti-mate of the ra-tio of scales. (Only present if ar-gu- ment [1258] Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov", "lm") \T1/ptm/m/n/ 10 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("maov", "aov", "mlm", "lm") \T1/ptm/m/n/10 or for mul-ti-ple e r-ror strata of class Underfull \hbox (badness 1490) in paragraph at lines 1508--1512 \T1/pcr/m/n/10 c("aovlist", "[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\ T1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \ T1/ptm/m/n/10 meth-ods avail-able for [1259] [1260] [1261] [1262] Underfull \hbox (badness 10000) in paragraph at lines 1773--1777 []\T1/ptm/m/n/10 function to be called to han-dle miss-ing val-ues. Cur-rently, via Underfull \hbox (badness 2197) in paragraph at lines 1773--1777 \T1/pcr/m/n/10 na.action = na.pass\T1/ptm/m/n/10 , only Yule-Walker method can han-dle miss- [1263] [1264] Underfull \hbox (badness 4303) in paragraph at lines 1874--1876 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 x \T1/ptm/m/n/10 con-tains miss-ing val-ues, see [][]\T1/pcr/m/n/10 NA[][][]\T1/ptm/m/n/10 , also con-sider us-ing [][]\T1/ pcr/m/n/10 arima[][][]()\T1/ptm/m/n/10 , pos-si-bly with [1265] [1266] [1267] Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 []\T1/ptm/m/n/10 logical; if true, the AR pa-ram-e-ters are trans-formed to en- sure Underfull \hbox (badness 10000) in paragraph at lines 2096--2101 \T1/ptm/m/n/10 that they re-main in the re-gion of sta-tion-ar-ity. Not used fo r Underfull \hbox (badness 1371) in paragraph at lines 2096--2101 \T1/pcr/m/n/10 method = "CSS"\T1/ptm/m/n/10 . For \T1/pcr/m/n/10 method = "ML"\ T1/ptm/m/n/10 , it has been ad-van-ta-geous Underfull \hbox (badness 1221) in paragraph at lines 2102--2108 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2102--2108 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1268] [1269] Underfull \hbox (badness 3965) in paragraph at lines 2183--2185 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1270] [1271] [1272] Underfull \hbox (badness 1221) in paragraph at lines 2457--2462 []\T1/ptm/m/n/10 optional nu-meric vec-tor of the same length as the to-tal num -ber of pa- Underfull \hbox (badness 4608) in paragraph at lines 2457--2462 \T1/ptm/m/n/10 ram-e-ters. If sup-plied, only \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 en-tries in \T1/pcr/m/n/10 fixed \T1/ptm/m/n/10 will be var-ied. [1273] Underfull \hbox (badness 3965) in paragraph at lines 2534--2536 []\T1/ptm/m/n/10 the AIC value cor-re-spond-ing to the log-likelihood. Only val id for [1274] [1275] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2679--2679 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1276] [1277] [1278] [1279] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1280] [1281] [1282] Overfull \hbox (19.88992pt too wide) in paragraph at lines 3128--3130 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of variances"\T1/ptm/m/n/10 . [1283] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3176--3176 []\T1/pcr/m/n/10 pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3177--3177 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1284] Underfull \hbox (badness 2726) in paragraph at lines 3260--3276 \T1/ptm/m/n/10 We have slightly tweaked the orig-i-nal ``TOMS 708'' al-go-rithm , and en-hanced for [1285] [1286] [1287] [1288] [1289] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3568--3568 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1290] [1291] [1292] [1293] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3846--3846 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1294] [1295] [1296] [1297] [1298] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4135--4135 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4136--4136 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1299] [1300] [1301] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4374--4374 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1302] [1303] [1304] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4542--4542 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1305] Underfull \hbox (badness 3989) in paragraph at lines 4634--4641 []\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 = [1306] [1307] Underfull \hbox (badness 2080) in paragraph at lines 4754--4756 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "aov" \T1/ptm/m/n/10 method does not re-por t aliased co-ef-fi-cients (see [][]\T1/pcr/m/n/10 alias[][][]\T1/ptm/m/n/10 ) b y de-fault where Underfull \hbox (badness 2050) in paragraph at lines 4757--4763 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 complete \T1/ptm/m/n/10 ar-gu-ment also ex- ists for com-pat-i-bil-ity with [][]\T1/pcr/m/n/10 vcov[][][] \T1/ptm/m/n/10 me th-ods, and \T1/pcr/m/n/10 coef Underfull \hbox (badness 4954) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aov \T1/ptm/m/n/10 meth-ods for other classes should typ-i-cally also keep the \T1/pcr/m/n/10 complete = * Underfull \hbox (badness 4726) in paragraph at lines 4757--4763 \T1/ptm/m/n/10 be-hav-ior in sync. By that, with \T1/pcr/m/n/10 p <- length(coe f(obj, complete = TF))\T1/ptm/m/n/10 , [1308] [1309] [1310] [1311] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5019--5019 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5021--5021 []\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))[] [1312] Underfull \hbox (badness 7397) in paragraph at lines 5108--5112 []\T1/ptm/m/n/10 For con-sis-tency, \T1/pcr/m/n/10 sparse \T1/ptm/m/n/10 is an ar-gu-ment to all these con-trast func-tions, how-ever Underfull \hbox (badness 7326) in paragraph at lines 5108--5112 \T1/pcr/m/n/10 sparse = TRUE \T1/ptm/m/n/10 for \T1/pcr/m/n/10 contr.poly \T1/p tm/m/n/10 is typ-i-cally point-less and is rarely use-ful for [1313] [1314] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5242--5242 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5260--5260 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5287--5289 []\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 [1315] Underfull \hbox (badness 10000) in paragraph at lines 5292--5294 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 r <- convolve(x, y, type = "open") \T1/ptm/m /n/10 and \T1/pcr/m/n/10 n <- length(x)\T1/ptm/m/n/10 , [1316] [1317] Underfull \hbox (badness 1436) in paragraph at lines 5470--5475 []\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 5470--5475 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5470--5475 \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 , [1318] [1319] [1320] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5668--5668 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1321] Underfull \hbox (badness 1168) in paragraph at lines 5740--5745 []\T1/ptm/m/n/10 For Spear-man's test, p-values are com-puted us-ing al-go-rith m AS 89 for $\OML/cmm/m/it/10 n < \OT1/cmr/m/n/10 1290$ \T1/ptm/m/n/10 and [1322] [1323] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5835--5835 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1324] [1325] [1326] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6020--6020 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1327] [1328] Underfull \hbox (badness 10000) in paragraph at lines 6183--6188 []\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 [1329] [1330] [1331] Underfull \hbox (badness 5954) in paragraph at lines 6379--6381 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1332] Underfull \hbox (badness 2503) in paragraph at lines 6461--6464 []\T1/ptm/m/n/10 Objects of class \T1/pcr/m/n/10 "hclust" \T1/ptm/m/n/10 can be con-verted to class \T1/pcr/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method Underfull \hbox (badness 5563) in paragraph at lines 6465--6467 []\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 6468--6473 \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, [1333] Underfull \hbox (badness 7238) in paragraph at lines 6504--6507 [][][]\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 [1334] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6539--6539 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6554--6554 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6569--6569 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] [1335] [1336] [1337] [1338] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6813--6813 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1339] [1340] Underfull \vbox (badness 10000) has occurred while \output is active [1341] [1342] [1343] [1344] Underfull \hbox (badness 10000) in paragraph at lines 7211--7215 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1345] Underfull \hbox (badness 6493) in paragraph at lines 7310--7313 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1346] [1347] Underfull \hbox (badness 10000) in paragraph at lines 7447--7450 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1348] [1349] [1350] [1351] [1352] [1353] Underfull \hbox (badness 10000) in paragraph at lines 7857--7862 []\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 , ..., [1354] [1355] Overfull \hbox (33.6622pt too wide) in paragraph at lines 7995--7997 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -pexp(t, r, lower = FALSE, log = TRUE)\T1/ptm/m/n/10 . [1356] [1357] [1358] Underfull \hbox (badness 1210) in paragraph at lines 8212--8214 []\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 [1359] [1360] [1361] [1362] [1363] [1364] [1365] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8687--8687 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8690--8690 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1366] [1367] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8828--8828 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1368] Underfull \hbox (badness 1859) in paragraph at lines 8867--8872 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 inverse \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\ T1/ptm/m/n/10 , the (un-nor-mal-ized) in-verse Fourier trans-form is re-turned, i.e., if [1369] [1370] [1371] Underfull \hbox (badness 2865) in paragraph at lines 9113--9122 []\T1/ptm/m/n/10 For larger than $\OT1/cmr/m/n/10 2 \OMS/cmsy/m/n/10 ^^B \OT1/c mr/m/n/10 2$ \T1/ptm/m/n/10 ta-bles and \T1/pcr/m/n/10 hybrid = TRUE\T1/ptm/m/n /10 , asymp-totic chi-squared prob-a-bil-i- Underfull \hbox (badness 1331) in paragraph at lines 9113--9122 \T1/ptm/m/n/10 ties are only used if the `Cochran con-di-tions' (or mod-i-fied ver-sion thereof) spec-i-fied by [1372] [1373] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9255--9255 [] \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 9256--9256 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1374] [1375] [1376] Overfull \hbox (61.88992pt too wide) in paragraph at lines 9435--9437 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of variances"\T1/ptm/m/n/10 . [1377] [1378] [1379] [1380] [1381] [1382] [1383] Underfull \hbox (badness 2443) in paragraph at lines 9888--9894 [][][]\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); [1384] [1385] [1386] Underfull \hbox (badness 3758) in paragraph at lines 10101--10104 []\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 [1387] [1388] [1389] [1390] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10337--10337 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10363--10368 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1391] Underfull \hbox (badness 4132) in paragraph at lines 10402--10406 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od [1392] Underfull \hbox (badness 10000) in paragraph at lines 10507--10510 []\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 [1393] [1394] [1395] Underfull \hbox (badness 2142) in paragraph at lines 10711--10714 []\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 ^^@ [1396] Underfull \hbox (badness 1708) in paragraph at lines 10792--10796 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1397] Underfull \hbox (badness 10000) in paragraph at lines 10834--10840 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, Underfull \hbox (badness 1418) in paragraph at lines 10872--10877 \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 (= [1398] [1399] Underfull \hbox (badness 2635) in paragraph at lines 11005--11008 \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 [1400] [1401] [1402] Underfull \hbox (badness 1694) in paragraph at lines 11190--11193 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to Underfull \hbox (badness 1337) in paragraph at lines 11209--11218 []\T1/ptm/m/n/10 If ei-ther is a vec-tor (of `weights') then the ap-pro-pri-ate den-dro-gram is re-ordered ac-cord- Underfull \hbox (badness 3049) in paragraph at lines 11209--11218 \T1/ptm/m/n/10 ing to the sup-plied val-ues sub-ject to the con-straints im-pos ed by the den-dro-gram, by [1403] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11291--11291 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1404] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11324--11324 [] \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 11337--11341 []\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 [1405] [1406] [1407] Underfull \hbox (badness 7379) in paragraph at lines 11517--11520 []\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[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1408] [1409] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11656--11656 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.11671 \aliasA{hat}{influence.measures}{hat} [1410] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11724--11724 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11736--11736 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] [1411] Underfull \hbox (badness 1062) in paragraph at lines 11785--11790 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1412] [1413] Underfull \hbox (badness 3623) in paragraph at lines 11956--11958 []\T1/pcr/m/n/10 rel.tol \T1/ptm/m/n/10 can-not be less than \T1/pcr/m/n/10 max (50*.Machine$double.eps, 0.5e-28) \T1/ptm/m/n/10 if [1414] [1415] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12052--12052 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1416] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12145--12145 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1417] Underfull \hbox (badness 10000) in paragraph at lines 12193--12196 []\T1/ptm/m/n/10 For nor-mally $\OML/cmm/m/it/10 N\OT1/cmr/m/n/10 (\OML/cmm/m/i t/10 m; \OT1/cmr/m/n/10 1)$ \T1/ptm/m/n/10 dis-tributed $\OML/cmm/m/it/10 X$\T1 /ptm/m/n/10 , the ex-pected value of \T1/pcr/m/n/10 IQR(X) \T1/ptm/m/n/10 is [1418] [1419] [1420] Underfull \hbox (badness 4441) in paragraph at lines 12388--12390 []\T1/ptm/m/n/10 vector of dif-fer-enc-ing co-ef-fi-cients, so an ARMA model is fit-ted to Underfull \hbox (badness 10000) in paragraph at lines 12395--12397 []\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 [1421] Underfull \hbox (badness 4739) in paragraph at lines 12418--12420 []\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 [1422] Underfull \hbox (badness 2753) in paragraph at lines 12487--12489 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1423] [1424] Underfull \hbox (badness 1292) in paragraph at lines 12612--12616 \T1/ptm/m/n/10 than one, it means the con-vo-lu-tion of ker-nels of di-men-sion \T1/pcr/m/n/10 m[j]\T1/ptm/m/n/10 , for [1425] Underfull \hbox (badness 10000) in paragraph at lines 12725--12727 []\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 Underfull \hbox (badness 2894) in paragraph at lines 12731--12735 []\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 12731--12735 \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 [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13438--13438 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1437] Underfull \hbox (badness 4518) in paragraph at lines 13481--13486 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1438] [1439] Underfull \hbox (badness 10000) in paragraph at lines 13680--13684 []\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 , [1440] [1441] [1442] Underfull \hbox (badness 6995) in paragraph at lines 13865--13867 [][][]\T1/pcr/m/n/10 naresid[][][] \T1/ptm/m/n/10 is ap-plied to the re-sults a nd so will fill in with \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 s it the fit had [1443] [1444] Underfull \hbox (badness 1163) in paragraph at lines 14013--14021 \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 , [1445] [1446] Underfull \hbox (badness 4518) in paragraph at lines 14133--14138 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 14271--14275 []\T1/ptm/m/n/10 Only for the (de-fault) case \T1/pcr/m/n/10 (surface = Underfull \hbox (badness 7133) in paragraph at lines 14271--14275 \T1/pcr/m/n/10 "interpolate", statistics = "approximate")\T1/ptm/m/n/10 : shoul d the [1449] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14319--14319 []\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 14320--14320 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1450] Underfull \hbox (badness 10000) in paragraph at lines 14375--14378 []\T1/ptm/m/n/10 The dis-tri-bu-tion func-tion is a rescaled hy-per-bolic tan-g ent, Underfull \hbox (badness 1715) in paragraph at lines 14375--14378 \T1/pcr/m/n/10 plogis(x) == (1+ [][]tanh[][][](x/2))/2\T1/ptm/m/n/10 , and it i s called a \T1/ptm/m/it/10 sig-moid func-tion \T1/ptm/m/n/10 in con-texts [1451] [1452] [1453] [1454] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14663--14663 []\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 14664--14664 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1455] Overfull \hbox (45.6622pt too wide) in paragraph at lines 14714--14716 []\T1/ptm/m/n/10 The cu-mu-la-tive haz-ard $\OML/cmm/m/it/10 H\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 t\OT1/cmr/m/n/10 ) = \OMS/cmsy/m/n/10 ^^@ []\OT1/cmr/m/n/10 (1 \OMS/cmsy/m/n/10 ^^@ \OML/cmm/m/it/10 F\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 t\OT1 /cmr/m/n/10 ))$ \T1/ptm/m/n/10 is \T1/pcr/m/n/10 -plnorm(t, r, lower = FALSE, l og = TRUE)\T1/ptm/m/n/10 . Overfull \hbox (18.78088pt too wide) in paragraph at lines 14757--14757 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1456] [1457] [1458] [1459] [1460] [1461] [1462] Underfull \hbox (badness 2726) in paragraph at lines 15164--15167 []\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 , [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15879--15879 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1474] [1475] Underfull \hbox (badness 1014) in paragraph at lines 16017--16022 \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 [1476] Underfull \hbox (badness 1648) in paragraph at lines 16083--16085 []\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 16097--16106 \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 16097--16106 \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 [1477] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16165--16165 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = "contr.poly"))[] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16719--16719 []\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[] [1486] [1487] [1488] [1489] Overfull \hbox (25.98041pt too wide) in paragraph at lines 16947--16947 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497] Underfull \hbox (badness 2359) in paragraph at lines 17533--17535 []\T1/ptm/m/n/10 Douglas M. Bates and Saikat De-bRoy: David M. Gay for the For- tran code used by [1498] [1499] Underfull \vbox (badness 10000) has occurred while \output is active [1500] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17705--17705 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1501] Underfull \hbox (badness 10000) in paragraph at lines 17785--17789 []\T1/ptm/m/n/10 Fits the asymp-totic re-gres-sion model, in the form \T1/pcr/m /n/10 b0 + [1502] [1503] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17865--17865 []\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 17912--17912 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1504] Overfull \hbox (20.58041pt too wide) in paragraph at lines 17959--17959 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] Underfull \hbox (badness 1248) in paragraph at lines 18450--18453 []\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 1127) in paragraph at lines 18463--18467 \T1/ptm/m/n/10 value by a fac-tor of \T1/pcr/m/n/10 reltol * (abs(val) + reltol ) \T1/ptm/m/n/10 at a step. De-faults to [1513] Underfull \hbox (badness 1478) in paragraph at lines 18471--18475 \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 18529--18531 []\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 [1514] [1515] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18635--18635 [] \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 [1516] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18677--18677 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18695--18695 []\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 18698--18698 []\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 18718--18718 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18721--18721 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1517] Underfull \hbox (badness 2564) in paragraph at lines 18756--18767 []\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 18756--18767 \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 [1518] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18819--18819 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1519] [1520] [1521] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19044--19044 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1522] Underfull \hbox (badness 1337) in paragraph at lines 19120--19123 []\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 [1523] [1524] [1525] [1526] [1527] [1528] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19439--19439 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1529] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19527--19527 [] \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 (6.78088pt too wide) in paragraph at lines 19530--19530 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1530] Underfull \hbox (badness 3049) in paragraph at lines 19609--19613 []\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 [1531] [1532] [1533] [1534] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19857--19857 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] Underfull \hbox (badness 4779) in paragraph at lines 19864--19866 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , add to al-read y ex-ist-ing plot. Only valid for Underfull \hbox (badness 1194) in paragraph at lines 19867--19870 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1535] Underfull \hbox (badness 1107) in paragraph at lines 19925--19927 []\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 [1536] Overfull \hbox (20.58041pt too wide) in paragraph at lines 19980--19980 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1537] Overfull \hbox (31.3804pt too wide) in paragraph at lines 19987--19987 []\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)[] Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 function(x, col, bg, pch, type, ...) \T1/ptm/ m/n/10 which gives Underfull \hbox (badness 10000) in paragraph at lines 20037--20040 \T1/ptm/m/n/10 the ac-tion to be car-ried out in each panel of the dis-play for [1538] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20081--20081 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1539] [1540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20206--20206 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1541] Underfull \hbox (badness 10000) in paragraph at lines 20269--20271 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or Overfull \hbox (6.78088pt too wide) in paragraph at lines 20317--20317 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1542] Underfull \hbox (badness 10000) in paragraph at lines 20372--20374 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 poly(*, simple=TRUE)\T1/ptm/m/n/10 , \T1/pc r/m/n/10 polym(*, coefs=)\T1/ptm/m/n/10 , and [1543] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20409--20409 [] \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 20414--20414 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1544] [1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21264--21264 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1557] Underfull \hbox (badness 6859) in paragraph at lines 21331--21338 [][][]\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 21342--21348 []\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 , [1558] [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22080--22080 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1570] [1571] [1572] [1573] [1574] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22364--22364 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22365--22365 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1575] [1576] [1577] [1578] [1579] Underfull \hbox (badness 1337) in paragraph at lines 22689--22695 []\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 [1580] [1581] [1582] [1583] [1584] [1585] [1586] [1587] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23251--23251 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1588] [1589] Underfull \hbox (badness 1028) in paragraph at lines 23392--23395 []\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 [1590] [1591] Underfull \hbox (badness 10000) in paragraph at lines 23502--23505 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by Underfull \hbox (badness 5091) in paragraph at lines 23502--23505 \T1/pcr/m/n/10 cutree(hclust.obj, k = k)\T1/ptm/m/n/10 , can be spec-i-fied for ef-fi-ciency if [1592] Underfull \hbox (badness 10000) in paragraph at lines 23557--23559 []\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 Underfull \hbox (badness 10000) in paragraph at lines 23619--23621 []\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 [1593] [1594] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23721--23721 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1595] [1596] [1597] Overfull \hbox (31.3804pt too wide) in paragraph at lines 23941--23941 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1598] [1599] [1600] Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\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 Underfull \hbox (badness 2134) in paragraph at lines 24139--24143 [][][]\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 [1601] Overfull \hbox (9.78043pt too wide) in paragraph at lines 24152--24152 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1602] [1603] [1604] [1605] [1606] [1607] [1608] Underfull \hbox (badness 6268) in paragraph at lines 24616--24621 [][]\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 , [1609] Overfull \hbox (58.38037pt too wide) in paragraph at lines 24644--24644 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1610] [1611] Underfull \hbox (badness 1867) in paragraph at lines 24821--24823 []\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 24834--24838 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <- [][]nobs[][][](object, use.fallback = use.fallback) \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 24834--24838 \T1/pcr/m/n/10 PP <- sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- wher e in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 24870--24870 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1613] [1614] [1615] Underfull \hbox (badness 2495) in paragraph at lines 25060--25069 []\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 [][]$\T1/pcr/m/n/10 https : / / en . [1616] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25142--25142 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25149--25151 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1617] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25236--25236 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] [1618] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25261--25261 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25264--25264 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1619] Underfull \hbox (badness 10000) in paragraph at lines 25306--25311 []\T1/ptm/m/n/10 integer or [][]\T1/pcr/m/n/10 function[][][] \T1/ptm/m/n/10 gi v-ing the num-ber of knots to use when Underfull \hbox (badness 2435) in paragraph at lines 25306--25311 \T1/pcr/m/n/10 all.knots = FALSE\T1/ptm/m/n/10 . If a func-tion (as by de-fault ), the num-ber of [1620] Underfull \hbox (badness 2980) in paragraph at lines 25451--25453 []\T1/ptm/m/n/10 the value of \T1/pcr/m/n/10 spar \T1/ptm/m/n/10 com-puted or g iven, un-less it has been given as [1621] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25487--25487 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25536--25536 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] [1622] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25557--25557 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] Underfull \vbox (badness 10000) has occurred while \output is active [1623] [1624] Overfull \hbox (15.18042pt too wide) in paragraph at lines 25661--25661 []\T1/pcr/m/n/9 legend(1, 470, paste("endrule", c("keep","constant","median"), sep = " = "),[] [1625] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25728--25728 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1626] [1627] [1628] [1629] [1630] [1631] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26107--26107 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] Underfull \hbox (badness 6477) in paragraph at lines 26161--26164 []\T1/ptm/m/n/10 Method \T1/pcr/m/n/10 "hyman" \T1/ptm/m/n/10 com-putes a \T1/p tm/m/it/10 mono-tone \T1/ptm/m/n/10 cu-bic spline us-ing Hy-man fil-ter-ing of an [1632] [1633] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26292--26292 []\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 26293--26293 []\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 [1634] Underfull \hbox (badness 2922) in paragraph at lines 26362--26367 []\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 [1635] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26399--26399 [] \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 26402--26402 [] \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 26411--26411 [] \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 26412--26412 [] \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 26416--26416 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1636] Underfull \hbox (badness 2922) in paragraph at lines 26458--26463 []\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 Underfull \hbox (badness 3240) in paragraph at lines 26470--26473 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff Overfull \hbox (36.7804pt too wide) in paragraph at lines 26491--26491 [] \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 26494--26494 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1637] Underfull \hbox (badness 2922) in paragraph at lines 26544--26549 []\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 [1638] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26577--26577 [] \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 26581--26581 [] \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 26591--26591 [] \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 26596--26596 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1639] Underfull \hbox (badness 2922) in paragraph at lines 26632--26638 []\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 26654--26654 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26670--26670 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1640] [1641] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26784--26784 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1642] Underfull \hbox (badness 2922) in paragraph at lines 26846--26851 []\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 [1643] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26884--26884 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1644] Underfull \hbox (badness 2922) in paragraph at lines 26933--26938 []\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 26964--26964 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1645] Underfull \hbox (badness 2922) in paragraph at lines 26998--27003 []\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 27023--27023 []\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 27027--27027 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27047--27047 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] [1646] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27057--27057 [] \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 27092--27097 []\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 [1647] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27114--27114 []\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 27132--27132 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1648] Underfull \hbox (badness 6493) in paragraph at lines 27184--27189 []\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 27211--27211 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27213--27213 []\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 27216--27216 []\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 27219--27219 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1649] [1650] [1651] [1652] [1653] [1654] [1655] [1656] Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex- Underfull \hbox (badness 10000) in paragraph at lines 27714--27717 \T1/ptm/m/n/10 trac-tion, which should be odd. If \T1/pcr/m/n/10 NULL\T1/ptm/m/ n/10 , the de-fault, [1657] [1658] [1659] [1660] [1661] [1662] [1663] Underfull \hbox (badness 3396) in paragraph at lines 28143--28145 []\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 [1664] [1665] [1666] Underfull \hbox (badness 2237) in paragraph at lines 28320--28322 []\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 [1667] [1668] Underfull \hbox (badness 2591) in paragraph at lines 28484--28486 []\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 [1669] Underfull \hbox (badness 2237) in paragraph at lines 28530--28533 []\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 [1670] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28603--28603 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1671] [1672] Underfull \hbox (badness 3407) in paragraph at lines 28711--28715 []\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) [1673] [1674] Underfull \hbox (badness 1337) in paragraph at lines 28844--28848 []\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 [1675] [1676] Underfull \hbox (badness 10000) in paragraph at lines 28961--28964 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for \T1/pcr/m/n/10 rt()\T1/ptm/m/n/10 , only for [1677] [1678] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29090--29090 []\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 29118--29118 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1679] Underfull \hbox (badness 1616) in paragraph at lines 29144--29147 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1680] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29223--29223 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1681] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29300--29300 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1682] Underfull \hbox (badness 5050) in paragraph at lines 29336--29341 []\T1/ptm/m/n/10 A [][]\T1/pcr/m/n/10 terms.object[][][] \T1/ptm/m/n/10 ob-ject is re-turned. The ob-ject it-self is the re-ordered (un-less [1683] Underfull \hbox (badness 2205) in paragraph at lines 29389--29394 []\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 [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29984--29984 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) [1692] Overfull \hbox (12.78088pt too wide) in paragraph at lines 29985--29985 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1693] [1694] [1695] [1696] Underfull \hbox (badness 10000) in paragraph at lines 30274--30278 []\T1/ptm/m/n/10 Setting \T1/pcr/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/p cr/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect Underfull \hbox (badness 1596) in paragraph at lines 30274--30278 \T1/pcr/m/n/10 interval = c(lower,upper) \T1/ptm/m/n/10 if \T1/pcr/m/n/10 sign( f(x)) \T1/ptm/m/n/10 does not sat-isfy the re-quire-ments at Overfull \hbox (30.78088pt too wide) in paragraph at lines 30285--30285 [] \T1/pcr/m/n/10 extendInt = c("no", "yes", "downX", "upX"), check.con v = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 30286--30286 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1697] [1698] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30412--30412 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30421--30421 []\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:[] [1699] [1700] [1701] [1702] Underfull \hbox (badness 1337) in paragraph at lines 30638--30642 []\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 [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] Underfull \hbox (badness 1337) in paragraph at lines 31165--31169 []\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 [1711] Underfull \hbox (badness 1946) in paragraph at lines 31242--31247 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 (and \T1/pcr/m/n/10 y \T1 /ptm/m/n/10 if ap-pli-ca-ble) are valid, the func-tion now al-ways re-turns, al so in the Underfull \hbox (badness 5161) in paragraph at lines 31264--31266 []\T1/ptm/m/n/10 an es-ti-mate of the lo-ca-tion pa-ram-e-ter. (Only present if ar-gu-ment [1712] [1713] [1714] [1715] [1716] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31590--31590 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1717] Underfull \hbox (badness 6775) in paragraph at lines 31647--31652 []\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 [1718] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31710--31710 []\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 "")[] [1719]) (./stats4-pkg.tex [1720] Chapter 11. [1721] [1722] [1723] Overfull \hbox (15.18042pt too wide) in paragraph at lines 192--192 [] \T1/pcr/m/n/9 -sum(stats::dpois(y, lambda = exp(lymax)/(1+x/exp(lxhalf)) , log = TRUE))[] [1724] [1725] [1726]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdash.methods}) has been already used, duplicate ignored \relax l.407 ...Package \pkg{stats4}}{show.Rdash.methods} [1727] Underfull \hbox (badness 10000) in paragraph at lines 440--443 []\T1/ptm/m/n/10 Generate a sum-mary as an ob-ject of class [1728] [1729]) (./tcltk-pkg.tex [1730] Chapter 12. [1731] [1732] [1733] [1734] Overfull \hbox (4.38043pt too wide) in paragraph at lines 349--349 []\T1/pcr/m/n/9 ls(envir = .TkRoot$env, all = TRUE) # .Tcl.args put a callback ref in here[] [1735] [1736] [1737] Underfull \vbox (badness 10000) has occurred while \output is active [1738] Underfull \hbox (badness 1292) in paragraph at lines 664--671 []\T1/pcr/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing any Tk or Tcl com-mand by sim-ply run-ning [1739] [1740] [1741] [1742] [1743] [1744] [1745] [1746] [1747] [1748] [1749] Underfull \hbox (badness 1189) in paragraph at lines 1407--1410 [][][]\T1/pcr/m/n/10 select.list[][][] \T1/ptm/m/n/10 (a text ver-sion ex-cept on Win-dows and the ma-cOS GUI), [][]\T1/pcr/m/n/10 menu[][][] \T1/ptm/m/n/10 ( whose [1750]) (./tools-pkg.tex Chapter 13. [1751] Overfull \hbox (9.78043pt too wide) in paragraph at lines 69--69 []\T1/pcr/m/n/9 ## is used for simple print methods in R, and as prototype for new methods.[] [1752] Underfull \hbox (badness 10000) in paragraph at lines 138--140 []\T1/ptm/m/n/10 an un-eval-u-ated \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion which will be eval-u-ated via Underfull \hbox (badness 1253) in paragraph at lines 164--167 []\T1/pcr/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [1753] Overfull \hbox (4.38043pt too wide) in paragraph at lines 215--215 []\T1/pcr/m/n/9 assertCondition(ff(), "error", "warning") # ok (quietly, catch ing warning)[] [1754] Underfull \hbox (badness 5147) in paragraph at lines 285--298 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 Underfull \hbox (badness 4792) in paragraph at lines 285--298 \T1/ptm/m/n/10 types of bib-li-o-graphic en-try sup-ported by [][]\T1/pcr/m/n/1 0 bibentry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou- Underfull \hbox (badness 2237) in paragraph at lines 285--298 \T1/ptm/m/n/10 tines de-scribed be-low. The for-mer must be named \T1/pcr/m/n/1 0 formatArticle\T1/ptm/m/n/10 , \T1/pcr/m/n/10 formatBook\T1/ptm/m/n/10 , [1755] Overfull \hbox (42.78088pt too wide) in paragraph at lines 370--370 []\T1/pcr/m/n/10 buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, ta ngle = TRUE, Underfull \hbox (badness 2460) in paragraph at lines 389--391 []\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 [1756] [1757] [1758] [1759] [1760] [1761] [1762] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1763] [1764] Overfull \hbox (0.78088pt too wide) in paragraph at lines 905--905 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 960--960 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1765] [1766] Underfull \hbox (badness 1635) in paragraph at lines 1060--1062 []\T1/ptm/m/n/10 Delete files in the tem-po-rary di-rec-tory? This op-tion is i g-nored when [1767] Underfull \hbox (badness 5431) in paragraph at lines 1135--1138 []\T1/ptm/m/n/10 a named list of char-ac-ter vec-tors with ar-gu-ments to be pa ssed to Underfull \hbox (badness 4441) in paragraph at lines 1138--1148 \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- [1768] Underfull \hbox (badness 1014) in paragraph at lines 1160--1162 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1166--1168 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us- Underfull \hbox (badness 10000) in paragraph at lines 1203--1206 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1769] Underfull \hbox (badness 10000) in paragraph at lines 1211--1214 []\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 [1770] [1771] Underfull \hbox (badness 10000) in paragraph at lines 1360--1363 []\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 Underfull \hbox (badness 10000) in paragraph at lines 1381--1383 []\T1/ptm/m/n/10 Re-save PDF files (es-pe-cially vi-gnettes) more com-pactly. S up-port func-tion for [1772] [1773] [1774] [1775] [1776] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1683--1683 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1693--1698 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 1693--1698 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1777] [1778] [1779]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1897 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1780] [1781] [1782] [1783] Underfull \hbox (badness 1142) in paragraph at lines 2165--2171 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 loadPkgRdMacros \T1/ptm/m/n/10 func-tion fi rst looks for an \T1/pcr/m/n/10 "RdMacros" \T1/ptm/m/n/10 en-try in the pack-ag e Overfull \hbox (101.58032pt too wide) in paragraph at lines 2199--2199 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1784] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2200--2200 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2227--2234 []\T1/ptm/m/n/10 Package main-tain-ers can use these func-tions to em-ploy user and site spe-cific com-pi-la- Underfull \hbox (badness 1102) in paragraph at lines 2227--2234 \T1/ptm/m/n/10 tion set-tings also for com-pi-la-tions not us-ing \T1/phv/m/n/1 0 R\T1/ptm/m/n/10 's mech-a-nisms (in par-tic-u-lar, cus-tom com- Underfull \hbox (badness 4168) in paragraph at lines 2227--2234 \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 [1785] Underfull \hbox (badness 1342) in paragraph at lines 2279--2285 \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 [1786] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2355--2355 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2368--2374 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (44.55087pt too wide) in paragraph at lines 2368--2374 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . [1787] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2401--2401 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2410--2410 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2427--2427 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1788] [1789] [1790] [1791] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1792] Underfull \hbox (badness 2486) in paragraph at lines 2737--2745 []\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 [1793] [1794] [1795] [1796] [1797] Underfull \hbox (badness 1072) in paragraph at lines 3115--3117 []\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 [1798] [1799] [1800] [1801] [1802] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3451--3451 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1803] [1804] [1805] [1806] Underfull \hbox (badness 4108) in paragraph at lines 3695--3702 []\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 [1807] [1808] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3795--3795 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3798--3798 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3815--3817 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , Underfull \hbox (badness 2932) in paragraph at lines 3832--3838 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1809] [1810] Underfull \hbox (badness 7832) in paragraph at lines 3954--3957 []\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 [1811] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4029--4029 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1812] Underfull \hbox (badness 1137) in paragraph at lines 4052--4054 []\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 [1813] [1814] [1815] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4226--4226 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4237--4240 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and Underfull \hbox (badness 6859) in paragraph at lines 4253--4258 []\T1/ptm/m/n/10 All ex-ist-ing files in di-rec-tory \T1/pcr/m/n/10 po \T1/ptm/ m/n/10 with names `\T1/pcr/m/n/10 R-\T1/ptm/m/sl/10 lang\T1/pcr/m/n/10 .po\T1/p tm/m/n/10 ' are up-dated from Underfull \hbox (badness 1184) in paragraph at lines 4261--4267 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/pcr/m/n/10 po /\T1/ptm/m/sl/10 pkgname\T1/pcr/m/n/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. T he Underfull \hbox (badness 2941) in paragraph at lines 4261--4267 \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 [1816] Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 reduce \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 , the sys-tem will col-lapse the fields in the \T1/pcr/m/n/10 De pendsList Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 ob-ject such that a min-i-mal set of de-pen-den-cies are spec-i- fied (for in-stance if Underfull \hbox (badness 10000) in paragraph at lines 4341--4346 \T1/ptm/m/n/10 there was `\T1/pcr/m/n/10 foo, foo (>= 1.0.0), foo (>= 1.3.0)\T1 /ptm/m/n/10 ', it would only re-turn [1817] [1818] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4473--4473 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4474--4474 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4486--4489 []\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 ', [1819] Underfull \hbox (badness 1742) in paragraph at lines 4490--4500 \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 4525--4531 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4525--4531 \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 ', Underfull \hbox (badness 1571) in paragraph at lines 4553--4557 []\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 [1820] [1821] [1822]) (./utils-pkg.tex Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1823] [1824] [1825] Underfull \hbox (badness 6316) in paragraph at lines 212--216 []\T1/pcr/m/n/10 find \T1/ptm/m/n/10 is a dif-fer-ent user in-ter-face for a si m-i-lar task to \T1/pcr/m/n/10 apropos\T1/ptm/m/n/10 . By de-fault [1826] Overfull \hbox (4.38043pt too wide) in paragraph at lines 256--256 []\T1/pcr/m/n/9 find("cor", numeric = TRUE) # numbers with these names[] [1827] Overfull \hbox (60.78088pt too wide) in paragraph at lines 370--370 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1828] [1829] [1830] Underfull \hbox (badness 1946) in paragraph at lines 527--531 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ Overfull \hbox (0.78088pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/10 aspell_package_Rd_files(dir, drop = c("\\author", "\\referenc es"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 583--583 []\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 584--584 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 585--585 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] [1831] Overfull \hbox (0.78088pt too wide) in paragraph at lines 586--586 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 620--626 []\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 620--626 \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- [1832] Overfull \hbox (0.78088pt too wide) in paragraph at lines 689--689 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1833] Underfull \hbox (badness 4505) in paragraph at lines 753--759 \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 [1834] Underfull \hbox (badness 1603) in paragraph at lines 870--876 \T1/ptm/m/n/10 ory avail-able and con-trol-ling the load/save pro-cess. If \T1/ pcr/m/n/10 infile \T1/ptm/m/n/10 starts Underfull \hbox (badness 3029) in paragraph at lines 870--876 \T1/ptm/m/n/10 with a `\T1/pcr/m/n/10 -\T1/ptm/m/n/10 ', use `\T1/pcr/m/n/10 -- \T1/ptm/m/n/10 ' as the fi-nal op-tion. The de-fault op-tions are [1835] Overfull \hbox (6.78088pt too wide) in paragraph at lines 927--927 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1836] Underfull \hbox (badness 1817) in paragraph at lines 992--999 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1003--1005 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1837] [1838] Underfull \hbox (badness 10000) in paragraph at lines 1111--1114 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1839] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1194--1194 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1840] [1841] [1842] [1843] [1844] Underfull \hbox (badness 1859) in paragraph at lines 1565--1574 []\T1/ptm/m/n/10 For ex-am-ple, sup-pose that on a data set which you know to b e quite large the com- [1845] [1846] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1666--1666 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] [1847] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1701--1701 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1848] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1847--1847 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1849] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1867--1867 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, Overfull \hbox (6.78088pt too wide) in paragraph at lines 1919--1919 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1850] Underfull \hbox (badness 2213) in paragraph at lines 1953--1956 []\T1/pcr/m/n/10 ind \T1/ptm/m/n/10 chooses a row in the list of cur-rent mir-r ors, by num-ber. It is best used with [1851] [1852] Underfull \hbox (badness 10000) in paragraph at lines 2054--2056 []\T1/ptm/m/n/10 One can in-clude an auto-generated pack-age ci-ta-tion in the `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' file via Overfull \hbox (36.7804pt too wide) in paragraph at lines 2088--2088 [] \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")[] [1853] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2111--2111 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] Underfull \hbox (badness 5189) in paragraph at lines 2156--2158 []\T1/ptm/m/n/10 A list of keys that have been pre-vi-ously cited, to be used w hen [1854] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2231--2231 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1855] Underfull \hbox (badness 1082) in paragraph at lines 2305--2309 [][][]\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; [1856] Underfull \hbox (badness 10000) in paragraph at lines 2342--2344 []\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 Underfull \hbox (badness 1057) in paragraph at lines 2374--2381 \T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 ); if FALSE, the func-tion re-turns a [][]\T1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 . Note that w hen [1857] [1858] [1859] Underfull \hbox (badness 10000) in paragraph at lines 2563--2565 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1860] [1861] [1862] [1863] Underfull \hbox (badness 10000) in paragraph at lines 2800--2804 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .tab\T1/ptm/m/n/10 ', `\T1/pcr/m /n/10 .txt\T1/ptm/m/n/10 ' or `\T1/pcr/m/n/10 .TXT\T1/ptm/m/n/10 ' are read us- ing Underfull \hbox (badness 5203) in paragraph at lines 2800--2804 [][]\T1/pcr/m/n/10 read.table[][][](..., header = TRUE, as.is=FALSE)\T1/ptm/m/n /10 , and hence re-sult in a Overfull \hbox (133.10922pt too wide) in paragraph at lines 2805--2808 []\T1/ptm/m/n/10 files end-ing `\T1/pcr/m/n/10 .csv\T1/ptm/m/n/10 ' or `\T1/pcr /m/n/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/pcr/m/n/10 read.table[][][ ](..., header = TRUE, sep = ";", as.is=FALSE)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2854--2857 []\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 [1864] Overfull \hbox (25.98041pt too wide) in paragraph at lines 2941--2941 []\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 '[] [1865] Underfull \hbox (badness 2452) in paragraph at lines 3017--3020 []\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 [1866] [1867] [1868] [1869] [1870] [1871] [1872] Underfull \hbox (badness 1072) in paragraph at lines 3499--3507 []\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 [1873] Underfull \hbox (badness 1231) in paragraph at lines 3548--3554 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3555--3560 []\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 3555--3560 \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 3555--3560 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1874] [1875] Underfull \hbox (badness 4660) in paragraph at lines 3677--3680 \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 3701--3703 []\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 [1876] [1877] [1878] Underfull \hbox (badness 1565) in paragraph at lines 3886--3890 []\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 Underfull \hbox (badness 10000) in paragraph at lines 3907--3913 []\T1/ptm/m/n/10 For a data frame, the row names will be taken from the orig-i- nal ob-ject if [1879] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3969--3969 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] Overfull \hbox (2.55087pt too wide) in paragraph at lines 3997--4004 \T1/pcr/m/n/10 setRNG = {RNGkind("default", "default"); set.seed(1)}\T1/ptm/m/n /10 . [1880] [1881] [1882] [1883] [1884] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4324--4324 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1885]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4395 ...mat Unordered and Ordered Lists}{format} [1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5348--5348 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1901] Underfull \hbox (badness 10000) in paragraph at lines 5432--5434 []\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 [1902] Underfull \hbox (badness 1502) in paragraph at lines 5481--5486 []\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 5481--5486 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1903] [1904] Underfull \hbox (badness 10000) in paragraph at lines 5654--5663 []\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 5654--5663 \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 [1905] Underfull \hbox (badness 2150) in paragraph at lines 5717--5720 []\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 5733--5736 []\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 [1906] [1907] Underfull \hbox (badness 3118) in paragraph at lines 5854--5856 []\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 [1908] Underfull \hbox (badness 2409) in paragraph at lines 5887--5891 []\T1/ptm/m/n/10 To in-stall a source pack-age with com-piled code only for the sub-architecture used by [1909] Underfull \hbox (badness 5091) in paragraph at lines 5991--5993 []\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 Overfull \hbox (44.55087pt too wide) in paragraph at lines 6007--6012 \T1/pcr/m/n/10 c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")\T1/ ptm/m/n/10 . Overfull \hbox (48.30977pt too wide) in paragraph at lines 6020--6027 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends", " Imports", "LinkingTo", "Suggests") [1910] Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be passed Underfull \hbox (badness 10000) in paragraph at lines 6078--6081 \T1/ptm/m/n/10 to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a source pack -age in-stall. E.g., [1911] Underfull \hbox (badness 10000) in paragraph at lines 6137--6141 []\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 6151--6158 []\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 6151--6158 \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 6151--6158 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by [1912] Underfull \hbox (badness 1314) in paragraph at lines 6210--6217 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 6251--6256 [][][]\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 , [1913] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6274--6274 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] Underfull \hbox (badness 5133) in paragraph at lines 6310--6314 []\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 6324--6327 []\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 [1914] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6371--6371 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1915] [1916] Underfull \hbox (badness 4132) in paragraph at lines 6490--6492 []\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 [1917] [1918] [1919] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6648--6648 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1920] [1921] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6791--6791 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1922] Underfull \hbox (badness 10000) in paragraph at lines 6831--6833 []\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 [1923] [1924] Underfull \hbox (badness 10000) in paragraph at lines 6972--6974 []\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 6977--6979 []\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 [1925] [1926] [1927] Underfull \hbox (badness 1859) in paragraph at lines 7200--7203 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1928] Underfull \hbox (badness 1655) in paragraph at lines 7282--7285 []\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 7293--7293 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] [1929] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7297--7297 []\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 7305--7305 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1930] Underfull \hbox (badness 10000) in paragraph at lines 7390--7394 []\T1/ptm/m/n/10 For all stan-dards, \T1/pcr/m/n/10 unit = "auto" \T1/ptm/m/n/1 0 is also al-lowed. If [1931] [1932] [1933] [1934] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7654--7654 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 7655--7655 [] \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 7656--7656 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] [1935] Underfull \hbox (badness 10000) in paragraph at lines 7684--7686 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from Underfull \hbox (badness 10000) in paragraph at lines 7698--7700 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like Underfull \hbox (badness 1259) in paragraph at lines 7706--7711 []\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, [1936] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7752--7752 [] \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 7753--7753 [] \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[] [1937] [1938] Underfull \hbox (badness 10000) in paragraph at lines 7882--7887 []\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 7882--7887 [][]\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 10000) in paragraph at lines 7889--7892 []\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 7889--7892 [][]\T1/pcr/m/n/10 available.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els [1939] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8005--8005 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8006--8006 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8177--8177 [] \T1/pcr/m/n/9 "S original, "),[] [1943] Underfull \hbox (badness 1789) in paragraph at lines 8300--8302 []\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 [1944] Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8358--8362 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1945] [1946] Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8473--8477 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1947] Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 filename \T1/ptm/m/n/10 is \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 , a list-style rep-re-sen-ta-tion of the doc-u-men-ta-tion Underfull \hbox (badness 10000) in paragraph at lines 8538--8542 \T1/ptm/m/n/10 shell is cre-ated and re-turned. Writ-ing the shell to a file am ounts to [1948] [1949] [1950] [1951] Underfull \hbox (badness 5203) in paragraph at lines 8869--8872 []\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 [1952] [1953] [1954] Underfull \hbox (badness 1776) in paragraph at lines 9095--9102 []\T1/ptm/m/n/10 If you are un-com-fort-able with un-so-licited eval-u-a-tion o f pieces of code, you should set [1955] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9119--9119 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [1956] [1957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9280--9280 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [1958] [1959] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9461--9461 []\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[] [1960] [1961] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9547--9547 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 9550--9550 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 9555--9555 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [1962] Underfull \hbox (badness 1077) in paragraph at lines 9627--9630 []\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 [1963] [1964] [1965] [1966] [1967] [1968] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10067--10067 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [1969] Underfull \hbox (badness 10000) in paragraph at lines 10154--10156 []\T1/ptm/m/n/10 To re-move from the li-brary tree \T1/ptm/m/sl/10 lib \T1/ptm/ m/n/10 in-stead of the de-fault one, use [1970] [1971] Underfull \hbox (badness 2181) in paragraph at lines 10277--10281 []\T1/pcr/m/n/10 as.roman \T1/ptm/m/n/10 cre-ates ob-jects of class \T1/pcr/m/n /10 "roman" \T1/ptm/m/n/10 which are in-ter-nally rep-re-sented as in-te- Underfull \hbox (badness 2269) in paragraph at lines 10277--10281 \T1/ptm/m/n/10 gers, and have suit-able meth-ods for print-ing, for-mat-ting, s ub-set-ting, co-er-cion, etc, see Underfull \hbox (badness 10000) in paragraph at lines 10289--10293 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [1972] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10307--10307 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10311--10311 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [1973] [1974] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10443--10443 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [1975] Underfull \hbox (badness 1917) in paragraph at lines 10566--10569 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 10566--10569 \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 [1976] Overfull \hbox (106.98032pt too wide) in paragraph at lines 10589--10589 []\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 '[] [1977] Underfull \hbox (badness 8075) in paragraph at lines 10652--10654 []\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 [1978] Underfull \hbox (badness 6725) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 score\T1/ptm/m/n/10 , \T1/pcr/m/n/10 date:late \ T1/ptm/m/n/10 for sort-ing by date with lat-est re-sults first, Underfull \hbox (badness 6428) in paragraph at lines 10702--10711 \T1/pcr/m/n/10 date:early \T1/ptm/m/n/10 for ear-li-est first, \T1/pcr/m/n/10 s ubject \T1/ptm/m/n/10 for sub-ject in al-pha-bet-i- Underfull \hbox (badness 10000) in paragraph at lines 10702--10711 \T1/ptm/m/n/10 cal or-der, \T1/pcr/m/n/10 subject:descending \T1/ptm/m/n/10 for re-verse al-pha-bet-i-cal or-der, Underfull \hbox (badness 1997) in paragraph at lines 10702--10711 \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 [1979] Underfull \hbox (badness 3646) in paragraph at lines 10828--10830 [][][]$\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 / [1980] Overfull \hbox (30.78088pt too wide) in paragraph at lines 10866--10866 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [1981] [1982] [1983] Underfull \hbox (badness 10000) in paragraph at lines 11047--11051 []\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 11078--11084 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [1984] Underfull \hbox (badness 2012) in paragraph at lines 11173--11179 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 \includegraphics\T1/ptm/m/n/10 ' state-ments for fig-ures should be auto-generated. Use [1985] Underfull \hbox (badness 2096) in paragraph at lines 11186--11188 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether EPS fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 2698) in paragraph at lines 11189--11191 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 ), in-di-cat-ing wh ether PDF fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1527) in paragraph at lines 11196--11199 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether PNG fig-ures should be gen-er-ated. Ig-nored if Underfull \hbox (badness 1067) in paragraph at lines 11200--11203 []\T1/ptm/m/n/10 logical (\T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 ), in-di-cat-ing w hether JPEG fig-ures should be gen-er-ated. Ig-nored if Overfull \hbox (6.78088pt too wide) in paragraph at lines 11254--11254 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] [1986] Underfull \hbox (badness 1009) in paragraph at lines 11272--11283 []\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 [1987] Underfull \hbox (badness 2846) in paragraph at lines 11359--11369 \T1/ptm/m/n/10 con-trols the num-ber of lines that are saved (de-fault 512), an d \T1/pcr/m/n/10 R_HISTFILE \T1/ptm/m/n/10 (de-fault [1988] [1989] Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 []\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- Underfull \hbox (badness 10000) in paragraph at lines 11498--11501 \T1/ptm/m/n/10 der. Where sub-architectures are in use this is of the form Underfull \hbox (badness 10000) in paragraph at lines 11515--11518 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [1990] Underfull \hbox (badness 2158) in paragraph at lines 11594--11597 []\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 [1991] [1992] [1993] Underfull \hbox (badness 3333) in paragraph at lines 11774--11776 []\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- [1994] [1995] Overfull \hbox (42.78088pt too wide) in paragraph at lines 11939--11939 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] [1996] Underfull \hbox (badness 5970) in paragraph at lines 11972--11975 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive Underfull \hbox (badness 2600) in paragraph at lines 11972--11975 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less Underfull \hbox (badness 1052) in paragraph at lines 11983--11992 \T1/ptm/m/n/10 (see [][]\T1/pcr/m/n/10 options[][][]\T1/ptm/m/n/10 ) which de-f aults to \T1/pcr/m/n/10 "no" \T1/ptm/m/n/10 for back com-pat-i-bil-ity rea-sons ; [1997] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12027--12027 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12058--12058 []\T1/pcr/m/n/9 ## Truncation behavior (<-> correct width measurement) for "lo ng" non-ASCII:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12065--12065 []\T1/pcr/m/n/9 ## nchar.max: 1st line needs an increase of 2 in order to se e 1 (in UTF-8!):[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 12067--12067 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [1998] [1999] [2000] Underfull \hbox (badness 10000) in paragraph at lines 12235--12237 []\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 [2001] [2002] Underfull \hbox (badness 4492) in paragraph at lines 12392--12399 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault) then the avail-able syn-tax ob-jects are con-sulted in Underfull \hbox (badness 6252) in paragraph at lines 12392--12399 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 2452) in paragraph at lines 12392--12399 \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$"\T1/ptm/m/n/10 ) and [2003] [2004] [2005] Underfull \hbox (badness 2020) in paragraph at lines 12555--12571 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 12555--12571 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2006] Underfull \hbox (badness 2809) in paragraph at lines 12675--12679 []\T1/ptm/m/n/10 NetBSD prior to 8.0 used flag `\T1/pcr/m/n/10 --xz\T1/ptm/m/n/ 10 ' rather than `\T1/pcr/m/n/10 -J\T1/ptm/m/n/10 ', so this should be used \T1 /ptm/m/it/10 via Underfull \hbox (badness 1596) in paragraph at lines 12675--12679 \T1/pcr/m/n/10 extra_flags = "--xz" \T1/ptm/m/n/10 rather than \T1/pcr/m/n/10 c ompression = "xz"\T1/ptm/m/n/10 . The com-mands from Underfull \hbox (badness 5022) in paragraph at lines 12690--12694 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 [][][]$\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 . Underfull \hbox (badness 10000) in paragraph at lines 12697--12700 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2007] [2008] [2009] Overfull \hbox (18.78088pt too wide) in paragraph at lines 12862--12862 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2010] [2011] [2012] [2013] [2014] [2015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13246--13246 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 13252--13252 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 13273--13275 []\T1/ptm/m/n/10 Download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 4660) in paragraph at lines 13286--13290 \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 Overfull \hbox (36.87935pt too wide) in paragraph at lines 13300--13304 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = lib.loc)\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 []\T1/ptm/m/n/10 Arguments such as \T1/pcr/m/n/10 destdir \T1/ptm/m/n/10 and \T 1/pcr/m/n/10 dependencies \T1/ptm/m/n/10 to be Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \T1/ptm/m/n/10 passed to [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 and \T1/pcr/m/n/10 ignore_repo_cache\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13306--13311 \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[][][] [2016] Underfull \hbox (badness 1052) in paragraph at lines 13312--13314 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 []\T1/ptm/m/n/10 For how the list of suit-able avail-able pack-ages is de-ter-m ined see Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 . \T1/pcr/m/n/10 avai lable = NULL \T1/ptm/m/n/10 make a call to Underfull \hbox (badness 10000) in paragraph at lines 13342--13347 \T1/pcr/m/n/10 available.packages(contriburl = contriburl, method = method) \T1 /ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13363--13368 []\T1/ptm/m/n/10 Take care when us-ing \T1/pcr/m/n/10 dependencies \T1/ptm/m/n/ 10 (passed to [][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 ) with Underfull \hbox (badness 10000) in paragraph at lines 13371--13374 [][][]\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 , [2017] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13425--13425 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2018] [2019] [2020] Underfull \hbox (badness 10000) in paragraph at lines 13613--13616 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Overfull \hbox (42.18039pt too wide) in paragraph at lines 13629--13629 []\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:[] [2021] Overfull \hbox (4.38043pt too wide) in paragraph at lines 13696--13696 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] [2022] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13718--13718 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 13737--13737 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2023] Underfull \hbox (badness 1454) in paragraph at lines 13764--13768 []\T1/ptm/m/n/10 the char-ac-ter(s) to print at the end of each line (row). For ex-am-ple, Underfull \hbox (badness 1715) in paragraph at lines 13789--13792 []\T1/ptm/m/n/10 arguments to \T1/pcr/m/n/10 write.table\T1/ptm/m/n/10 : \T1/pc r/m/n/10 append\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.names\T1/ptm/m/n/10 , \T1/pc r/m/n/10 sep\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dec \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 13834--13836 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion [2024] Underfull \hbox (badness 3271) in paragraph at lines 13846--13850 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 sep \T1/ptm/m/n/10 and \T1/pcr/m/n/10 dec \T1 /ptm/m/n/10 (see be-low), \T1/pcr/m/n/10 qmethod = "double"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 col.names \T1/ptm/m/n/10 to \T1/pcr/m/n/10 NA \T1/ptm/m/n/10 if [2025] [2026]) [2027] [2028] (./KernSmooth-pkg.tex Chapter 15. [2029] Overfull \hbox (24.78088pt too wide) in paragraph at lines 124--124 []\T1/pcr/m/n/10 bkde2D(x, bandwidth, gridsize = c(51L, 51L), range.x, truncat e = TRUE) [2030] [2031] [2032] [2033] [2034] Overfull \hbox (18.78088pt too wide) in paragraph at lines 519--519 []\T1/pcr/m/n/10 dpill(x, y, blockmax = 5, divisor = 20, trim = 0.01, proptrun = 0.05, [2035] [2036] [2037] [2038]) (./MASS-pkg.tex Chapter 16. [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048] [2049] Overfull \hbox (20.58041pt too wide) in paragraph at lines 774--774 []\T1/pcr/m/n/9 dreg <- cbind(sin = sin(2*pi*beav2$hours/24), cos = cos(2*pi*b eav2$hours/24))[] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] Underfull \hbox (badness 7256) in paragraph at lines 1604--1606 []\T1/ptm/m/n/10 logical. If true and the re-sult would be sparse (only true fo r [2062] [2063] [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2412--2412 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2416--2416 []\T1/pcr/m/n/10 dropterm(object, scope, scale = 0, test = c("none", "Chisq", "F"),[] [2073] [2074] [2075] [2076] Underfull \hbox (badness 6559) in paragraph at lines 2694--2697 []\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 [2077] [2078] [2079] Underfull \hbox (badness 10000) in paragraph at lines 2864--2869 \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "geometric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "log-normal"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lognormal"\T1/pt m/m/n/10 , Underfull \hbox (badness 8189) in paragraph at lines 2864--2869 \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 , Underfull \hbox (badness 3557) in paragraph at lines 2900--2908 []\T1/ptm/m/n/10 For the fol-low-ing named dis-tri-bu-tions, rea-son-able start -ing val-ues will be com-puted if Underfull \hbox (badness 3118) in paragraph at lines 2900--2908 \T1/pcr/m/n/10 start \T1/ptm/m/n/10 is omit-ted or only par-tially spec-i-fied: \T1/pcr/m/n/10 "cauchy"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gamma"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 , [2080] [2081] Underfull \hbox (badness 4686) in paragraph at lines 3032--3034 []\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 Underfull \hbox (badness 1515) in paragraph at lines 3046--3050 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2082] [2083] [2084] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3227--3227 [] \T1/pcr/m/n/10 eps.max = .Machine$double.eps^0.25, verbose = FAL SE, ...)[] Underfull \hbox (badness 5817) in paragraph at lines 3234--3236 []\T1/ptm/m/n/10 Fitted model ob-ject from a \T1/pcr/m/n/10 Gamma \T1/ptm/m/n/1 0 fam-ily or \T1/pcr/m/n/10 quasi \T1/ptm/m/n/10 fam-ily with [2085] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3357--3357 []\T1/pcr/m/n/9 survreg(Surv(time, cens) ~ factor(pair) + treat, gehan, dist = "exponential")[] [2086] [2087] [2088] [2089] [2090] [2091] [2092] [2093] [2094] [2095] [2096] [2097] Underfull \hbox (badness 1845) in paragraph at lines 4143--4145 []\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 [2098] [2099] [2100] [2101] [2102] [2103] [2104] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4639--4639 [] \T1/pcr/m/n/10 col = 5, xlab = deparse(substitute(data)), bty = "n", ...)[] [2105] [2106] Underfull \hbox (badness 10000) in paragraph at lines 4791--4794 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2107] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/10 lm.ridge(formula, data, subset, na.action, lambda = 0, model = FALSE, Underfull \hbox (badness 10000) in paragraph at lines 4869--4872 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2108] [2109] [2110] [2111] [2112] Underfull \hbox (badness 5681) in paragraph at lines 5269--5271 []\T1/ptm/m/n/10 the quan-tile to be used: see \T1/pcr/m/n/10 Details\T1/ptm/m/ n/10 . This is over-ridden if Underfull \hbox (badness 5022) in paragraph at lines 5273--5276 []\T1/ptm/m/n/10 the cut-off / tun-ing con-stant used for $\OML/cmm/m/it/10 ^^_ \OT1/cmr/m/n/10 ()$ \T1/ptm/m/n/10 and $\OML/cmm/m/it/10 \OT1/cmr/m/n/10 ()$ \ T1/ptm/m/n/10 func-tions when [2113] Underfull \hbox (badness 1975) in paragraph at lines 5322--5324 []\T1/ptm/m/n/10 the value of the cri-te-rion for the best so-lu-tion found, in the case of [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] Overfull \hbox (42.78088pt too wide) in paragraph at lines 5908--5908 []\T1/pcr/m/n/10 mvrnorm(n = 1, mu, Sigma, tol = 1e-6, empirical = FALSE, EISP ACK = FALSE) [2122] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5969--5969 []\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") [2123] [2124]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.npk}) has been already used, duplicate ignored \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 \relax l.6111 ...sical N, P, K Factorial Experiment}{npk} [2125] Underfull \hbox (badness 1783) in paragraph at lines 6229--6233 []\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 [2126] [2127] [2128] [2129] Underfull \vbox (badness 10000) has occurred while \output is active [2130] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6527--6527 [] \T1/pcr/m/n/9 start = list(fixed=c(L75=c(48.7, -0.03), lsc=0.24)), verb ose = TRUE)))[] [2131] Overfull \hbox (18.78088pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/10 dimen, abbrev = FALSE, ..., cex=0.7, type = c("std", "tr ellis"))[] [2132] [2133] [2134] [2135] [2136] [2137] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7054--7054 []\T1/pcr/m/n/9 nlmod <- nls(y ~ Const + A * exp(B * x), start=list(Const=100 , A=10, B=1))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7071--7071 [] \T1/pcr/m/n/10 method = c("logistic", "probit", "loglog", "cloglog", "c auchit"))[] Underfull \hbox (badness 10000) in paragraph at lines 7078--7085 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [2138] Underfull \hbox (badness 10000) in paragraph at lines 7094--7096 []\T1/ptm/m/n/10 initial val-ues for the pa-ram-e-ters. This is in the for-mat Underfull \hbox (badness 3138) in paragraph at lines 7149--7155 []\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 ) = [2139] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7219--7219 []\T1/pcr/m/n/9 house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, da ta = housing)[] [2140] [2141] Underfull \hbox (badness 5091) in paragraph at lines 7328--7331 \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 [2142] [2143] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7458--7458 []\T1/pcr/m/n/9 fm <- lqs(stack.loss ~ ., data = stackloss, method = "S", nsam p = "exact")[] [2144] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7523--7523 [] \T1/pcr/m/n/10 method = c("plug-in", "predictive", "debiased", "looC V"), ...)[] [2145] [2146] [2147] [2148] [2149] [2150] Underfull \hbox (badness 4686) in paragraph at lines 7961--7963 []\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 Underfull \hbox (badness 1515) in paragraph at lines 7977--7981 []\T1/ptm/m/n/10 where \T1/pcr/m/n/10 p1\T1/ptm/m/n/10 , \T1/pcr/m/n/10 p2\T1/p tm/m/n/10 , ...are pos-i-tive in-te-gers, ter-mi-nat-ing ei-ther at \T1/pcr/m/n /10 cycles \T1/ptm/m/n/10 terms or when a [2151] [2152] Overfull \hbox (6.78088pt too wide) in paragraph at lines 8080--8080 [] \T1/pcr/m/n/10 maxit = 20, acc = 1e-4, test.vec = "resid", lqs.control = NULL)[] Underfull \hbox (badness 1590) in paragraph at lines 8104--8108 []\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 [2153] [2154] [2155] [2156] [2157] [2158] [2159] [2160] [2161] [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9483--9483 []\T1/pcr/m/n/10 summary(object, method = c("XtX", "XtWX"), correlation = FALS E, ...)[] [2173] Underfull \hbox (badness 1158) in paragraph at lines 9610--9613 []\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), [2174] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9692--9692 []\T1/pcr/m/n/10 theta.md(y, mu, dfr, weights, limit = 20, eps = .Machine$doub le.eps^0.25) Overfull \hbox (30.78088pt too wide) in paragraph at lines 9694--9694 []\T1/pcr/m/n/10 theta.ml(y, mu, n, weights, limit = 10, eps = .Machine$double .eps^0.25,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 9697--9697 []\T1/pcr/m/n/10 theta.mm(y, mu, dfr, weights, limit = 10, eps = .Machine$doub le.eps^0.25)[] [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186] [2187]) (./Matrix-pkg.tex [2188] 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 [2189] 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 [2190] 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 [2191] Underfull \hbox (badness 10000) in paragraph at lines 257--260 []\T1/ptm/m/n/10 these three meth-ods are sim-ply us-ing Underfull \hbox (badness 10000) in paragraph at lines 263--265 []\T1/ptm/m/n/10 There are more meth-ods, no-tably also for \T1/pcr/m/n/10 "[][ ]sparseVector[][][]"\T1/ptm/m/n/10 's, see [2192] [2193] 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) Underfull \hbox (badness 5147) in paragraph at lines 495--498 []\T1/ptm/m/n/10 integer vec-tor of ``di-ag-o-nal num-bers'', with iden-ti-cal mean-ing as in [2194] Underfull \hbox (badness 5119) in paragraph at lines 508--512 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class Underfull \hbox (badness 4621) in paragraph at lines 512--516 []\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 Overfull \hbox (4.38043pt too wide) in paragraph at lines 535--535 []\T1/pcr/m/n/9 s1 <- bandSparse(13, k = -c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 537--537 []\T1/pcr/m/n/9 s2 <- bandSparse(13, k = c(0:2, 6), diag = c(diags, diags[2]) , symm=TRUE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 546--546 []\T1/pcr/m/n/9 lLis <- lapply(list(rpois(20, 2), rpois(20,1), rpois(20,3))[c( 1:3,2:3,3:2)],[] [2195] [2196] 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:[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 @param lmat list(, , ....., ) where each mat_j is a k x k \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 matrix\TS1/pcr/m/n/9 '[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 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}"}.[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 675--675 [] \T1/pcr/m/n/9 ## \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 i :\TS1/pcr/m/n/9 ' \ T1/pcr/m/n/9 maybe there\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s a faster way (w/o matri x indexing), but elegant?[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 676--676 [] \T1/pcr/m/n/9 i = as.vector(matrix(0L:(M-1L), nrow=k)[, rep(seq_len( N), each=k)]),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 681--681 []\T1/pcr/m/n/9 l12 <- replicate(12, matrix(rpois(16, lambda = 6.4), 4,4), sim plify=FALSE)[] [2197] 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 . [2198] [2199] [2200] Overfull \hbox (72.78088pt too wide) in paragraph at lines 947--947 []\T1/pcr/m/n/10 ## solve(a, b, system = c("A","LDLt","LD","DLt","L","Lt","D ","P","Pt"), ...)[] [2201] Underfull \hbox (badness 10000) in paragraph at lines 1022--1024 []\T1/pcr/m/n/10 signature(from = "CHMfactor", to = "sparseMatrix") \T1/ptm/m/n /10 (or equiv-a- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 []\T1/pcr/m/n/10 signature(x = "CHMfactor"): \T1/ptm/m/n/10 Plot the im-age of the lower tri- Underfull \hbox (badness 10000) in paragraph at lines 1045--1050 \T1/ptm/m/n/10 an-gu-lar fac-tor, $\OML/cmm/m/it/10 L$\T1/ptm/m/n/10 , from the de-com-po-si-tion. This method is equiv-a-lent to Underfull \hbox (badness 1092) in paragraph at lines 1045--1050 \T1/pcr/m/n/10 image(as(x, "sparseMatrix")) \T1/ptm/m/n/10 so the com-ments in the above de-scrip-tion of Underfull \hbox (badness 10000) in paragraph at lines 1068--1075 []\T1/pcr/m/n/10 signature(x = "CHMfactor", logarithm = "logical") [2202]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cho l}) has been already used, duplicate ignored \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 \relax l.1134 ...- 'Matrix' S4 Generic and Methods}{chol} [2203pdfTeX 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' ] [2204] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1266--1266 []\T1/pcr/m/n/9 ## --> see Cholesky() and its examples, for the pivot structur e & factorization[] [2205] Overfull \hbox (18.78088pt too wide) in paragraph at lines 1360--1360 []\T1/pcr/m/n/10 Cholesky(A, perm = TRUE, LDL = !super, super = FALSE, Imult = 0, ...) Underfull \hbox (badness 2277) in paragraph at lines 1388--1391 []\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 [2206] 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 [2207] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1462--1462 []\T1/pcr/m/n/9 ## hence, the identical() check *should* work, but fails on so me GOTOblas:[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1476--1476 []\T1/pcr/m/n/9 dq <- function(ch) paste(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/p cr/m/n/9 '\T1/pcr/m/n/9 ,ch,\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 "\TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 , sep="") ## dQuote() gives bad plots[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1484--1484 []\T1/pcr/m/n/9 (opts <- expand.grid(perm = c(TRUE,FALSE), LDL = c(TRUE,FALSE) , super = c(FALSE,TRUE)))[] [2208] Underfull \hbox (badness 6445) 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 3861) 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 Underfull \hbox (badness 1783) in paragraph at lines 1566--1570 []\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1 /ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend Underfull \hbox (badness 1221) in paragraph at lines 1582--1588 \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 [2209]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col Sums}) has been already used, duplicate ignored \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 \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 \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 \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 \relax l.1656 \aliasA{rowSums}{colSums}{rowSums} [2210] 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 [2211] Underfull \hbox (badness 10000) in paragraph at lines 1801--1805 []\T1/pcr/m/n/10 signature(x = "compMatrix", value = "list")\T1/ptm/m/n/10 : se t the [2212] 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 [2213] [2214] [2215] Underfull \hbox (badness 10000) in paragraph at lines 2112--2114 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "ddenseMatrix ", where = [2216] [2217] Underfull \hbox (badness 10000) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" , where = Underfull \hbox (badness 3068) in paragraph at lines 2295--2299 \T1/ptm/m/n/10 i-cally via \T1/pcr/m/n/10 as(*, "CsparseMatrix") \T1/ptm/m/n/10 or sim-i-lar. Of-ten how-ever, more eas-ily via [2218] Underfull \hbox (badness 4713) 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 [2219] Underfull \hbox (badness 10000) in paragraph at lines 2447--2450 []\T1/pcr/m/n/10 signature(x = "dgeMatrix", norm = "character") \T1/ptm/m/n/10 or [2220] Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dgTMatrix", ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2549--2553 \T1/ptm/m/n/10 but more typ-i-cally via \T1/pcr/m/n/10 as(*, "dgTMatrix")\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 spMatrix[][][]()\T1/ptm/m/n/10 , or [2221] Underfull \hbox (badness 2707) 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 ; [2222] 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 [2223] 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 [2224] 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 2973--2974 []\T1/pcr/m/n/10 signature(from = "diagonalMatrix", to = "triangularMatrix")\T1 /ptm/m/n/10 : Underfull \hbox (badness 1810) in paragraph at lines 2980--2982 []\T1/pcr/m/n/10 signature(a = "diagonalMatrix", b, ...)\T1/ptm/m/n/10 : is tri v-ially im-ple-mented, of 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 3803) 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 [2225] Underfull \hbox (badness 1371) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix", e2="denseMatrix")\T1/ptm/m/n/10 : the re-sult is from class 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 [2226] [2227] Underfull \hbox (badness 1859) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix", digits = "numeric")\T1/ptm/m/n/10 : t his 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 pre fer-able to (and more ef-fi-cient than) [2228] Underfull \hbox (badness 1168) 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 [2229] [2230] Underfull \hbox (badness 4967) 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 [2231] Overfull \hbox (2.39853pt too wide) in paragraph at lines 3533--3535 []\T1/ptm/m/n/10 Creation ``from scratch'' most ef-fi-ciently hap-pens via [][] \T1/pcr/m/n/10 sparseMatrix[][][](*, symmetric=TRUE)\T1/ptm/m/n/10 . Underfull \hbox (badness 6364) in paragraph at lines 3575--3578 []\T1/pcr/m/n/10 signature(a = "dsCMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2232] [2233] 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 10000) in paragraph at lines 3735--3737 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "missing")\T1/ptm/m/n/10 : a triv-ial Underfull \hbox (badness 10000) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix", uplo = "character")\T1/ptm/m/n/10 : if [2234] Underfull \hbox (badness 4967) 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 Underfull \hbox (badness 10000) in paragraph at lines 3852--3855 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 1735) in paragraph at lines 3852--3855 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the ma-trix norm of the [2235] Underfull \hbox (badness 10000) in paragraph at lines 3855--3858 []\T1/pcr/m/n/10 signature(x = "dspMatrix", type = "character")\T1/ptm/m/n/10 , or Underfull \hbox (badness 2318) in paragraph at lines 3855--3858 \T1/pcr/m/n/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/pcr/m/n/10 type = "missing "\T1/ptm/m/n/10 : Com-putes the re-cip-ro-cal con-di-tion Underfull \hbox (badness 6364) in paragraph at lines 3859--3862 []\T1/pcr/m/n/10 signature(a = "dsyMatrix", b = "....")\T1/ptm/m/n/10 : \T1/pcr /m/n/10 x <- solve(a,b) \T1/ptm/m/n/10 solves [2236] Underfull \hbox (badness 4060) in paragraph at lines 3983--3986 []\T1/pcr/m/n/10 signature(a = "dtCMatrix", b = "....")\T1/ptm/m/n/10 : sparse tri-an-gu-lar solve (aka [2237] 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 [2238] 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 - Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix", logarithm = "logical")\T1/ptm/m/n/1 0 : the [2239] [2240] [2241] [2242] Underfull \hbox (badness 10000) in paragraph at lines 4393--4398 []\T1/ptm/m/n/10 The ex-po-nen-tial of a ma-trix is de-fined as the in-fi-nite Tay-lor se-ries [2243] [2244] 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():[] [2245] [2246] Underfull \hbox (badness 10000) in paragraph at lines 4702--4704 [][][]\T1/pcr/m/n/10 symmpart[][][] \T1/ptm/m/n/10 for the sym-met-ric part of a ma-trix, or the co-er-cions [2247] [2248] 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 , [2249] 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))[] [2250] 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 '[] [2251] Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/pcr/m/n/10 NA \ T1/ptm/m/n/10 means Underfull \hbox (badness 10000) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 no bor-der is drawn. When \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 as by de-fault, Underfull \hbox (badness 2644) in paragraph at lines 5068--5073 \T1/pcr/m/n/10 border.col <- if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is used. Con- Underfull \hbox (badness 4108) in paragraph at lines 5068--5073 \T1/ptm/m/n/10 sider us-ing an opaque color in-stead of \T1/pcr/m/n/10 NULL \T1 /ptm/m/n/10 which cor-re-sponds to [2252] 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")) ||[] [2253] 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[] [2254] 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 5637) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix", y = "indMatrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use [2255] Underfull \hbox (badness 3138) in paragraph at lines 5303--5305 []\T1/pcr/m/n/10 signature(x = "indMatrix")\T1/ptm/m/n/10 : re-turn the [2256] 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,[] Underfull \hbox (badness 1603) in paragraph at lines 5391--5393 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 p \T1/ptm/m/n/10 con-t ains val-ues \T1/pcr/m/n/10 0:(n-1) \T1/ptm/m/n/10 or rather (by de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 []\T1/ptm/m/n/10 an in-te-ger vec-tor of the same length (\T1/pcr/m/n/10 n\T1/p tm/m/n/10 ) as \T1/pcr/m/n/10 p\T1/ptm/m/n/10 . By de-fault, Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 zero.p = FALSE, zero.res = FALSE\T1/ptm/m/n/10 ) , \T1/pcr/m/n/10 invPerm(p) \T1/ptm/m/n/10 is the same as Underfull \hbox (badness 10000) in paragraph at lines 5399--5404 [][]\T1/pcr/m/n/10 order[][][](p) \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 sort.lis t[][][](p) \T1/ptm/m/n/10 and for that case, the func-tion is equiv-a-lent to [2257] [2258] [2259] 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[] [2260] 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"[] [2261] 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 [2262] 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)))[] [2263] 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 [2264] Underfull \hbox (badness 2809) 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 [2265] 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., [2266] 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 [2267] Underfull \hbox (badness 1184) 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 [2268] 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., [2269] 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[] [2270] 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 [2271] 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[] [2272] [2273] 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''), [2274] 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 ``e mpty'' [][]sparse-Ma-trix[][][], as does [2275]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det }) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 1348) in paragraph at lines 6948--6951 []\T1/pcr/m/n/10 signature(x = "Matrix")\T1/ptm/m/n/10 : As [][]\T1/pcr/m/n/10 diff[][][]() \T1/ptm/m/n/10 for tra-di-tional ma-tri-ces, i.e., ap-ply-ing Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 []\T1/pcr/m/n/10 signature(x = "Matrix", value = "ANY")\T1/ptm/m/n/10 : where \ T1/pcr/m/n/10 value \T1/ptm/m/n/10 is Underfull \hbox (badness 10000) in paragraph at lines 6953--6956 \T1/ptm/m/n/10 in-te-ger of length 2. Al-lows to \T1/ptm/m/it/10 re-shape \T1/p tm/m/n/10 Ma-trix ob-jects, but only when Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 7326) 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 [2276]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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 \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 \relax l.7252 ...tcrossprod}{matrix-products}{tcrossprod} [2277] 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 [2278pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cros sprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.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 - Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 trix mul-ti-pli-ca-tion; ditto for sev-eral other sig-na-ture co m-bi-na-tions, see Underfull \hbox (badness 5637) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and ot her sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 7435--7437 []\T1/pcr/m/n/10 signature(x = "CsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7437--7439 []\T1/pcr/m/n/10 signature(x = "TsparseMatrix", y = "missing") \T1/ptm/m/n/10 r e-turns Underfull \hbox (badness 10000) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix", y = "matrix") \T1/ptm/m/n/10 and [2279] [2280] 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 [2281] Underfull \hbox (badness 2809) 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 [2282] 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/ ptm/m/n/10 should be done, af-ter [2283] Underfull \hbox (badness 1406) in paragraph at lines 7748--7752 []\T1/ptm/m/n/10 Higham (2002) uses Dyk-stra's cor-rec-tion, but the ver-sion b y Jens Oehlschlaegel did not Underfull \hbox (badness 1019) in paragraph at lines 7748--7752 \T1/ptm/m/n/10 use it (ac-ci-den-tally), and has still lead to good re-sults; t his sim-pli-fi-ca-tion, now only via [2284] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7846--7846 []\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 [2285] Underfull \hbox (badness 2635) in paragraph at lines 7911--7916 []\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 7911--7916 \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 7919--7922 []\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., [2286] [2287] Underfull \hbox (badness 10000) in paragraph at lines 8113--8115 []\T1/ptm/m/n/10 fast [2288]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8153 \HeaderA{norm}{Matrix Norms}{norm} [2289] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8240--8240 []\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 8241--8241 []\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 8242--8242 []\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 8355--8365 []\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 , [2290] Underfull \hbox (badness 1184) in paragraph at lines 8426--8429 []\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 [2291] Underfull \hbox (badness 10000) in paragraph at lines 8516--8519 []\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., [2292] Underfull \hbox (badness 10000) in paragraph at lines 8592--8595 []\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., [2293] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8608--8608 []\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 [2294] Underfull \hbox (badness 10000) in paragraph at lines 8718--8720 []\T1/pcr/m/n/10 signature(x = "matrix", y = "pMatrix") \T1/ptm/m/n/10 and othe r sig-na-tures (use Underfull \hbox (badness 1596) in paragraph at lines 8734--8736 []\T1/pcr/m/n/10 signature(from = "pMatrix", to = "ngTMatrix")\T1/ptm/m/n/10 : co-er-cion to sparse Underfull \hbox (badness 1721) in paragraph at lines 8740--8744 \T1/ptm/m/n/10 ma-trix; note that \T1/pcr/m/n/10 solve(P) \T1/ptm/m/n/10 is ide n-ti-cal to \T1/pcr/m/n/10 t(P) \T1/ptm/m/n/10 for per-mu-ta-tion ma-tri-ces. S ee [2295] [2296] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8819--8819 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8824--8824 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8829--8829 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8852--8862 []\T1/ptm/m/n/10 logical or string spec-i-fy-ing if and how col-umn names of \T 1/pcr/m/n/10 x \T1/ptm/m/n/10 should Underfull \hbox (badness 10000) in paragraph at lines 8852--8862 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2297] [2298]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8953 \aliasA{qr}{qr-methods}{qr} Underfull \hbox (badness 5119) in paragraph at lines 8999--9002 []\T1/ptm/m/n/10 QR de-com-po-si-tion of a gen-eral sparse double-precision ma- trix with Overfull \hbox (9.78043pt too wide) in paragraph at lines 9026--9026 []\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![] [2299] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9037--9037 []\T1/pcr/m/n/9 qxrLA <- qr(m(Xr), LAPACK=TRUE) # => qr.fitted(), qr.resid() n ot supported[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9041--9041 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9058--9058 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9066--9066 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] [2300] Underfull \hbox (badness 10000) in paragraph at lines 9119--9125 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9136--9139 []\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 [2301] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9208--9208 []\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"[] [2302] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9229--9229 []\T1/pcr/m/n/9 (st1 <- system.time(r1 <- rankMatrix(L))) # war ning+ ~1.5 sec (2013)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 9230--9230 []\T1/pcr/m/n/9 (st2 <- system.time(r2 <- rankMatrix(L, method = "qr"))) # con siderably faster![] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.9249 ... the Reciprocal Condition Number}{rcond} [2303] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9362--9362 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 9547--9549 []\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 Underfull \hbox (badness 1325) in paragraph at lines 9553--9561 \T1/ptm/m/n/10 gets \T1/pcr/m/n/10 x <- rand.x(nnz) \T1/ptm/m/n/10 and calls [] []\T1/pcr/m/n/10 sparseMatrix[][][](i=i, j=j, x=x, ..)\T1/ptm/m/n/10 . When [2307] [2308] Underfull \hbox (badness 1558) in paragraph at lines 9698--9701 []\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 [2309] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9760--9760 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9764--9764 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2310]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9826 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9923--9923 [] \T1/pcr/m/n/10 system = c("A", "LDLt", "LD", "DLt", "L", "Lt", "D", "P ", "Pt"), ...)[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9928--9928 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2311] Underfull \hbox (badness 6047) in paragraph at lines 9963--9975 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods Underfull \hbox (badness 10000) in paragraph at lines 9980--9983 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 7203) in paragraph at lines 9985--9986 []\T1/ptm/m/n/10 basically com-putes uses tri-an-gu-lar Underfull \hbox (badness 7851) in paragraph at lines 9989--9996 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 10000) in paragraph at lines 9989--9996 \T1/pcr/m/n/10 ( sparse = FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : U ses the sparse Underfull \hbox (badness 10000) in paragraph at lines 10002--10012 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list Underfull \hbox (badness 2165) in paragraph at lines 10002--10012 \T1/pcr/m/n/10 ( sparse=FALSE, tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Che cks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym- [2312] Underfull \hbox (badness 1194) in paragraph at lines 10036--10038 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10050--10053 []\T1/ptm/m/n/10 , and sim-i-lar \T1/pcr/m/n/10 b\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 10000) in paragraph at lines 10059--10060 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10065--10067 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10069--10070 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10077--10080 [][][]\T1/pcr/m/n/10 solve[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lu[][][]\T1 /ptm/m/n/10 , and class doc-u-men-ta-tions [][]\T1/pcr/m/n/10 CHMfactor[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 sparseLU[][][]\T1/ptm/m/n/10 , and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10095--10095 []\T1/pcr/m/n/9 image(ia0 <- solve(a)) # checker board, dense [but really, a i s singular!][] Overfull \hbox (25.98041pt too wide) in paragraph at lines 10099--10099 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2313] Underfull \hbox (badness 10000) in paragraph at lines 10120--10123 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu la and data frame Underfull \hbox (badness 1648) in paragraph at lines 10148--10150 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 10000) in paragraph at lines 10156--10159 []\T1/ptm/m/n/10 character string or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or (co- er-ca-ble to) Underfull \hbox (badness 2591) in paragraph at lines 10156--10159 \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 [2314] Underfull \hbox (badness 10000) in paragraph at lines 10167--10171 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for Underfull \hbox (badness 2828) in paragraph at lines 10167--10171 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for Underfull \hbox (badness 6592) in paragraph at lines 10178--10180 []\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 [2315] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10255--10255 [] \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 10256--10256 [] \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 10257--10257 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2316] [2317] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10441--10441 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10442--10442 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2318] Underfull \hbox (badness 4621) in paragraph at lines 10482--10486 []\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 [2319] Underfull \hbox (badness 10000) in paragraph at lines 10558--10561 []\T1/ptm/m/n/10 The stan-dard \T1/phv/m/n/10 R [][]\T1/pcr/m/n/10 xtabs[][][]( *, sparse=TRUE)\T1/ptm/m/n/10 , for sparse ta-bles and Overfull \hbox (4.38043pt too wide) in paragraph at lines 10570--10570 []\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 10574--10574 []\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 10575--10575 []\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 10580--10580 []\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 10583--10583 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10606--10606 []\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 10607--10607 []\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 10633--10633 []\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 10635--10635 [] \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 10637--10637 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2321] Underfull \hbox (badness 10000) in paragraph at lines 10730--10738 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class Underfull \hbox (badness 1325) in paragraph at lines 10751--10755 []\T1/pcr/m/n/10 signature(x = "sparseMatrix", value = "ANY")\T1/ptm/m/n/10 : a l-lows to \T1/ptm/m/it/10 re-shape \T1/ptm/m/n/10 a [2322] Underfull \hbox (badness 10000) in paragraph at lines 10781--10785 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*, sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10821 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2323] [2324] Underfull \hbox (badness 1430) in paragraph at lines 10951--10953 []\T1/pcr/m/n/10 signature(a = "sparseQR", b = "ANY")\T1/ptm/m/n/10 : For \T1/p cr/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10979--10979 [] \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 11007--11009 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2325] Underfull \hbox (badness 2970) in paragraph at lines 11140--11146 []\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 11140--11146 \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 , [2326] Underfull \hbox (badness 10000) in paragraph at lines 11191--11194 []\T1/pcr/m/n/10 signature(x = "sparseVector", mode = "character") \T1/ptm/m/n/ 10 co-erces Underfull \hbox (badness 10000) in paragraph at lines 11213--11216 []\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 [2327] Underfull \hbox (badness 10000) in paragraph at lines 11231--11236 []\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 11246--11248 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2328] [2329] Underfull \hbox (badness 3525) in paragraph at lines 11364--11368 []\T1/ptm/m/n/10 The ma-trix $\OML/cmm/m/it/10 M$ \T1/ptm/m/n/10 will have \T1/ pcr/m/n/10 M[i[k], j[k]] == x[k]\T1/ptm/m/n/10 , for $\OML/cmm/m/it/10 k \OT1/c mr/m/n/10 = 1\OML/cmm/m/it/10 ; \OT1/cmr/m/n/10 2\OML/cmm/m/it/10 ; [] ; n$\T1/ ptm/m/n/10 , where Underfull \hbox (badness 1831) in paragraph at lines 11371--11377 [][][]\T1/pcr/m/n/10 Matrix[][][](*, sparse=TRUE) \T1/ptm/m/n/10 for the more u sual con-struc-tor of such ma-tri-ces. Then, [2330] Underfull \hbox (badness 10000) in paragraph at lines 11466--11470 []\T1/pcr/m/n/10 signature(object = "symmetricMatrix")\T1/ptm/m/n/10 : re-turns \T1/ptm/m/it/10 sym-met-ric Underfull \hbox (badness 1043) in paragraph at lines 11466--11470 [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , even when the \T1/pcr/m/n/10 Dimnames \T1/ptm/m/n/10 slot only has row or col-umn names. This Underfull \hbox (badness 10000) in paragraph at lines 11482--11487 []\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 1259) in paragraph at lines 11482--11487 \T1/pcr/m/n/10 list(NULL, )\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. How-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11490--11495 \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 [2331] Underfull \hbox (badness 2057) in paragraph at lines 11562--11564 []\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., [2332] [2333] Underfull \hbox (badness 6641) in paragraph at lines 11648--11651 []\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 11688--11692 []\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 11688--11692 \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 [2334] Underfull \hbox (badness 7649) in paragraph at lines 11795--11797 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2335] [2336] [2337] Underfull \hbox (badness 7362) in paragraph at lines 11996--11998 []\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 [2338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12034--12034 []\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 12035--12035 []\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)[] [2339] [2340] Underfull \hbox (badness 6910) in paragraph at lines 12285--12287 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2341] [2342] [2343]) (./boot-pkg.tex [2344] Chapter 18. [2345] [2346] [2347] [2348] [2349] [2350] [2351] 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"), [2352] 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- Underfull \hbox (badness 1264) in paragraph at lines 583--588 \T1/ptm/m/n/10 lems. This may be spec-i-fied for any sim-u-la-tion, but is ig-n ored when [2353] Overfull \hbox (43.25928pt too wide) in paragraph at lines 643--649 []\T1/ptm/m/n/10 logical, only al-lowed to be \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/1 0 for \T1/pcr/m/n/10 sim = "ordinary", stype = "i", n = 0 [2354] Underfull \hbox (badness 6268) in paragraph at lines 797--807 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 parallel = "snow" \T1/ptm/m/n/10 us-ing the de -fault clus-ter, a sec-ond ap-proach is used if [2355] 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 , [2356] 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 [2357] [2358] 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 [2359] 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 [2360] [2361] [2362] [2363] 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- [2364] [2365] [2366] [2367] [2368] 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), [2369] [2370] [2371] Underfull \vbox (badness 10000) has occurred while \output is active [2372] 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),[] [2373] 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. [2374] [2375] [2376] 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 [2377] 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 , [2378] [2379] 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 [2380] [2381] [2382] [2383] [2384] 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,[] [2385] [2386] [2387] 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 , [2388] 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)) [2389] [2390] [2391] 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 [2392] [2393] [2394] [2395] [2396] [2397] [2398] 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)[] [2399] [2400] 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])[] [2401] [2402] [2403] 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 [2404] 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 [2405] [2406] 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 Underfull \hbox (badness 2269) in paragraph at lines 4386--4389 []\T1/ptm/m/n/10 The lin-ear ap-prox-i-ma-tion to a boot-strap repli-cate with fre-quency vec-tor \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is given by [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] 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 [2416] [2417] [2418] [2419] 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 [2420] 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])[] [2421] [2422] [2423] [2424] [2425] [2426] [2427] [2428] 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][] [2429] 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 [2430] 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 [2431] [2432] [2433] [2434] 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). [2435] [2436] 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[] [2437] [2438] [2439] 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 [2440] [2441] 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),[] [2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449]) (./class-pkg.tex [2450] Chapter 19. [2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/ptm/m/n/10 the size of the code-book. De-faults to [2459] [2460] [2461] [2462] [2463] [2464] [2465] [2466]) (./cluster-pkg.tex Chapter 20. [2467] Underfull \hbox (badness 3098) 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- Underfull \hbox (badness 2253) in paragraph at lines 133--142 \T1/ptm/m/n/10 larly for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is spec-i-fied of longer length than one. Since Underfull \hbox (badness 3323) in paragraph at lines 133--142 \T1/ptm/b/n/10 clus-ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-val id \T1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 as \T1/pcr/m/n/10 method="flexible", par.method = 0.5\T1/ptm/m/n /10 . Fur-ther, \T1/pcr/m/n/10 method= "single" Underfull \hbox (badness 10000) in paragraph at lines 133--142 \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/10 method="flexible", par.method = c(.5,.5,0,-.5)\T1/ptm/m/n/10 , and Overfull \hbox (48.49016pt too wide) in paragraph at lines 133--142 \T1/pcr/m/n/10 method="complete" \T1/ptm/m/n/10 is equiv-a-lent to \T1/pcr/m/n/ 10 method="flexible", par.method = c(.5,.5,0,+.5)\T1/ptm/m/n/10 . [2468] Underfull \hbox (badness 10000) in paragraph at lines 167--169 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 method = "gaverage", par.method = 0 \ T1/ptm/m/n/10 (or \T1/pcr/m/n/10 par.method = [2469] 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]))[] [2470] [2471] Underfull \vbox (badness 10000) has occurred while \output is active [2472] [2473] 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, ...)[] [2474] Underfull \hbox (badness 5374) in paragraph at lines 539--541 []\T1/ptm/m/n/10 logical in-di-cat-ing the ban-ner should be framed; mainly use d when [2475] 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)[] [2476] 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 [2477] [2478] Underfull \hbox (badness 2941) in paragraph at lines 778--781 [][][]\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 816--816 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2479] Underfull \hbox (badness 10000) in paragraph at lines 863--865 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 928--928 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2481] Underfull \hbox (badness 4872) in paragraph at lines 974--976 []\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 988--992 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2482] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1095--1095 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2483] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1112--1112 []\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 1150--1150 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2484] Underfull \hbox (badness 4144) in paragraph at lines 1182--1186 []\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 [2485] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1258--1258 [] \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 1264--1264 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2486] [2487] Underfull \hbox (badness 10000) in paragraph at lines 1403--1408 []\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 1451--1454 [2488] Underfull \hbox (badness 10000) in paragraph at lines 1468--1472 [][][]\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 1492--1492 []\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 1502--1502 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2489] Underfull \hbox (badness 5741) in paragraph at lines 1542--1545 []\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 [2490] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1608--1608 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2491] Underfull \hbox (badness 5008) in paragraph at lines 1725--1733 \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 [2492] [2493] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1816--1816 []\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 1835--1835 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2494] [2495] [2496] [2497] Underfull \hbox (badness 10000) in paragraph at lines 2143--2145 []\T1/ptm/m/n/10 logical in-di-cat-ing if the con-verged. This is de-fined as Underfull \hbox (badness 10000) in paragraph at lines 2154--2157 Underfull \hbox (badness 3179) in paragraph at lines 2168--2174 [][][]\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. [2498] [2499] [2500] Underfull \hbox (badness 10000) in paragraph at lines 2326--2329 [][][]\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 , [2501] Underfull \hbox (badness 1292) in paragraph at lines 2394--2397 []\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 2403--2405 []\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 2426--2429 [][][]\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 , [2502] [2503] [2504] [2505] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2642--2642 []\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 ):[] [2506] [2507] Underfull \hbox (badness 1067) in paragraph at lines 2829--2834 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 (or in-te-ger \T1/pcr/m/n/10 0\T1/ptm/m/n/10 ) cor-re-sponds to the orig-i-nal ``swap'' al-g o-rithm, whereas [2508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2888--2888 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2509] [2510] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2991--2991 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2511] [2512] [2513] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3187--3187 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3188--3188 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2514] Underfull \hbox (badness 10000) in paragraph at lines 3255--3258 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by [2515] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3305--3305 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3306--3306 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2516] [2517] [2518] Underfull \hbox (badness 10000) in paragraph at lines 3491--3494 []\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 Underfull \hbox (badness 3471) in paragraph at lines 3491--3494 [][]\T1/pcr/m/n/10 pam[][][](*, keep.diss=FALSE)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 dist \T1/ptm/m/n/10 must be the dis-sim-i-lar-ity if a [2519] Underfull \hbox (badness 10000) in paragraph at lines 3554--3559 [][][]\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 , [2520] Underfull \hbox (badness 4621) in paragraph at lines 3616--3621 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/pc r/m/n/10 plot([][]as.hclust[][][](x), ...)\T1/ptm/m/n/10 , Underfull \hbox (badness 1990) in paragraph at lines 3616--3621 \T1/ptm/m/n/10 which 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 Underfull \hbox (badness 6268) in paragraph at lines 3628--3631 [][][]\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 , [2521] [2522] [2523] Underfull \hbox (badness 10000) in paragraph at lines 3813--3816 [][][]\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 3844--3847 [][][]\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 , [2524] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3897--3897 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3908--3910 []\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 [2525] [2526] [2527] [2528] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4101--4101 [] \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 4103--4103 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] Underfull \hbox (badness 1946) in paragraph at lines 4132--4137 []\T1/ptm/m/n/10 arguments passed [][]\T1/pcr/m/n/10 barplot[][][]()\T1/ptm/m/n /10 ; note that the de-fault used to be \T1/pcr/m/n/10 col [2529] Underfull \hbox (badness 10000) in paragraph at lines 4199--4207 \T1/pcr/m/n/10 attr(sil, "Ordered") \T1/ptm/m/n/10 is a log-i-cal in-di-cat-ing if \T1/pcr/m/n/10 sil \T1/ptm/m/it/10 is \T1/ptm/m/n/10 or-dered as by [2530] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4241--4241 []\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 4250--4250 [] \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 4252--4252 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4255--4255 []\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 4257--4257 [] \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 4264--4264 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 10000) in paragraph at lines 4622--4628 []\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 4638--4640 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side Overfull \hbox (52.98038pt too wide) in paragraph at lines 4651--4651 []\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 4653--4653 []\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)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4663--4663 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] [2537] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4667--4667 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2538]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2539] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2540] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2541] [2542] [2543]) (./foreign-pkg.tex [2544] Chapter 22. [2545] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2546] [2547] 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 , [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 296--296 []\T1/pcr/m/n/10 read.epiinfo(file, read.deleted = FALSE, guess.broken.dates = FALSE, [2549] [2550] [2551] 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,[] [2552] 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"),[] Underfull \hbox (badness 10000) in paragraph at lines 506--515 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer- Underfull \hbox (badness 6001) in paragraph at lines 506--515 \T1/ptm/m/n/10 ent lev-els. For \T1/pcr/m/n/10 "append" \T1/ptm/m/n/10 (the de- fault), the first orig-i-nal value Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named to Underfull \hbox (badness 10000) in paragraph at lines 506--515 \T1/pcr/m/n/10 paste0(label, duplicated.value.labels.infix, level)\T1/ptm/m/n/1 0 , Underfull \hbox (badness 10000) in paragraph at lines 516--519 []\T1/ptm/m/n/10 character: the in-fix used for la-bels of fac-tor lev-els with du- Underfull \hbox (badness 10000) in paragraph at lines 516--519 \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 [2553] 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 [2554] 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.[] Overfull \hbox (112.38031pt too wide) in paragraph at lines 625--625 []\T1/pcr/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2555] Overfull \hbox (9.78043pt too wide) in paragraph at lines 658--658 []\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="")[] [2556] [2557] 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])[] [2558] [2559] 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) [2560] Overfull \hbox (0.78088pt too wide) in paragraph at lines 963--963 []\T1/pcr/m/n/10 write.arff(x, file, eol = "\n", relation = deparse(substitute (x))) Underfull \hbox (badness 6708) in paragraph at lines 989--992 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2561] [2562] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\T1/pcr/m/n/10 http : / / www . clicketyclick . dk / databases / xbase / format / data _ types . Overfull \hbox (24.78088pt too wide) in paragraph at lines 1109--1109 [] \T1/pcr/m/n/10 convert.factors = c("labels", "string", "numeric", "codes"))[] [2563] Underfull \hbox (badness 1286) in paragraph at lines 1194--1198 []\T1/ptm/m/n/10 Unless dis-abled by ar-gu-ment \T1/pcr/m/n/10 convert.dates = FALSE\T1/ptm/m/n/10 , \T1/phv/m/n/10 R \T1/ptm/m/n/10 date and date-time ob-jec ts [2564] 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 , [2565] Underfull \hbox (badness 6725) 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 [2566]) (./lattice-pkg.tex Chapter 23. [2567] [2568] [2569] Overfull \hbox (12.78088pt too wide) in paragraph at lines 286--286 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 290--290 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .xyplot"),[] [2570] Overfull \hbox (42.78088pt too wide) in paragraph at lines 298--298 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defaul t.dotplot"),[] Overfull \hbox (54.78088pt too wide) in paragraph at lines 305--305 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.barchart"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 313--313 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.stripplot"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 334--334 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 338--338 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .bwplot"),[] [2571] Underfull \hbox (badness 4060) in paragraph at lines 357--369 []\T1/ptm/m/n/10 For the func-tions doc-u-mented here, the for-mula is gen-er-a lly of the Underfull \hbox (badness 10000) in paragraph at lines 357--369 \T1/ptm/m/n/10 form \T1/pcr/m/n/10 y ~ x | g1 * g2 * ... \T1/ptm/m/n/10 (or equ iv-a-lently, \T1/pcr/m/n/10 y ~ x | Underfull \hbox (badness 1028) in paragraph at lines 397--412 \T1/ptm/m/n/10 This for-mula would be taken to mean that the user wants to plot both Underfull \hbox (badness 10000) in paragraph at lines 413--415 []\T1/ptm/m/n/10 To in-ter-pret \T1/pcr/m/n/10 y1 + y2 \T1/ptm/m/n/10 as a sum, one can ei-ther set [2572] Underfull \hbox (badness 7631) in paragraph at lines 479--484 []\T1/ptm/m/n/10 A po-ten-tially use-ful com-po-nent of \T1/pcr/m/n/10 scales \ T1/ptm/m/n/10 in this case may be [2573] [2574] 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 [2575] [2576] [2577] [2578] Underfull \hbox (badness 2005) in paragraph at lines 986--998 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the un-used lev-els of fac-tors will be Underfull \hbox (badness 1199) in paragraph at lines 986--998 \T1/ptm/m/n/10 some-times ap-pro-pri-ate to sup-press drop-ping to pre-serve a use-ful lay-out. [2579] 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 [2580] [2581] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a Underfull \hbox (badness 1917) in paragraph at lines 1239--1240 []\T1/ptm/m/n/10 Space be-tween col-umn blocks, in ad-di-tion to [2582] [2583] [2584] 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 , [2585] 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 , [2586] Underfull \vbox (badness 10000) has occurred while \output is active [2587] 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 [2588] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see [2589] 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 [2590] [2591] [2592] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] Underfull \hbox (badness 10000) in paragraph at lines 2086--2093 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, \T1/pcr/ m/n/10 x \T1/ptm/m/n/10 can be a for-mula of the form Underfull \hbox (badness 1997) in paragraph at lines 2086--2093 \T1/pcr/m/n/10 ~ x | g1 * g2 * ...\T1/ptm/m/n/10 , in-di-cat-ing that his-togra ms or ker-nel den-sity [2593] 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 [2594] [2595] [2596] 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"),[] Underfull \hbox (badness 4441) in paragraph at lines 2362--2366 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2597] [2598] [2599] Underfull \hbox (badness 4441) in paragraph at lines 2547--2554 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 method, \T1/pc r/m/n/10 x \T1/ptm/m/n/10 should be a for-mula of the form [2600] [2601] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2602] Underfull \hbox (badness 10000) in paragraph at lines 2761--2766 []\T1/ptm/m/n/10 for the \T1/pcr/m/n/10 formula \T1/ptm/m/n/10 method, a for-mu la of the form \T1/pcr/m/n/10 z ~ x * y [2603] 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 Underfull \hbox (badness 6758) in paragraph at lines 2877--2881 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether the col-orkey should be Underfull \hbox (badness 7576) in paragraph at lines 2877--2881 \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 [2604] 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- Underfull \hbox (badness 1400) in paragraph at lines 2935--2941 \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 [2605] [2606] 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),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3073--3073 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. cloud"),[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 3085--3085 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defa ult.wireframe"),[] [2607] Underfull \hbox (badness 10000) in paragraph at lines 3110--3118 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 "formula" \T1/ptm/m/n/10 meth-ods, a fo r-mula of the form \T1/pcr/m/n/10 z ~ x 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 [2608] [2609] [2610] [2611]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \relax l.3431 \aliasA{parallel}{B\_08\_splom}{parallel} Overfull \hbox (18.78088pt too wide) in paragraph at lines 3473--3473 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default. splom"),[] [2612] 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"),[] [2613] [2614] [2615] [2616] [2617] 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))) [2618] Underfull \hbox (badness 10000) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 fy-ing \T1/pcr/m/n/10 lattice.options(default.theme = "col.white bg")\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3922--3926 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2619] [2620] 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) Underfull \hbox (badness 1173) in paragraph at lines 4061--4065 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4088--4090 []\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 [2621] 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 [2622] [2623] 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 , Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "plot.line"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "plot.polygon"\T1/ptm /m/n/10 , \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 , Underfull \hbox (badness 1735) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.line"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "superpose.p olygon"\T1/ptm/m/n/10 . \T1/pcr/m/n/10 col.points Underfull \hbox (badness 10000) in paragraph at lines 4284--4294 \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col\T1/ptm/m/n/10 , but is used only f or \T1/pcr/m/n/10 "plot.symbol" \T1/ptm/m/n/10 and Underfull \hbox (badness 5231) in paragraph at lines 4284--4294 \T1/pcr/m/n/10 "superpose.symbol"\T1/ptm/m/n/10 . Sim-i-larly, \T1/pcr/m/n/10 c ol.line \T1/ptm/m/n/10 over-rides \T1/pcr/m/n/10 col \T1/ptm/m/n/10 for Underfull \hbox (badness 1701) in paragraph at lines 4309--4312 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/pcr/m/n/10 plot .symbol\T1/ptm/m/n/10 , \T1/pcr/m/n/10 plot.polygon\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4312--4314 []\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 [2624] [2625] [2626] [2627] [2628] [2629] 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")[] [2630] [2631] 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 . [2632] [2633] Underfull \hbox (badness 1442) in paragraph at lines 5035--5038 []\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 [2634] [2635] [2636] [2637] [2638] [2639] 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 Overfull \hbox (36.78088pt too wide) in paragraph at lines 5397--5397 [] \T1/pcr/m/n/10 bg = trellis.par.get("strip.background")$col[wh ich.given],[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5398--5398 [] \T1/pcr/m/n/10 fg = trellis.par.get("strip.shingle")$col[which .given],[] [2640] Underfull \hbox (badness 10000) in paragraph at lines 5486--5489 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 2103) in paragraph at lines 5486--5489 \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 Underfull \hbox (badness 6412) in paragraph at lines 5503--5509 []\T1/ptm/m/n/10 default strip func-tion for trel-lis func-tions. Use-ful mostl y be-cause of the \T1/pcr/m/n/10 style Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 ar-gu-ment --- non-default styles are of-ten more in-for-ma-tive , es-pe-cially when Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/ptm/m/n/10 the names of the lev-els of the fac-tor \T1/pcr/m/n/10 x \T1/ptm /m/n/10 are small. Tra-di-tional use is as Underfull \hbox (badness 10000) in paragraph at lines 5503--5509 \T1/pcr/m/n/10 strip = function(...) strip.default(style=2,...)\T1/ptm/m/n/10 , though this can be [2641] Underfull \hbox (badness 1635) in paragraph at lines 5512--5517 []\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 [2642] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 panel.identify.qqmath(x, distribution, groups, subscripts, la bels,[] [2643] Overfull \hbox (18.78088pt too wide) in paragraph at lines 5675--5675 []\T1/pcr/m/n/10 panel.link.splom(threshold = 18, verbose = getOption("verbose "), ...)[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5676--5676 []\T1/pcr/m/n/10 panel.brush.splom(threshold = 18, verbose = getOption("verbos e"), ...)[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5679--5679 []\T1/pcr/m/n/10 trellis.vpname(name = c("position", "split", "split.location" , "toplevel",[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 5682--5682 [] \T1/pcr/m/n/10 "xlab", "ylab", "xlab.top", "ylab.rig ht", "page"),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 5684--5684 [] \T1/pcr/m/n/10 side = c("left", "top", "right", "bottom", "in side"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5690--5690 [] \T1/pcr/m/n/10 which.given = lattice.getStatus("current.whi ch.given",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5691--5691 [] \T1/pcr/m/n/10 prefix = pre fix),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 5692--5692 [] \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),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5694--5694 [] \T1/pcr/m/n/10 column = lattice.getStatus("current.focus.co lumn",[] Underfull \hbox (badness 10000) in paragraph at lines 5710--5712 []\T1/ptm/m/n/10 variables defin-ing the con-tents of the panel. In the case of [2644] Underfull \hbox (badness 2376) in paragraph at lines 5721--5723 []\T1/ptm/m/n/10 an op-tional vec-tor of la-bels as-so-ci-ated with each point. De-faults to [2645] 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 Underfull \hbox (badness 4205) in paragraph at lines 5857--5864 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-tr a pa-ram-e-ters are passed on to Underfull \hbox (badness 4792) in paragraph at lines 5857--5864 \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 [2646] [2647] 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 , [2648] [2649] 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- [2650] [2651] 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 Underfull \hbox (badness 2486) in paragraph at lines 6273--6278 \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 [2652] [2653] Overfull \hbox (60.78088pt too wide) in paragraph at lines 6360--6360 [] \T1/pcr/m/n/10 shade.colors.palette = trellis.par.get("shade.co lors")$palette,[] [2654] 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 [2655] Underfull \hbox (badness 10000) in paragraph at lines 6549--6552 []\T1/ptm/m/n/10 All three num-bers should be be-tween 0 and 1. The Underfull \hbox (badness 1558) in paragraph at lines 6549--6552 \T1/pcr/m/n/10 shade.colors.palette \T1/ptm/m/n/10 func-tion should re-turn a v alid color. The [2656] Underfull \hbox (badness 1005) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 fer-ent pur-poses. For cloud, the data is un-struc-tured, and \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 z \T1/ptm/m/n/10 are all passed to Underfull \hbox (badness 1571) in paragraph at lines 6599--6607 \T1/ptm/m/n/10 the \T1/pcr/m/n/10 panel.3d.cloud \T1/ptm/m/n/10 func-tion. For wire-frame, on the other hand, \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/ 10 y \T1/ptm/m/n/10 are in- [2657] [2658] [2659] [2660] [2661] 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- Underfull \hbox (badness 1715) in paragraph at lines 6955--6962 \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 [2662] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2663] Underfull \hbox (badness 10000) in paragraph at lines 7055--7059 []\T1/ptm/m/n/10 The panel func-tion used for the di-ag-o-nals. See ar-gu-ments to Underfull \hbox (badness 1584) in paragraph at lines 7055--7059 \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 [2664] 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 [2665] [2666] 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 [2667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7372--7372 [] \T1/pcr/m/n/9 panel.qqmath(..., f.value = ppoints(100), ta ils.n = 50))[] [2668] [2669] 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 Underfull \hbox (badness 4242) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 which is called with those ar-gu-ments. If spec-i-fied as a (pos -si-bly Underfull \hbox (badness 1147) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 named) nu-meric vec-tor, \T1/pcr/m/n/10 abline \T1/ptm/m/n/10 is co-erced to a list. This al-lows ar- Underfull \hbox (badness 2351) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 gu-ments of the form \T1/pcr/m/n/10 abline = c(0, 1)\T1/ptm/ m/n/10 , which adds the di- Underfull \hbox (badness 1675) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 ag-o-nal line, or \T1/pcr/m/n/10 abline = c(h = 0, v = 0)\T1 /ptm/m/n/10 , which adds the Underfull \hbox (badness 1769) in paragraph at lines 7540--7548 \T1/ptm/m/n/10 x- and y-axes to the plot. Use the list form for finer con-trol; e.g., [2670] 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)),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7606--7606 [] \T1/pcr/m/n/9 scales = list(alternating = c(0, 2), tck = c(0, 0.7), d raw = FALSE),[] [2671] Overfull \hbox (12.78088pt too wide) in paragraph at lines 7667--7667 [] \T1/pcr/m/n/10 font, fontfamily, fontface, cex, ..., identifier, nam e.type)[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 7672--7672 [] \T1/pcr/m/n/10 adj = c(0.5, 0.5), pos = NULL, offset = 0.5, ..., ident ifier, name.type)[] [2672] [2673] [2674] Overfull \hbox (66.78088pt too wide) in paragraph at lines 7857--7857 []\T1/pcr/m/n/10 panel.grid(h=3, v=3, col, col.line, lty, lwd, x, y, ..., iden tifier = "grid")[] [2675] 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 Underfull \hbox (badness 1231) in paragraph at lines 7912--7918 \T1/ptm/m/n/10 tings. The de-fault is to take them from the ``add.line'' set-ti ngs. The [2676] [2677] [2678] [2679] [2680] [2681] [2682] [2683] 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 [2684] [2685] 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, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 8646--8646 []\T1/pcr/m/n/10 prepanel.default.histogram(x, breaks, equal.widths, type, nin t, ...)[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8658--8658 []\T1/pcr/m/n/10 prepanel.default.densityplot(x, darg, groups, weights, subscr ipts, ...)[] [2686] 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 [2687] 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 [2688] 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 [2689] [2690] 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)[] [2691] [2692] 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)),[] [2693] Overfull \hbox (84.94879pt 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 (104.63074pt 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 [2694] [2695] [2696] [2697] [2698] [2699] [2700] Underfull \hbox (badness 4205) 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 4518) 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 , Underfull \hbox (badness 6300) in paragraph at lines 9627--9630 []\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/pcr/m/n/10 "Grand Rapids"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Duluth"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "University Farm" \T1/ptm/m/n/10 , [2701] [2702] [2703]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2704] [2705] [2706] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 []\T1/ptm/m/n/10 Cause of death. A fac-tor with lev-els \T1/pcr/m/n/10 Alzheime rs\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Cancer\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Cerebrovascular 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 , Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 Heart disease\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower respiratory\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 Nephritis\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Suicide\ T1/ptm/m/n/10 , and [2707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10088--10088 [] \T1/pcr/m/n/9 par.settings = simpleTheme(pch = 16), auto.key = list( columns = 2),[] [2708]) (./mgcv-pkg.tex Chapter 24. [2709] [2710] Overfull \hbox (6.78088pt too wide) in paragraph at lines 147--147 []\T1/pcr/m/n/10 bam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL, Overfull \hbox (18.78088pt too wide) in paragraph at lines 150--150 [] \T1/pcr/m/n/10 paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discret e=FALSE,[] [2711] Overfull \hbox (72.78088pt too wide) in paragraph at lines 152--152 [] \T1/pcr/m/n/10 coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.in tercept=NULL,...)[] Underfull \hbox (badness 1142) in paragraph at lines 171--175 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 196--201 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2712] [2713] [2714] [2715] Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 361--368 [][]\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 , [2716] Overfull \hbox (4.38043pt too wide) in paragraph at lines 404--404 []\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)+[] [2717] [2718] [2719] Underfull \hbox (badness 2922) in paragraph at lines 603--604 []\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 [2720] [2721] Underfull \hbox (badness 10000) in paragraph at lines 697--698 []\T1/ptm/m/n/10 First con-sider \T1/pcr/m/n/10 choldrop\T1/ptm/m/n/10 . If \T1 /pcr/m/n/10 R \T1/ptm/m/n/10 is up-per tri-an-gu-lar then [2722] Underfull \hbox (badness 1158) in paragraph at lines 749--751 []\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 [2723] Underfull \hbox (badness 1259) in paragraph at lines 812--813 []\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). [2724] Underfull \vbox (badness 10000) has occurred while \output is active [2725] [2726] [2727] [2728] [2729] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1160--1160 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h + 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1161--1161 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1167--1167 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] [2730] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1174--1174 []\T1/pcr/m/n/9 ## create index picking out elements of stored hazard info for this stratum...[] Overfull \hbox (74.58035pt too wide) in paragraph at lines 1176--1176 []\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),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1178--1178 [] \T1/pcr/m/n/9 lines(bs$family$data$tr[ind],exp(-bs$family$data$h[ind]) ,lwd=2,col=i)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1209--1209 []\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)[] [2731] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1270--1270 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] [2732] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1281--1281 [] \T1/pcr/m/n/9 if (um[[et]][1]==max(tr)&&um[[status]][1]==1) um[[event]][ nrow(um)] <- 1[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1315--1315 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] Underfull \vbox (badness 10000) has occurred while \output is active [2733] [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1818--1818 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2742] [2743] [2744] [2745] [2746] [2747] Underfull \hbox (badness 1052) in paragraph at lines 2193--2201 \T1/ptm/m/n/10 an isotropic smooth is in-ap-pro-pri-ate), and users can add smo oths. Lin-ear func-tion-als of Overfull \hbox (6.78088pt too wide) in paragraph at lines 2210--2210 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2222--2225 []\T1/ptm/m/n/10 A GAM for-mula, or a list of for-mu-lae (see [][]\T1/pcr/m/n/1 0 formula.gam[][][] \T1/ptm/m/n/10 and also Underfull \hbox (badness 1142) in paragraph at lines 2235--2239 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2748] Underfull \hbox (badness 1043) in paragraph at lines 2261--2266 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2749] [2750] Underfull \hbox (badness 1043) in paragraph at lines 2424--2430 \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 [2751] [2752] Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][][]\T1/pcr/m/n/10 mgcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamO bject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\T1/pcr/m/n/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][] [][]predict.gam[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 2560--2566 [][]\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 , [2753] Underfull \vbox (badness 10000) has occurred while \output is active [2754] Underfull \vbox (badness 10000) has occurred while \output is active [2755] Underfull \vbox (badness 10000) has occurred while \output is active [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3216--3216 [] \T1/pcr/m/n/10 mustart = NULL, offset = rep(0, nobs), U1 = diag(nco l(x)),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2764] [2765] [2766] [2767] [2768] [2769] Underfull \hbox (badness 5189) in paragraph at lines 3580--3584 []\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 [2770] [2771] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3697--3697 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2772] [2773] [2774] Underfull \hbox (badness 1184) in paragraph at lines 3866--3870 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2775] [2776] [2777] [2778] [2779] [2780] [2781] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4312--4312 [] \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)+[] [2782] [2783] [2784] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4462--4462 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2785] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4556--4556 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2786] Underfull \hbox (badness 1142) in paragraph at lines 4587--4591 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2787] Underfull \hbox (badness 10000) in paragraph at lines 4656--4665 []\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 [2788] [2789] Underfull \hbox (badness 5970) in paragraph at lines 4773--4779 [][][]\T1/pcr/m/n/10 magic[][][] \T1/ptm/m/n/10 for an al-ter-na-tive for cor-r e-lated data, [][]\T1/pcr/m/n/10 te[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gam[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 plot.gam[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 1418) in paragraph at lines 4773--4779 [][]\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 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2790] Underfull \vbox (badness 10000) has occurred while \output is active [2791] [2792] [2793] Underfull \hbox (badness 1577) in paragraph at lines 5053--5056 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5060--5061 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2794] [2795] [2796] [2797] [2798] [2799] [2800] Underfull \hbox (badness 6708) in paragraph at lines 5449--5450 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(..., fit=FALSE) \T1/ptm/m/n/10 or [2801] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5498--5498 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2802] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5523--5523 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5552--5552 [] \T1/pcr/m/n/9 fv <- predict(b,se=TRUE) ## usual Gaussian approximation, fo r comparison[] Underfull \vbox (badness 10000) has occurred while \output is active [2803] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5605--5605 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2804] [2805] [2806] [2807] [2808] [2809] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5929--5929 []\T1/pcr/m/n/10 jagam(formula,family=gaussian,data=list(),file,weights=NULL,n a.action, Overfull \hbox (36.78088pt too wide) in paragraph at lines 5931--5931 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5952--5956 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2810] [2811] [2812] [2813] [2814] [2815] Overfull \hbox (72.78088pt too wide) in paragraph at lines 6267--6267 []\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) [2816] [2817] [2818] [2819] Underfull \vbox (badness 10000) has occurred while \output is active [2820] Underfull \vbox (badness 10000) has occurred while \output is active [2821] [2822] [2823] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6696--6696 []\T1/pcr/m/n/9 "The world is ruled by idiots because only an idiot would want to rule the world.",[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6723--6723 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1242) in paragraph at lines 7266--7267 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2833] [2834] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7353--7353 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2835] [2836] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7416--7416 []\T1/pcr/m/n/9 for (sim in c(1,7)) { ## cycle over uncorrelated and correlate d covariates[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7435--7435 [] \T1/pcr/m/n/9 dat1[[dname[i]]][dat1[[by.name]]] <- mean(dat1[[dname[i]]] ,na.rm=TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] [2853] [2854] Underfull \vbox (badness 10000) has occurred while \output is active [2855] [2856] Underfull \hbox (badness 10000) in paragraph at lines 8655--8658 []\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 8655--8658 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8655--8658 \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 . [2857] Underfull \hbox (badness 10000) in paragraph at lines 8711--8714 []\T1/ptm/m/n/10 These func-tions (\T1/pcr/m/n/10 pdTens\T1/ptm/m/n/10 , \T1/pc r/m/n/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdFactor.pdTens\T1/p tm/m/n/10 , Underfull \hbox (badness 3108) in paragraph at lines 8711--8714 \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 [2858] [2859] [2860] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8931--8931 []\T1/pcr/m/n/10 plot(x,residuals=FALSE,rug=NULL,se=TRUE,pages=0,select=NULL,s cale=-1,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8932--8932 [] \T1/pcr/m/n/10 n=100,n2=40,n3=3,pers=FALSE,theta=30,phi=30,jit=FALS E,xlab=NULL,[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8935--8935 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2861] [2862] [2863] Underfull \hbox (badness 1629) in paragraph at lines 9093--9098 \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 [2864] [2865] [2866] [2867] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9304--9304 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2868] [2869] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9468--9468 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2870] [2871] [2872] [2873] Underfull \vbox (badness 10000) has occurred while \output is active [2874] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9736--9736 [] \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[] [2875] Underfull \hbox (badness 1205) in paragraph at lines 9774--9776 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9774--9776 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 9780--9785 []\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 [2876] Underfull \hbox (badness 1205) in paragraph at lines 9864--9866 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9864--9866 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2877] Underfull \hbox (badness 10000) in paragraph at lines 9933--9936 []\T1/ptm/m/n/10 The smooth ob-ject will be largely what is re-turned from Underfull \hbox (badness 2057) in paragraph at lines 9933--9936 [][]\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, [2878] [2879] Underfull \hbox (badness 1253) in paragraph at lines 10063--10065 []\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, [2880] [2881] [2882] [2883] Underfull \hbox (badness 1946) in paragraph at lines 10241--10248 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10241--10248 \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 10241--10248 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10249--10252 []\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 10249--10252 \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. [2884] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10315--10315 []\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 10344--10347 []\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 , [2885] [2886] [2887] [2888] [2889] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10631--10631 []\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) [2890] [2891] [2892] [2893] [2894] [2895] Underfull \hbox (badness 3861) in paragraph at lines 10972--10975 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10979--10979 []\T1/pcr/m/n/10 Sl.initial.repara(Sl, X, inverse = FALSE, both.sides = TRUE, cov = TRUE, Underfull \hbox (badness 10000) in paragraph at lines 10992--10996 []\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- [2896] Underfull \hbox (badness 10000) in paragraph at lines 11032--11036 []\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- [2897] [2898] [2899] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11173--11173 [] \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 11184--11189 []\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 [2900] Underfull \hbox (badness 1803) in paragraph at lines 11261--11265 \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 11273--11285 \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 11290--11294 \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 11290--11294 \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 , [2901] [2902] [2903] Underfull \vbox (badness 10000) has occurred while \output is active [2904] Underfull \hbox (badness 6876) in paragraph at lines 11485--11491 [][][]\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 11526--11527 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2905] [2906] Underfull \hbox (badness 10000) in paragraph at lines 11643--11644 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2907] [2908] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11697--11697 [] \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 11709--11709 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11720--11720 [] \T1/pcr/m/n/9 "1st order penalties: red tps; blue bs over (0,1); black bs over (-.5,1.5)")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11721--11721 [] \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 11726--11726 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2909] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11732--11732 [] \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 11733--11733 [] \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:[] [2910] Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term Underfull \hbox (badness 10000) in paragraph at lines 11802--11804 \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 [2911] [2912] Underfull \hbox (badness 10000) in paragraph at lines 11930--11931 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2913] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12011--12011 []\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 12012--12012 []\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[] [2914] [2915] [2916] Underfull \hbox (badness 10000) in paragraph at lines 12162--12163 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2917] [2918] [2919] [2920] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12401--12401 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2921] Underfull \hbox (badness 10000) in paragraph at lines 12462--12464 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2922] [2923] Underfull \vbox (badness 10000) has occurred while \output is active [2924] Underfull \hbox (badness 10000) in paragraph at lines 12621--12624 []\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 12621--12624 \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 12621--12624 \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" [2925] [2926] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12703--12703 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] Underfull \hbox (badness 10000) in paragraph at lines 12748--12754 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 2698) in paragraph at lines 12748--12754 \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- [2927] [2928] [2929] Underfull \vbox (badness 10000) has occurred while \output is active [2930] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12962--12962 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 13065--13073 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like Underfull \hbox (badness 10000) in paragraph at lines 13091--13092 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2933] [2934] [2935] [2936] Underfull \hbox (badness 3396) in paragraph at lines 13352--13355 [][][]\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 [2937] Underfull \hbox (badness 10000) in paragraph at lines 13397--13399 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2938] [2939] [2940] [2941] Underfull \hbox (badness 10000) in paragraph at lines 13621--13624 []\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 13621--13624 \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 [2942] Underfull \hbox (badness 10000) in paragraph at lines 13654--13658 [][][]\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 13654--13658 [][]\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 13654--13658 [][]\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 , [2943] [2944] [2945] [2946] [2947] Underfull \hbox (badness 2158) in paragraph at lines 13944--13944 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [2948] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14023--14023 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [2949] [2950] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14157--14157 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [2951] [2952] [2953] Underfull \hbox (badness 4846) in paragraph at lines 14288--14291 []\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 [2954] [2955] [2956] [2957] [2958] Underfull \vbox (badness 10000) has occurred while \output is active [2959] [2960] [2961] [2962] [2963] [2964] [2965] [2966] Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 []\T1/ptm/m/n/10 Suppose that \T1/pcr/m/n/10 m=1 \T1/ptm/m/n/10 and you fill an ar-ray us-ing code like Underfull \hbox (badness 10000) in paragraph at lines 15113--15121 \T1/pcr/m/n/10 for(i in 1:K) for(j in i:K) for(k in j:K) for(l in k:K) [2967] [2968] [2969] [2970] [2971] [2972] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15477--15477 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [2973] [2974] [2975] [2976] [2977] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15771--15771 []\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 15772--15772 []\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 15784--15784 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [2978] [2979] [2980]) (./nlme-pkg.tex Chapter 25. [2981] 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 [2982] 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 [2983] [2984] [2985] [2986] [2987] 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,[] [2988] [2989] 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 --------------------------- ---------------[] [2990] [2991] [2992] [2993] [2994] [2995] [2996] [2997] 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"),[] [2998] 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 [2999] [3000] [3001] [3002] [3003] [3004] [3005] 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 , [3006] 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 [3007] [3008] [3009] [3010] [3011] 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 , [3012] 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")[] [3013] Underfull \hbox (badness 1132) in paragraph at lines 2144--2146 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3014] [3015] Underfull \hbox (badness 4168) in paragraph at lines 2255--2261 [][][]\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 , [3016] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2280--2280 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] Underfull \hbox (badness 10000) in paragraph at lines 2843--2847 [][][]\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 , [3025] [3026] [3027] [3028] [3029] [3030] [3031] [3032] [3033] [3034] [3035] [3036] Underfull \hbox (badness 6493) in paragraph at lines 3579--3587 [][][]\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 , [3037] [3038] [3039] [3040] [3041] [3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] Underfull \hbox (badness 10000) in paragraph at lines 5159--5163 [][][]\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 , [3061] [3062] [3063] [3064] [3065] Underfull \hbox (badness 10000) in paragraph at lines 5476--5480 []\T1/ptm/m/n/10 Note that as from ver-sion 3.1-102, this only omits rows omit- ted in the fit if Underfull \hbox (badness 2671) in paragraph at lines 5476--5480 \T1/pcr/m/n/10 na.action = na.omit\T1/ptm/m/n/10 , and does not omit at all if \T1/pcr/m/n/10 na.action = na.exclude\T1/ptm/m/n/10 . [3066] [3067] Underfull \hbox (badness 10000) in paragraph at lines 5591--5594 [][][]\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 , [3068] [3069] [3070] [3071] [3072] [3073] [3074] [3075] [3076] Underfull \hbox (badness 2799) in paragraph at lines 6097--6103 \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 [3077] Underfull \hbox (badness 7133) in paragraph at lines 6158--6162 []\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 , [3078] Underfull \hbox (badness 2057) in paragraph at lines 6242--6253 [][][]\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 , [3079] Underfull \hbox (badness 10000) in paragraph at lines 6306--6308 []\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 6338--6338 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3080] [3081] [3082] [3083] Underfull \hbox (badness 7133) in paragraph at lines 6556--6560 []\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 , [3084] Underfull \hbox (badness 10000) in paragraph at lines 6655--6661 [][][]\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 6682--6682 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3085] Underfull \hbox (badness 10000) in paragraph at lines 6720--6722 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3086] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6750--6750 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 6993--7000 [][][]\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 , [3090] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7010--7010 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7018--7018 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7040--7042 []\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 [3091] [3092] [3093] Underfull \hbox (badness 10000) in paragraph at lines 7255--7260 [][][]\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 , [3094] [3095] [3096] Underfull \hbox (badness 10000) in paragraph at lines 7407--7415 []\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 7407--7415 \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 1817) in paragraph at lines 7407--7415 \T1/pcr/m/n/10 list(niterEM=20, gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 20 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7430--7433 [][][]\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 , [3097] [3098] [3099] Underfull \hbox (badness 3354) in paragraph at lines 7645--7647 []\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 [3100] [3101] [3102] [3103] [3104] [3105] Underfull \hbox (badness 1642) in paragraph at lines 8037--8059 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3106] [3107] Underfull \hbox (badness 10000) in paragraph at lines 8157--8174 [][][]\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 8157--8174 [][]\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 8200--8200 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8209--8231 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3108] [3109] [3110] [3111] [3112] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8474--8474 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8520--8522 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8558--8558 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8565 \aliasA{sigma}{lmeObject}{sigma} [3114] [3115] [3116] Underfull \hbox (badness 10000) in paragraph at lines 8726--8738 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 lmList\T1/ptm/m/n/10 , ei-ther a lin-ear fo r-mula ob-ject of the form [3117] [3118] [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 9317--9324 [][][]\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 9328--9328 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3126] Underfull \hbox (badness 6300) in paragraph at lines 9410--9413 []\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 [3127] [3128] [3129] [3130]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9679 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3131] Underfull \hbox (badness 10000) in paragraph at lines 9699--9702 []\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 9743--9746 []\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 9743--9746 \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 [3132] [3133] [3134] Underfull \hbox (badness 2435) in paragraph at lines 9917--9922 []\T1/ptm/m/n/10 The model ma-tri-ces for each el-e-ment of \T1/pcr/m/n/10 form ula(object)\T1/ptm/m/n/10 , cal-cu-lated us-ing \T1/pcr/m/n/10 data\T1/ptm/m/n/ 10 , [3135] [3136] [3137] [3138] [3139] Underfull \hbox (badness 7291) in paragraph at lines 10207--10209 []\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 [3140] [3141] [3142] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10423--10423 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3143] Underfull \hbox (badness 1596) in paragraph at lines 10452--10478 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3144] [3145] [3146] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10628--10628 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3147] [3148] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10779--10779 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10790--10795 []\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[][][] [3149] Underfull \hbox (badness 10000) in paragraph at lines 10812--10816 []\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 Underfull \hbox (badness 10000) in paragraph at lines 10831--10833 []\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 10867--10867 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3150] [3151] [3152] [3153] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11123--11123 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3154] [3155] [3156] [3157] [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 6268) in paragraph at lines 11902--11912 [][][]\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 , [3166] [3167] [3168] [3169] Underfull \hbox (badness 10000) in paragraph at lines 12163--12169 [][][]\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 , [3170] [3171] [3172] [3173] [3174] Underfull \hbox (badness 6876) in paragraph at lines 12485--12487 []\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 [3175] [3176] Underfull \hbox (badness 2452) in paragraph at lines 12641--12648 [][][]\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 , [3177] Underfull \hbox (badness 10000) in paragraph at lines 12706--12712 [][][]\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 , [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] [3189] [3190] [3191] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13658--13658 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3192] Underfull \hbox (badness 10000) in paragraph at lines 13685--13688 []\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 Underfull \hbox (badness 6016) in paragraph at lines 13713--13716 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with the la-bel for the hor-i- zon-tal axis. Underfull \hbox (badness 2653) in paragraph at lines 13713--13716 \T1/ptm/m/n/10 De-fault is the \T1/pcr/m/n/10 y \T1/ptm/m/n/10 el-e-ments of \T 1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 1975) in paragraph at lines 13720--13723 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 dotplot Underfull \hbox (badness 1838) in paragraph at lines 13728--13735 []\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 13728--13735 \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 [3193] Overfull \hbox (12.78088pt too wide) in paragraph at lines 13785--13785 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] Underfull \hbox (badness 10000) in paragraph at lines 13792--13795 []\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 13792--13795 \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 [3194] Underfull \hbox (badness 4582) in paragraph at lines 13820--13823 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 2418) in paragraph at lines 13820--13823 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object, "labels") \T1/ptm/m/n/10 and Underfull \hbox (badness 2990) in paragraph at lines 13824--13827 []\T1/ptm/m/n/10 an op-tional func-tion passed as the \T1/pcr/m/n/10 strip \T1/ ptm/m/n/10 ar-gu-ment to the \T1/pcr/m/n/10 xyplot [3195] Underfull \hbox (badness 10000) in paragraph at lines 13900--13903 []\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 Underfull \hbox (badness 1472) in paragraph at lines 13925--13932 \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 , [3196] Underfull \hbox (badness 10000) in paragraph at lines 13994--13996 [][][]\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 , [3197] [3198] [3199] [3200] Underfull \hbox (badness 1540) in paragraph at lines 14209--14214 \T1/ptm/m/n/10 a \T1/pcr/m/n/10 loess \T1/ptm/m/n/10 smoother is added to the p lot. If \T1/pcr/m/n/10 showModel = TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n/10 x \T1 /ptm/m/n/10 in-cludes an Underfull \hbox (badness 1215) in paragraph at lines 14256--14258 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3201] [3202] [3203] [3204] [3205] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14500--14500 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213] [3214]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15153 ...Extract Random Effects}{random.effects} [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \hbox (badness 1009) in paragraph at lines 15810--15819 \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 [3225] [3226] [3227] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15957--15957 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3228] [3229] [3230] [3231] Underfull \hbox (badness 10000) in paragraph at lines 16235--16253 []\T1/ptm/m/n/10 any of the fol-low-ing: (i) a one-sided for-mula of the form Underfull \hbox (badness 1708) in paragraph at lines 16235--16253 \T1/pcr/m/n/10 ~x1+...+xn | g1/.../gm\T1/ptm/m/n/10 , with \T1/pcr/m/n/10 x1+.. .+xn \T1/ptm/m/n/10 spec-i-fy-ing the model [3232] Underfull \hbox (badness 10000) in paragraph at lines 16292--16298 [][][]\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 , [3233] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16323--16323 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3234] [3235] [3236] [3237] [3238] [3239] [3240] Underfull \hbox (badness 1728) in paragraph at lines 16812--16815 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3241] [3242] [3243] [3244] [3245] Underfull \hbox (badness 1867) in paragraph at lines 17147--17156 \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 17147--17156 \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" Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multip le of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17147--17156 \T1/pcr/m/n/10 "General Positive-Definite, Natural Parametrization" [3246] Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 []\T1/ptm/m/n/10 an op-tional char-ac-ter string with a de-scrip-tion of the Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 varFunc \T1/ptm/m/n/10 class. De-fault de-pends on the method fu nc-tion: Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Combination of variance functions" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varComb\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Constant plus power of covariate" \T1/ptm/m/n/10 for \T1/pcr/m/ n/10 varConstPower\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Exponential of variance covariate" \T1/ptm/m/n/10 for \T1/pcr/m /n/10 varExp\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \T1/pcr/m/n/10 "Different standard deviations per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 10000) in paragraph at lines 17211--17219 \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 , [3247] [3248] [3249] [3250] Underfull \hbox (badness 10000) in paragraph at lines 17458--17465 [][][]\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 , [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] Underfull \hbox (badness 10000) in paragraph at lines 17993--18003 [][][]\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 17993--18003 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18031--18036 \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 [3259] Underfull \hbox (badness 3579) in paragraph at lines 18095--18100 \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 [3260] Underfull \hbox (badness 3579) in paragraph at lines 18158--18163 \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 [3261] Underfull \hbox (badness 1577) in paragraph at lines 18219--18221 []\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 18221--18226 \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 [3262] Underfull \hbox (badness 3579) in paragraph at lines 18284--18289 \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 [3263] Underfull \hbox (badness 10000) in paragraph at lines 18317--18326 [][][]\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 18317--18326 [][]\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 , Underfull \hbox (badness 3579) in paragraph at lines 18356--18361 \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 [3264] [3265] [3266] Underfull \hbox (badness 1009) in paragraph at lines 18505--18514 \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 [3267] [3268] Underfull \hbox (badness 1009) in paragraph at lines 18639--18648 \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 [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.multinom.1}) has been already used, du plicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} [3277] 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,[] Underfull \hbox (badness 10000) in paragraph at lines 78--87 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm [3278] [3279] [3280] 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,[] [3281] 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)[] [3282] Underfull \hbox (badness 4013) in paragraph at lines 474--477 \T1/ptm/m/n/10 the cor-re-spond-ing class (which is prob-a-bly only use-ful if the net was gen-er-ated by [3283] 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,[] [3284]) (./rpart-pkg.tex Chapter 27. [3285] [3286] [3287] [3288] 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, ...)[] [3289] Underfull \hbox (badness 10000) in paragraph at lines 373--377 []\T1/ptm/m/n/10 Vector of split la-bels (\T1/pcr/m/n/10 collapse = TRUE\T1/ptm /m/n/10 ) or ma-trix of left and right splits [3290] [3291] [3292] 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 [3293] [3294] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3295] Underfull \hbox (badness 2941) in paragraph at lines 785--787 []\T1/ptm/m/n/10 a plot of \T1/pcr/m/n/10 rpart \T1/ptm/m/n/10 is cre-ated us-i ng the \T1/pcr/m/n/10 postscript \T1/ptm/m/n/10 driver, or the cur-rent de-vice if [3296] Overfull \hbox (25.98041pt too wide) in paragraph at lines 902--902 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3297] Overfull \hbox (48.78088pt too wide) in paragraph at lines 921--921 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3298] [3299] [3300] Underfull \hbox (badness 2310) in paragraph at lines 1113--1116 []\T1/ptm/m/n/10 For re-gres-sion or \T1/pcr/m/n/10 anova \T1/ptm/m/n/10 trees all three resid-ual def-i-ni-tions re-duce to Overfull \hbox (6.78088pt too wide) in paragraph at lines 1163--1163 []\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 1164--1164 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] Underfull \hbox (badness 2837) in paragraph at lines 1187--1196 []\T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "anova"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " poisson"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "class" \T1/ptm/m/n/10 or \T1/pcr/m/n/1 0 "exp"\T1/ptm/m/n/10 . If \T1/pcr/m/n/10 method Underfull \hbox (badness 2088) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is miss-ing then the rou-tine tries to make an in-tel-li-gent gu ess. If \T1/pcr/m/n/10 y Underfull \hbox (badness 1817) in paragraph at lines 1187--1196 \T1/ptm/m/n/10 is a sur-vival ob-ject, then \T1/pcr/m/n/10 method = "exp" \T1/p tm/m/n/10 is as-sumed, if \T1/pcr/m/n/10 y \T1/ptm/m/n/10 has 2 [3301] Underfull \hbox (badness 2846) in paragraph at lines 1226--1228 []\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 [3302] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1270--1270 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1286--1286 []\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 1287--1287 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3303] [3304] [3305] [3306] [3307] [3308] Underfull \hbox (badness 1565) in paragraph at lines 1739--1742 []\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 ', [3309] [3310] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1833--1833 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3311] [3312] [3313]) (./spatial-pkg.tex [3314] Chapter 28. [3315] [3316] [3317] [3318] [3319] [3320] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3321] [3322] [3323] [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333]) (./survival-pkg.tex [3334] Chapter 29. [3335] [3336] Overfull \hbox (31.3804pt too wide) in paragraph at lines 171--171 []\T1/pcr/m/n/9 aareg(formula = Surv(time, status) ~ age + sex + ph.ecog, data = lung, nmin = 1[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 190--190 []\T1/pcr/m/n/9 ## Not run: lines(lfit2[4], col=2) # Nearly the same, until t he last point[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 193--193 []\T1/pcr/m/n/9 # Chronic Granuomatous Disease. See section 8.5 of Therneau a nd Grambsch.[] [3337] [3338]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.aml}) has been already used, duplicate ignored \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 \relax l.326 ... Myelogenous Leukemia survival data}{aml} [3339] [3340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 423--423 []\T1/pcr/m/n/9 fit <- coxph(Surv(futime, fustat) ~ resid.ds *rx + ecog.ps, da ta = ovarian) Overfull \hbox (4.38043pt too wide) in paragraph at lines 425--425 []\T1/pcr/m/n/9 fit2 <- coxph(Surv(futime, fustat) ~ resid.ds +rx + ecog.ps, d ata=ovarian)[] [3341] Overfull \hbox (6.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 survreg(Surv(time, status) ~ age + sex + factor(ph.ecog), lung)[] [3342] [3343] Underfull \vbox (badness 10000) has occurred while \output is active [3344] Overfull \hbox (36.78088pt too wide) in paragraph at lines 661--661 []\T1/pcr/m/n/10 cch(formula, data = sys.parent(), subcoh, id, stratum=NULL, c ohort.size, Overfull \hbox (48.78088pt too wide) in paragraph at lines 662--662 [] \T1/pcr/m/n/10 method =c("Prentice","SelfPrentice","LinYing","I.Borgan", "II.Borgan"),[] [3345] [3346] 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,[] [3347] [3348] [3349] 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[] [3350] [3351] 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) [3352]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3353] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1271--1271 [] \T1/pcr/m/n/10 cluster, ymin, ymax, timewt= c("n", "S", "S/G", "n/G", "n/G 2", "I"),[] [3354] [3355] [3356] [3357] [3358] [3359] Underfull \hbox (badness 1337) in paragraph at lines 1753--1757 [][][]\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 , [3360] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1808--1808 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3361] [3362] [3363] [3364] [3365] [3366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2246--2246 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] [3367] [3368] [3369] [3370] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2495--2495 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3371] [3372] [3373] [3374] [3375] Underfull \vbox (badness 2393) has occurred while \output is active [3376] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2812--2812 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) Overfull \hbox (36.7804pt too wide) in paragraph at lines 2848--2848 [] \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 2862--2864 []\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 [3377] Underfull \hbox (badness 1048) in paragraph at lines 2917--2919 []\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 [3378] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2995--2995 [] \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 )))[] [3379] [3380] [3381] [3382] [3383] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3241--3241 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3384] [3385] [3386] [3387] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3507--3507 [] \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 )))[] [3388] Underfull \vbox (badness 10000) has occurred while \output is active [3389] [3390] [3391] [3392] [3393] [3394] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3924--3924 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3395] [3396] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4119--4119 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3397] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4245--4245 []\T1/pcr/m/n/9 mresid <- (lung$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[] [3398] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4253--4253 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3399] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4339--4339 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3400] [3401] Underfull \hbox (badness 1852) in paragraph at lines 4487--4489 []\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 [3402] [3403] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4622--4622 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4623--4623 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3404] [3405] [3406] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4787--4787 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] Underfull \hbox (badness 1540) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 an ar-ray con-tain-ing the ex-pected num-ber of events (or per -son years if [3407] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4889--4889 []\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 4910--4910 []\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 4912--4912 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3408] [3409] [3410] [3411] [3412] Underfull \vbox (badness 2126) has occurred while \output is active [3413] [3414] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5387--5387 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5399--5402 \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 [3415] [3416] [3417] [3418] [3419] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5699--5699 []\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 5700--5700 []\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 \relax l.5705 ...ata from a soldering experiment}{solder} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.solder.1}) has been already used, dupl icate ignored \relax l.5705 ...ata from a soldering experiment}{solder} [3420] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5811--5811 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6166--6166 []\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 6167--6167 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3427] [3428] [3429] [3430] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6459--6459 [] \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 ),[] [3431] [3432] Underfull \vbox (badness 10000) has occurred while \output is active [3433] Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 length \T1/ptm/m/n/10 of a \T1/pcr/m/n/10 S urv \T1/ptm/m/n/10 ob-ject is the num-ber of sur-vival times Underfull \hbox (badness 10000) in paragraph at lines 6722--6729 \T1/ptm/m/n/10 it con-tains, not the num-ber of items re-quired to en-code it, e.g., Underfull \hbox (badness 1412) in paragraph at lines 6722--6729 \T1/pcr/m/n/10 x <- Surv(1:4, 5:9, c(1,0,1,0)); length(x) \T1/ptm/m/n/10 has a value of 4. Like- Underfull \hbox (badness 1253) in paragraph at lines 6733--6736 []\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 [3434] [3435] Underfull \hbox (badness 10000) in paragraph at lines 6876--6885 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6972--6972 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3437] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6990--6990 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7032--7038 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3438] Underfull \hbox (badness 3000) in paragraph at lines 7054--7056 []\T1/ptm/m/n/10 numeric value to scale the re-sults. If \T1/pcr/m/n/10 ratetab le \T1/ptm/m/n/10 is in units/day, Overfull \hbox (48.78088pt too wide) in paragraph at lines 7084--7084 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3439] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7170--7170 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3440] [3441] [3442] Underfull \hbox (badness 10000) in paragraph at lines 7395--7400 [][][]\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 , [3443] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7416--7416 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7633--7633 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3446] [3447] Underfull \hbox (badness 6332) in paragraph at lines 7740--7745 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the er-ror. Pos-si-ble val- ues are [3448] [3449] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7933--7933 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3450] [3451] [3452] [3453] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8223--8223 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3454] Underfull \hbox (badness 1354) in paragraph at lines 8264--8268 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3455] [3456] Underfull \hbox (badness 2035) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 it is as-sumed to name an el-e-ment from [][]\T1/pcr/m/n/10 surv reg.distributions[][][]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 8439--8446 \T1/ptm/m/n/10 These in-clude \T1/pcr/m/n/10 "weibull"\T1/ptm/m/n/10 , \T1/pcr/ m/n/10 "exponential"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "gaussian"\T1/ptm/m/n/10 , Underfull \hbox (badness 1297) in paragraph at lines 8439--8446 \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 [3457] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8515--8515 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3458] Overfull \vbox (31.11076pt too high) has occurred while \output is active [3459] [3460] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8672--8672 [] \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 )[] [3461] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8804--8804 [] \T1/pcr/m/n/9 temp/pi, -2 *x*temp, 2*temp^2*(4*x ^2*temp -1))[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8807--8807 [] \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 )[] [3462] [3463] [3464] [3465] [3466] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9109--9109 []\T1/pcr/m/n/9 # The first data set contains data on 312 subjects in a clinic al trial plus[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9110--9110 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9116--9116 [] \T1/pcr/m/n/9 protime = tdc(day, protime), alk.phos = tdc(day , alk.phos))[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9118--9118 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3467] [3468] [3469] [3470] [3471] [3472]pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.xtfrm.Surv}) has been already used, duplicate i gnored \relax l.9488 ...ting order for Surv objects}{xtfrm.Surv} [3473] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9556--9556 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3474] [3475] [3476]) (./fullrefman.ind [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2194--2196 []| \T1/pcr/m/n/10 smooth.construct.ad.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2196--2198 []| \T1/pcr/m/n/10 smooth.construct.bs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2198--2200 []| \T1/pcr/m/n/10 smooth.construct.cr.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2200--2202 []| \T1/pcr/m/n/10 smooth.construct.ds.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2202--2204 []| \T1/pcr/m/n/10 smooth.construct.fs.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2204--2206 []| \T1/pcr/m/n/10 smooth.construct.gp.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2206--2208 []| \T1/pcr/m/n/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2208--2210 []| \T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method [3572] Overfull \hbox (74.8567pt too wide) in paragraph at lines 13599--13601 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3573] [3574] [3575] Overfull \hbox (50.8567pt too wide) in paragraph at lines 14358--14360 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14364--14366 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 14366--14368 []\T1/pcr/m/n/10 Logic,ldenseMatrix,lsparseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14368--14370 []\T1/pcr/m/n/10 Logic,lgCMatrix,lgCMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14370--14372 []\T1/pcr/m/n/10 Logic,lgeMatrix,lgeMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 14372--14374 []\T1/pcr/m/n/10 Logic,lgTMatrix,lgTMatrix-method Overfull \hbox (8.8567pt too wide) in 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at lines 14416--14418 []\T1/pcr/m/n/10 Logic,nsparseVector,nsparseVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14424--14426 []\T1/pcr/m/n/10 Logic,sparseVector,dMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14426--14428 []\T1/pcr/m/n/10 Logic,sparseVector,lMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14428--14430 []\T1/pcr/m/n/10 Logic,sparseVector,nMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 14430--14432 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method [3576] Overfull \hbox (74.8567pt too wide) in paragraph at lines 14432--14434 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3577] [3578] [3579] [3580] Overfull \hbox (52.01662pt too wide) in paragraph at lines 15402--15404 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [3581] [3582] Overfull \hbox (8.8567pt too wide) in paragraph at lines 15955--15957 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 15974--15976 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 15976--15978 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 15982--15984 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method [3583] Overfull \hbox (14.8567pt too wide) in paragraph at lines 16000--16002 []\T1/pcr/m/n/10 norm,ldenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16006--16008 []\T1/pcr/m/n/10 norm,ndenseMatrix,character-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 16008--16010 []\T1/pcr/m/n/10 norm,sparseMatrix,character-method [3584] Overfull \hbox (26.8567pt too wide) in paragraph at lines 16253--16255 []\T1/pcr/m/n/10 Ops,atomicVector,sparseVector-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 16259--16261 []\T1/pcr/m/n/10 Ops,ddiMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16271--16273 []\T1/pcr/m/n/10 Ops,ddiMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 16273--16275 []\T1/pcr/m/n/10 Ops,diagonalMatrix,ddiMatrix-method Overfull \hbox (50.8567pt too wide) in paragraph at lines 16275--16277 []\T1/pcr/m/n/10 Ops,diagonalMatrix,diagonalMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16277--16279 []\T1/pcr/m/n/10 Ops,diagonalMatrix,sparseMatrix-method Overfull \hbox (62.8567pt too wide) in paragraph at lines 16279--16281 []\T1/pcr/m/n/10 Ops,diagonalMatrix,triangularMatrix-method [3585] Overfull \hbox (38.8567pt too wide) in paragraph at lines 16299--16301 []\T1/pcr/m/n/10 Ops,dsparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16301--16303 []\T1/pcr/m/n/10 Ops,ldenseMatrix,ldenseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 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)\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 16634--16636 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3588] [3589] [3590] [3591] [3592] Overfull \hbox (46.01662pt too wide) in paragraph at lines 17898--17900 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [3593] Overfull \hbox (4.01662pt too wide) in paragraph at lines 17901--17903 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17903--17905 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17905--17907 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 17907--17909 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 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(\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17923--17925 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17925--17927 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17927--17929 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17929--17931 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 17931--17933 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.cr.smooth\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3594] [3595] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18277--18279 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18349--18351 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3596] [3597] [3598] Overfull \hbox (26.8567pt too wide) in paragraph at lines 18812--18814 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 18821--18823 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18823--18825 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 18825--18827 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 18827--18829 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 18839--18841 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method 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rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19196--19198 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19198--19200 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19200--19202 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19202--19204 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19204--19206 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19206--19208 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19208--19210 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19214--19216 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19218--19220 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19228--19230 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19232--19234 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19234--19236 []\T1/pcr/m/n/10 rbind2,numeric,sparseMatrix-method [3601] Overfull \hbox (38.8567pt too wide) in paragraph at lines 19236--19238 []\T1/pcr/m/n/10 rbind2,sparseMatrix,denseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19238--19240 []\T1/pcr/m/n/10 rbind2,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19240--19242 []\T1/pcr/m/n/10 rbind2,sparseMatrix,matrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19242--19244 []\T1/pcr/m/n/10 rbind2,sparseMatrix,numeric-method Overfull \hbox (44.8567pt too wide) in paragraph at lines 19244--19246 []\T1/pcr/m/n/10 rbind2,sparseMatrix,sparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19273--19275 []\T1/pcr/m/n/10 rcond,ddenseMatrix,character-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19275--19277 []\T1/pcr/m/n/10 rcond,ddenseMatrix,missing-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19277--19279 []\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19279--19281 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19283--19285 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19287--19289 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19291--19293 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19295--19297 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19299--19301 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19303--19305 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19307--19309 []\T1/pcr/m/n/10 rcond,ldenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19311--19313 []\T1/pcr/m/n/10 rcond,ndenseMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19313--19315 []\T1/pcr/m/n/10 rcond,sparseMatrix,character-method [3602] [3603] [3604] [3605] [3606] Overfull \hbox (20.8567pt too wide) in paragraph at lines 20248--20250 []\T1/pcr/m/n/10 Schur,diagonalMatrix,logical-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 20250--20252 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Transcript written on fullrefman.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' + exit 0 Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.44593 + 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 + cd R-3.5.3 + make 'INSTALL=/bin/install -p' install DESTDIR=/usr/src/tmp/R-base-buildroot install-pdf install-info make: Entering directory '/usr/src/RPM/BUILD/R-3.5.3' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/m4' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/m4' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tools' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tools' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/doc' installing doc ... mkdir -p -- 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directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -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-3.5.3/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/bin/exec make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/src/main' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib make[3]: Leaving directory 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manually make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/doc/manual' make: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3' + mv /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so ++ relative /usr/lib64/libR.so /usr/lib64/R/lib/libR.so + ln -s ../../libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/R/lib/libR.so + ln -s libR.so /usr/src/tmp/R-base-buildroot/usr/lib64/libR-2.11.so ++ relative /usr/share/doc/R-3.5 /usr/lib64/R/doc + ln -s ../../share/doc/R-3.5 /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/mgcv/libs/mgcv.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/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/lattice/libs/lattice.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/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/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/spatial/libs/spatial.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/parallel/libs/parallel.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/graphics/libs/graphics.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/grDevices/libs/cairo.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/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) /usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -pthread -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -pthread -L${rlibdir} -lR' Checking contents of files in /usr/src/tmp/R-base-buildroot/ (default) Compressing files in /usr/src/tmp/R-base-buildroot (auto) Verifying info files in /usr/src/tmp/R-base-buildroot/usr/share/info (normal) Adjusting library links in /usr/src/tmp/R-base-buildroot ./usr/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.50074 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.5.3 + export TZ= + TZ= + make check make: Entering directory '/usr/src/RPM/BUILD/R-3.5.3' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... NOTE 6599c6599 < Grand Mean: 291.5937 --- > Grand Mean: 291.5938 15143c15143 < Grand Mean: 291.5937 --- > Grand Mean: 291.5938 17463c17463 < assertCondition: caught "error" --- > assertCondition: caught 'error' 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-3.5.3/tests/Examples' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running strict specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running sloppy specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/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-3.5.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' checking Sys.timezone ... make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running code in 'timezone.R' ...make[4]: *** [Makefile.common:105: timezone.Rout] Error 1 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' Sys.timezone() appears unknown make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running regression tests ... make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in '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-3.5.3/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running code in 'reg-tests-3.R' ... OK comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK running code in 'reg-examples3.R' ... OK comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ...340c340 < Achieved convergence tolerance: 9.33e-07 --- > Achieved convergence tolerance: 9.32e-07 407c407 < Achieved convergence tolerance: 2.19e-06 --- > Achieved convergence tolerance: 2.17e-06 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-3.5.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running tests of Internet functions make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.5.3/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [2] "" > [3] "" > [4] "" > [5] "" > [6] "" > [7] "" > [8] "" > [9] "" > [10] "" > [11] "" > [12] "" > [13] "" > [14] "" > [15] "" > [16] "" > [17] "" > [18] "<h1>The Comprehensive R Archive Network</h1>" > [19] "" > [20] "Your browser seems not to support frames," > [21] "here is the <A href=\"navbar.html\">contents page</A> of CRAN." > [22] "" > [23] "" > > close(zz) > > > > # and via read.table, test http and ftp. > > > > read.table("http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat") > V1 V2 V3 V4 V5 > 1 1 307 930 36.58 0 > 2 2 307 940 36.73 0 > 3 3 307 950 36.93 0 > 4 4 307 1000 37.15 0 > 5 5 307 1010 37.23 0 > 6 6 307 1020 37.24 0 > 7 7 307 1030 37.24 0 > 8 8 307 1040 36.90 0 > 9 9 307 1050 36.95 0 > 10 10 307 1100 36.89 0 > 11 11 307 1110 36.95 0 > 12 12 307 1120 37.00 0 > 13 13 307 1130 36.90 0 > 14 14 307 1140 36.99 0 > 15 15 307 1150 36.99 0 > 16 16 307 1200 37.01 0 > 17 17 307 1210 37.04 0 > 18 18 307 1220 37.04 0 > 19 19 307 1230 37.14 0 > 20 20 307 1240 37.07 0 > 21 21 307 1250 36.98 0 > 22 22 307 1300 37.01 0 > 23 23 307 1310 36.97 0 > 24 24 307 1320 36.97 0 > 25 25 307 1330 37.12 0 > 26 26 307 1340 37.13 0 > 27 27 307 1350 37.14 0 > 28 28 307 1400 37.15 0 > 29 29 307 1410 37.17 0 > 30 30 307 1420 37.12 0 > 31 31 307 1430 37.12 0 > 32 32 307 1440 37.17 0 > 33 33 307 1450 37.28 0 > 34 34 307 1500 37.28 0 > 35 35 307 1510 37.44 0 > 36 36 307 1520 37.51 0 > 37 37 307 1530 37.64 0 > 38 38 307 1540 37.51 0 > 39 39 307 1550 37.98 1 > 40 40 307 1600 38.02 1 > 41 41 307 1610 38.00 1 > 42 42 307 1620 38.24 1 > 43 43 307 1630 38.10 1 > 44 44 307 1640 38.24 1 > 45 45 307 1650 38.11 1 > 46 46 307 1700 38.02 1 > 47 47 307 1710 38.11 1 > 48 48 307 1720 38.01 1 > 49 49 307 1730 37.91 1 > 50 50 307 1740 37.96 1 > 51 51 307 1750 38.03 1 > 52 52 307 1800 38.17 1 > 53 53 307 1810 38.19 1 > 54 54 307 1820 38.18 1 > 55 55 307 1830 38.15 1 > 56 56 307 1840 38.04 1 > 57 57 307 1850 37.96 1 > 58 58 307 1900 37.84 1 > 59 59 307 1910 37.83 1 > 60 60 307 1920 37.84 1 > 61 61 307 1930 37.74 1 > 62 62 307 1940 37.76 1 > 63 63 307 1950 37.76 1 > 64 64 307 2000 37.64 1 > 65 65 307 2010 37.63 1 > 66 66 307 2020 38.06 1 > 67 67 307 2030 38.19 1 > 68 68 307 2040 38.35 1 > 69 69 307 2050 38.25 1 > 70 70 307 2100 37.86 1 > 71 71 307 2110 37.95 1 > 72 72 307 2120 37.95 1 > 73 73 307 2130 37.76 1 > 74 74 307 2140 37.60 1 > 75 75 307 2150 37.89 1 > 76 76 307 2200 37.86 1 > 77 77 307 2210 37.71 1 > 78 78 307 2220 37.78 1 > 79 79 307 2230 37.82 1 > 80 80 307 2240 37.76 1 > 81 81 307 2250 37.81 1 > 82 82 307 2300 37.84 1 > 83 83 307 2310 38.01 1 > 84 84 307 2320 38.10 1 > 85 85 307 2330 38.15 1 > 86 86 307 2340 37.92 1 > 87 87 307 2350 37.64 1 > 88 88 308 0 37.70 1 > 89 89 308 10 37.46 1 > 90 90 308 20 37.41 1 > 91 91 308 30 37.46 1 > 92 92 308 40 37.56 1 > 93 93 308 50 37.55 1 > 94 94 308 100 37.75 1 > 95 95 308 110 37.76 1 > 96 96 308 120 37.73 1 > 97 97 308 130 37.77 1 > 98 98 308 140 38.01 1 > 99 99 308 150 38.04 1 > 100 100 308 200 38.07 1 > > OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3/tests' make: Leaving directory '/usr/src/RPM/BUILD/R-3.5.3' + exit 0 Processing files: R-base-3.5.3-alt1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.77054 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.5.3 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.5.3 + exit 0 warning: File listed twice: /usr/lib64/R/library/KernSmooth/html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html 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/usr/lib64/R/library/utils/html/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/chooseBioCmirror.html warning: File listed twice: /usr/lib64/R/library/utils/html/chooseCRANmirror.html warning: File 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/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/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/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/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/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.FskeRd 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: 1193 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2020-12-06 03:14:46.539779531 +0000 +++ filter-provides-deps 2020-12-06 03:14:46.540779531 +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.2pJx5I 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:odjvQNYfHFGF6Xo9rSYpedG8BII3EakgydO9cuf3TxqqZyO7yMvQ7wSiUTrcy7nNqGiflliOlRYkEVx3WbfE9EMjzuK8DfBqYQcAifd5xG3BauIcFNL1sZ76iqxUM9hRH43rPONzmSAG7LsxwROHTsK033i8b0gJi5VZjAEWcRCCPuZbOjbw5ZapXarSwbze7OXk9oZitxqybLaksw9aaqOHEnB223TfEVsYBaZxnGEwKdkBoh0ZIRTiaMlYFyDDP9NEVlf0k9nKqTQLgGT84AEkyBhQwfRSwRA0YgRCkFogdJEmuP6RN1espwjZ9zAy0UdgjefE70tytnRStRZEXi0mTOn4e8bbq38e4clbqXZIOCcwWzxBuVc2C8BizZyXUg0lsMgMo7KG8LXMZ6juhZkkPEg9PEW1XNyiZjUYr88T0K4m1VyDBJMZzxU0obgFvsZrcjj2kzEsMVVoTeGyZi2tJk4mSb3VIkEM49lU87j7ZyIddk4Y0aLn19nimTu0LddCZCycnoIBi1r9TC7h8ZmccJLISk6aCoFpqQJ3iFKgSntpZk034k2VOoZ0L8ZHy30mTX4t1ZAsmGCEwS2V8foRvdfffpYq45gGEjgF100a60TrTexlIV4iOJZ9Wo5lC5t2rcS2qunxQqytYaTyPiUPSgdUvaWUpWXtuD72mg20Pa7T45brAXK91D6u5e8eG8IHh30gUCeUqNwVV0Y61vntnZfJvjmpZa4wr0Dbizdh51stjg0hVwQcHxgEE0uVgcZxz1LKkarm5KEtPzv0tDGiUtM6JIZ5jijeePeqEsvdkAuMij9Z3gnAh1y8jkuRTUgjuHRjXrw8pyTG8ihTY1w3ZBbZEoCp9S7TdN6Y8Lc6u2H6hkuTwSgUhl97T1KZxwx7nTZoq20bQuU7FwUbaOh7RVr54iYtw8fMj0q9s0EYGWBxatviZAgKsopVq81j1Z03OTyFJLuw8epTGv9cIjnWTax6Krqq4UuGuYn7V6Ru0Z2gbXMfwqnEs7runz9Xki9HbNJw0QfkEItxFOZ14XCppeiByhS88ANiDOCk60lubLQr8g453AU6RWd91Z5XHSYzA1o1qi2VS3l6wvvWZkngZG4oO4mwooIzBjCyvicnaMsAMdgbh92wsZuZKdylwyHcByxC90X2NCN9cBnQet0YgOjoRHEUWN3xL4zTp2Cik8hFDpDyC1tNeaOq2Ijuba7TcYWkp4pmOo0pkSNfBcy46cixBUFBJZDbl6nFvK3G3yZHV4IhuloZx6DFelZLVkfZ8gZBbSBd4uFpBb6c8BeOMo5NfiwbC7isMKiPiuPmatTNv7wc07q4WiDk8C29wrPbFPqcSgdLqQXm4ylx9eBZqwW9v1B4XGv7nm0Z57bxcsMZIhCpCaUSR8gM0WOoRL9kJVOIsodv0YizyDi4e8gaPIbbm3a0iCg8lDHHkL0Wry3z1lVY4tfY6ZygnmjOXBKaEDs6EV2gFN3TzWOJdZnP8WdufuSantDLrapEMoBmhoUcXisBmwYuBkBkgORF3VOlQhAfC3EkN7v8uN8KwK74s42QxL6m4yhod1xXUcExcU12kXTgRjy2QoSmJtgT61g53urvi0zjG7qO11aooCh2JsOv1S7f8yD4y64MGNY5gnYl1TkkWAn4YcEDNnkO0naPgTpu5taTaZiCroA0Ka94U1WycQhZ2nL9aqclymCa90bPssTagwluO881jZGTro2DWqORfQ5GdGsgP2kDr397h0YF9KCeKE8bcTxbOZzgS0Q0zZKjxHAzp3pBrZjZdCabv42EE112tc2IIYGa39ctTbpHSQoOx4kKcS9ZA7MUN0oZpqnqx2sV4vcBs0zdB5uAQsKeCh9Atc1rRm7Pv4eo1z0leEZufigxYwssXb92bbB7dSpe9deAF0WoJQShuhtLC9yWBGXdSRjwPwY0P0cvziOeQ8DMi2lvXYSfoyFFCZ0xZrV9Xn6IVcZ9WdoaxRLt6khTyoAyR1UHD0Wf3Dwsho05WHTnIdrsAqdvAcMcvIBBpKWFlc0kbCSOKvsUI0QmgsKQpvPRJEfRK3JNv8YDw8kx00Z2wZ8IzieQdsgz6j7ATazLZuX6g2NJhr4aIVyBhOWuLHMIvqZoSk8aw5Fo1U3EQKIT3vC1yulAYPDAcLUUe0NZ7BPX5fegeyXaudMKqduSDIVQGXmvq9NvbjjI9q9KBK1CuUZwNy7MVYqJLYFmlsAyZoVblDOkCED91dtYh288weYAnQZ5jPtZL5IE0OyF9qq5PSD3hw7srebwxZgcO6F9Jh0TZjkU1FCmwLVGcc9K95Mc7Mu5RlZA1viuU4gQGgiepzvZCAZ1UwUoP2UPFPZ6UKSmwQvCas26oMjiW4YcLeR9LIgTjZE9K4u8IzC8kc01uQELl2XoTdaiRVdddyqnjXm6kSZkNIa0JuXUXkMyxrodlCF18PZjkQW0jfpLXdo0vY053 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, 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:rme9dGe009CqZyeEKu0c959bA01WKVsu0KL3f0MzHG9G3SAPMCzdZ2ZyhPe7xLi5vYvWeHEOFls8vqO9WfXluFSG02, 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:nidQ8PMktsCwid18OsyEUS8ifZzElko8gle73YghFZmboE0sZwI3S2Gz6RwZADa29NiWZu0BVGKnVqwyZw4mp, 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.BDraAL Creating R-base-debuginfo package Processing files: R-full-3.5.3-alt1 Requires: R-devel = 3.5.3-alt1, R-tcltk = 3.5.3-alt1, R-doc-html = 3.5.3-alt1, gcc-c++, gcc-fortran, liblapack-devel, make Processing files: R-devel-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.yvcugS 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.jLEL61 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 rm rmdir Provides: pkgconfig(libR) = 3.5.3 Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils Requires(pre): R-base = 3.5.3-alt1 Requires(postun): R-base = 3.5.3-alt1 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.6hLeKh Processing files: R-tcltk-3.5.3-alt1 warning: File listed twice: /usr/lib64/R/library/tcltk/html warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.z2v7xA 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.YKAAvW 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 = 3.5.3-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.N43ZCl Creating R-tcltk-debuginfo package Processing files: R-doc-html-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.iwqXVN 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.lNwToj 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 = 3.5.3-alt1 Processing files: R-doc-pdf-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.uR8T6R 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.vVqTYt 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 > 3.5.3, R-base < 3.5.3 Processing files: R-doc-info-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.o7Ca18 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.75sxdR 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 > 3.5.3, R-base < 3.5.3 Processing files: R-base-debuginfo-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ax4nPC 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.d2NlBr find-requires: running scripts (debuginfo) Provides: debug64(libR.so) Requires: R-base = 3.5.3-alt1, /usr/lib/debug/lib64/ld-linux-x86-64.so.2.debug, debug64(ld-linux-x86-64.so.2), debug64(libX11.so.6), debug64(libXmu.so.6), debug64(libXt.so.6), debug64(libbz2.so.1), debug64(libc.so.6), debug64(libcairo.so.2), debug64(libcurl.so.4), debug64(libdl.so.2), debug64(libgobject-2.0.so.0), 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-3.5.3-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.YLZXNo find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.hdrvap find-requires: running scripts (debuginfo) Requires: R-tcltk = 3.5.3-alt1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so) Adding to R-devel a strict dependency on R-base Adding to R-tcltk a strict dependency on R-base Adding to R-doc-html a strict dependency on R-base Adding to R-base-debuginfo a strict dependency on R-base Adding to R-full a strict dependency on R-devel Adding to R-full a strict dependency on R-tcltk Adding to R-full a strict dependency on R-doc-html Adding to R-tcltk-debuginfo a strict dependency on R-tcltk Adding to R-devel a strict dependency on R-base Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo also prunning dir /usr/src/debug/R-3.5.3/include/R_ext also prunning dir /usr/src/debug/R-3.5.3/src/include also prunning dir /usr/src/debug/R-3.5.3/include Removing 1 extra deps from R-devel due to dependency on R-base Removing 1 extra deps from R-tcltk due to dependency on R-base Removing 1 extra deps from R-tcltk-debuginfo due to dependency on R-base-debuginfo Removing 2 extra deps from R-devel due to repentancy on R-base Removing 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-3.5.3-alt1.x86_64.rpm Wrote: /usr/src/RPM/RPMS/noarch/R-full-3.5.3-alt1.noarch.rpm Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-3.5.3-alt1.x86_64.rpm Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-3.5.3-alt1.x86_64.rpm Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-3.5.3-alt1.noarch.rpm Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-3.5.3-alt1.noarch.rpm Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-3.5.3-alt1.noarch.rpm Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-3.5.3-alt1.x86_64.rpm Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-3.5.3-alt1.x86_64.rpm 1062.30user 69.45system 9:42.79elapsed 194%CPU (0avgtext+0avgdata 362596maxresident)k 0inputs+0outputs (0major+20510600minor)pagefaults 0swaps 1177.61user 81.96system 11:53.31elapsed 176%CPU (0avgtext+0avgdata 362596maxresident)k 1588360inputs+0outputs (0major+21959551minor)pagefaults 0swaps --- R-base-3.5.3-alt1.x86_64.rpm.repo 2019-04-12 06:29:11.000000000 +0000 +++ R-base-3.5.3-alt1.x86_64.rpm.hasher 2020-12-06 03:15:51.242803700 +0000 @@ -4357,4 +4357,4 @@ Requires: libgobject-2.0.so.0()(64bit) >= set:ml6W90 -Requires: libicui18n.so.64()(64bit) >= set:rouin2ooZp9tgudEa9b7dNJZ60 -Requires: libicuuc.so.64()(64bit) >= set:pmj2RkjF3gfi2hEq1 +Requires: libicui18n.so.65()(64bit) >= set:rolIY5WucOij1kVmNEZ6KImTd0 +Requires: libicuuc.so.65()(64bit) >= set:pmfKgUVR3uSC2LbF2 Requires: libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0 --- R-base-debuginfo-3.5.3-alt1.x86_64.rpm.repo 2019-04-12 06:29:11.000000000 +0000 +++ R-base-debuginfo-3.5.3-alt1.x86_64.rpm.hasher 2020-12-06 03:15:51.440803774 +0000 @@ -639,4 +639,4 @@ Requires: debug64(libgobject-2.0.so.0) -Requires: debug64(libicui18n.so.64) -Requires: debug64(libicuuc.so.64) +Requires: debug64(libicui18n.so.65) +Requires: debug64(libicuuc.so.65) Requires: debug64(libjpeg.so.62)