<86>Sep 29 12:13:27 userdel[924499]: delete user 'rooter' <86>Sep 29 12:13:27 userdel[924499]: removed group 'rooter' owned by 'rooter' <86>Sep 29 12:13:27 userdel[924499]: removed shadow group 'rooter' owned by 'rooter' <86>Sep 29 12:13:27 groupadd[924543]: group added to /etc/group: name=rooter, GID=1304 <86>Sep 29 12:13:27 groupadd[924543]: group added to /etc/gshadow: name=rooter <86>Sep 29 12:13:27 groupadd[924543]: new group: name=rooter, GID=1304 <86>Sep 29 12:13:27 useradd[924560]: new user: name=rooter, UID=1304, GID=1304, home=/root, shell=/bin/bash <86>Sep 29 12:13:27 userdel[924597]: delete user 'builder' <86>Sep 29 12:13:27 userdel[924597]: removed group 'builder' owned by 'builder' <86>Sep 29 12:13:27 userdel[924597]: removed shadow group 'builder' owned by 'builder' <86>Sep 29 12:13:27 groupadd[924623]: group added to /etc/group: name=builder, GID=1305 <86>Sep 29 12:13:27 groupadd[924623]: group added to /etc/gshadow: name=builder <86>Sep 29 12:13:27 groupadd[924623]: new group: name=builder, GID=1305 <86>Sep 29 12:13:27 useradd[924645]: new user: name=builder, UID=1305, GID=1305, home=/usr/src, shell=/bin/bash warning: Macro %add_tcl_lib_path not found <13>Sep 29 12:13:43 rpmi: libpng16-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed <13>Sep 29 12:13:43 rpmi: xorg-proto-devel-2021.4-alt1 p9+272150.100.1.1 1621427342 installed <13>Sep 29 12:13:43 rpmi: libjpeg-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed <13>Sep 29 12:13:43 rpmi: libexpat-2.4.3-alt1 p9+293696.100.1.1 1643124786 installed <13>Sep 29 12:13:43 rpmi: perl-Try-Tiny-0.30-alt1 1514318058 installed <13>Sep 29 12:13:43 rpmi: perl-libnet-1:3.11-alt1 1511423541 installed <13>Sep 29 12:13:43 rpmi: javapackages-tools-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed <13>Sep 29 12:13:43 rpmi: perl-Module-Runtime-0.016-alt1 1509549848 installed <13>Sep 29 12:13:43 rpmi: perl-HTTP-Date-6.02-alt1 1348645274 installed <13>Sep 29 12:13:43 rpmi: perl-Term-ANSIColor-4.06-alt1 1479407083 installed <13>Sep 29 12:13:43 rpmi: libICE-1.0.9-alt1 1409902719 installed <13>Sep 29 12:13:43 rpmi: libgdbm-1.8.3-alt10 1454943313 installed <13>Sep 29 12:13:43 rpmi: libSM-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed <13>Sep 29 12:13:43 rpmi: libglvnd-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:43 rpmi: tex-common-0.2-alt4 1244804096 installed <13>Sep 29 12:13:43 rpmi: libopenblas-0.3.9-alt2 p9+274919.40.2.1 1624305203 installed <13>Sep 29 12:13:43 rpmi: perl-Unicode-Normalize-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Sep 29 12:13:43 rpmi: libpaper-1.1.26-alt1 sisyphus+221360.100.1.1 1549974198 installed <13>Sep 29 12:13:43 rpmi: libidn2-2.2.0-alt1 p9+229971.100.2.1 1558696275 installed <13>Sep 29 12:13:43 rpmi: psutils-2:1.23-alt2 sisyphus+226711.100.1.1 1554520810 installed <13>Sep 29 12:13:43 rpmi: perl-Dist-CheckConflicts-0.11-alt1 1397076608 installed <13>Sep 29 12:13:43 rpmi: perl-Module-Implementation-0.09-alt1 1418836057 installed <13>Sep 29 12:13:43 rpmi: libjasper-2.0.22-alt1 p9+259398.100.5.1 1602695042 installed <13>Sep 29 12:13:43 rpmi: rpm-macros-info-install-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Sep 29 12:13:43 rpmi: zlib-devel-1.2.11-alt1 sisyphus+221902.6000.4.1 1550600768 installed <13>Sep 29 12:13:43 rpmi: liblksctp-1.0.17-alt2 1523113258 installed <13>Sep 29 12:13:43 rpmi: libnspr-1:4.35-alt1 p9+319683.300.1.1 1683030815 installed <13>Sep 29 12:13:43 rpmi: libpixman-3:0.38.4-alt1 sisyphus+228006.100.1.1 1556013486 installed <13>Sep 29 12:13:43 rpmi: libwayland-server-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed <13>Sep 29 12:13:43 rpmi: libtcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Sep 29 12:13:43 rpmi: tcl-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Sep 29 12:13:43 rpmi: libsqlite3-3.33.0-alt1 p9+258834.40.2.1 1601364885 installed <13>Sep 29 12:13:43 rpmi: python-module-sphinxcontrib-2.1.1-alt2.1.2 sisyphus+227529.1100.1.2 1555924423 installed <13>Sep 29 12:13:43 rpmi: perl-Text-Unidecode-1.30-alt1 1480505027 installed <13>Sep 29 12:13:43 rpmi: perl-IO-stringy-2.111-alt1 1432302202 installed <13>Sep 29 12:13:43 rpmi: perl-Devel-StackTrace-1:2.03-alt1 1511420922 installed <13>Sep 29 12:13:43 rpmi: perl-Sub-Exporter-Progressive-0.001013-alt1 1479395404 installed <13>Sep 29 12:13:43 rpmi: perl-File-Which-1.23-alt1 sisyphus.218871.100 1546337313 installed <13>Sep 29 12:13:43 rpmi: perl-Tie-RefHash-1.39-alt1 1316492563 installed <13>Sep 29 12:13:43 rpmi: perl-TimeDate-2.32-alt1 p9+252601.500.11.1 1592659283 installed <13>Sep 29 12:13:43 rpmi: perl-IO-Socket-IP-0.39-alt1 1494508514 installed <13>Sep 29 12:13:43 rpmi: perl-LWP-MediaTypes-6.04-alt1 sisyphus+225468.100.1.1 1553186684 installed <13>Sep 29 12:13:43 rpmi: perl-Compress-Raw-Zlib-2.086-alt1 sisyphus+226395.100.1.2 1554269783 installed <13>Sep 29 12:13:43 rpmi: perl-HTML-Tagset-3.20-alt2 1317725093 installed <13>Sep 29 12:13:43 rpmi: libXau-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed <13>Sep 29 12:13:44 rpmi: libwebp7-1.0.3-alt1 p9+234901.200.1.1 1563552213 installed <13>Sep 29 12:13:44 rpmi: libjbig-2.1-alt1 1401380921 installed <13>Sep 29 12:13:44 rpmi: libtiff5-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed <13>Sep 29 12:13:44 rpmi: libopenjpeg2.0-2.3.1-alt1 sisyphus+226454.100.1.1 1554284336 installed <13>Sep 29 12:13:44 rpmi: libnettle6-3.4.1-alt1 sisyphus+226533.100.2.1 1554512181 installed <13>Sep 29 12:13:44 rpmi: libquadmath0-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:44 rpmi: libgfortran5-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:44 rpmi: libicu65-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed <13>Sep 29 12:13:44 rpmi: libgraphite2-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed <13>Sep 29 12:13:45 rpmi: libharfbuzz-2.8.1-alt1 p9+319683.500.4.1 1689082543 installed <13>Sep 29 12:13:45 rpmi: libfreetype-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed <13>Sep 29 12:13:45 rpmi: fontconfig-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed Updating fonts cache: <29>Sep 29 12:13:46 fontconfig: Updating fonts cache: succeeded [ DONE ] <13>Sep 29 12:13:46 rpmi: libp11-kit-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed <13>Sep 29 12:13:46 rpmi: libtasn1-4.14-alt1 p9+235792.100.2.1 1565425233 installed <13>Sep 29 12:13:46 rpmi: fonts-type1-urw-3:1.0.7pre44-alt3 sisyphus+224082.100.2.1 1552406640 installed <13>Sep 29 12:13:46 rpmi: fonts-type1-xorg-7.0.0-alt4 1188553211 installed <13>Sep 29 12:13:46 rpmi: libharfbuzz-icu-2.8.1-alt1 p9+319683.500.4.1 1689082543 installed <13>Sep 29 12:13:46 rpmi: libharfbuzz-gobject-2.8.1-alt1 p9+319683.500.4.1 1689082543 installed <13>Sep 29 12:13:46 rpmi: libgraphite2-devel-1.3.13-alt2 sisyphus+226799.100.1.1 1554648233 installed <13>Sep 29 12:13:46 rpmi: icu-utils-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed <13>Sep 29 12:13:46 rpmi: libicu-devel-1:6.5.1-alt2 p9+270410.100.1.1 1619007054 installed <13>Sep 29 12:13:46 rpmi: libquadmath8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:46 rpmi: libhogweed4-3.4.1-alt1 sisyphus+226533.100.2.1 1554512181 installed <13>Sep 29 12:13:46 rpmi: libgnutls30-3.6.16-alt6 p9+345962.100.2.1 1715786186 installed <13>Sep 29 12:13:46 rpmi: libXau-devel-1.0.9-alt1 sisyphus+223149.200.2.1 1551268156 installed <13>Sep 29 12:13:46 rpmi: perl-autodie-2.29-alt1 1445013559 installed <13>Sep 29 12:13:46 rpmi: perl-File-HomeDir-1.004-alt1 1525450444 installed <13>Sep 29 12:13:46 rpmi: perl-Devel-GlobalDestruction-1:0.14-alt1 1479389769 installed <13>Sep 29 12:13:46 rpmi: perl-OLE-Storage_Lite-0.20-alt1 p9+252601.400.11.1 1592659257 installed <13>Sep 29 12:13:46 rpmi: lksctp-tools-1.0.17-alt2 1523113258 installed <13>Sep 29 12:13:46 rpmi: libpng-devel-1.6.36-alt1 sisyphus+219478.100.1.1 1547633315 installed <13>Sep 29 12:13:46 rpmi: perl-unicore-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Sep 29 12:13:46 rpmi: perl-Net-IDN-Encode-2.500-alt1 sisyphus+221481.100.1.1 1550127189 installed <13>Sep 29 12:13:47 rpmi: libopenblas-devel-0.3.9-alt2 p9+274919.40.2.1 1624305203 installed <13>Sep 29 12:13:47 rpmi: libOpenGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:47 rpmi: libgdbm-devel-1.8.3-alt10 1454943313 installed <13>Sep 29 12:13:47 rpmi: libICE-devel-1.0.9-alt1 1409902719 installed <13>Sep 29 12:13:47 rpmi: libSM-devel-1.2.3-alt1 sisyphus+226734.100.2.1 1554586157 installed <13>Sep 29 12:13:47 rpmi: perl-Data-Dump-1.23-alt1 1444601978 installed <13>Sep 29 12:13:47 rpmi: perl-File-Listing-6.04-alt1 1329758996 installed <13>Sep 29 12:13:47 rpmi: java-common-1.6.0-alt1 p9+234085.100.1.1 1562573623 installed <13>Sep 29 12:13:47 rpmi: rpm-build-tcl-0.5.1-alt1 1519671307 installed <13>Sep 29 12:13:47 rpmi: tcl-devel-8.6.9-alt1 sisyphus+227145.100.1.2 1555606523 installed <13>Sep 29 12:13:47 rpmi: rpm-macros-java-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed <13>Sep 29 12:13:47 rpmi: perl-Algorithm-Diff-1.1903-alt1 1418755800 installed <13>Sep 29 12:13:47 rpmi: perl-Unicode-EastAsianWidth-1.40-alt1 sisyphus.217785.100 1544703272 installed <13>Sep 29 12:13:47 rpmi: libtre5-0.8.0-alt2.1 1334590818 installed <13>Sep 29 12:13:47 rpmi: libpcre16-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Sep 29 12:13:47 rpmi: pcretest-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Sep 29 12:13:47 rpmi: libgomp1-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:47 rpmi: libpcsclite-1.9.5-alt1 p9+294972.100.1.1 1644252424 installed <13>Sep 29 12:13:47 rpmi: javazi-2022d-alt1 p9+309237.200.1.1 1667106831 installed <13>Sep 29 12:13:47 rpmi: libgif-4.1.6-alt3 1299634266 installed <13>Sep 29 12:13:47 rpmi: libgtk+2-locales-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Sep 29 12:13:47 rpmi: libfribidi-1.0.7-alt1 p9+238309.200.1.1 1569787041 installed <13>Sep 29 12:13:47 rpmi: libatk-locales-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed <13>Sep 29 12:13:47 rpmi: libatk-2.32.0-alt1 sisyphus+225059.600.3.2 1552845198 installed <13>Sep 29 12:13:47 rpmi: icon-theme-hicolor-0.17-alt2 p9+248347.100.1.1 1584981172 installed <13>Sep 29 12:13:47 rpmi: shared-mime-info-1.13.1-alt1 p9+238204.100.1.1 1569496447 installed <13>Sep 29 12:13:47 rpmi: libgdk-pixbuf-locales-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed <13>Sep 29 12:13:47 rpmi: gsettings-desktop-schemas-data-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed <13>Sep 29 12:13:47 rpmi: libgio-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed <13>Sep 29 12:13:47 rpmi: gsettings-desktop-schemas-3.32.0-alt1 sisyphus+225059.300.3.2 1552843929 installed <13>Sep 29 12:13:47 rpmi: libgdk-pixbuf-2.38.2-alt1 p9+237353.1000.2.2 1568374008 installed <13>Sep 29 12:13:47 rpmi: gtk-update-icon-cache-3.24.29-alt0.M90P.1 p9+277455.200.2.1 1625582389 installed <13>Sep 29 12:13:47 rpmi: libkpathsea6-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Sep 29 12:13:47 rpmi: libptexenc1-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Sep 29 12:13:47 rpmi: libsynctex2-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Sep 29 12:13:47 rpmi: libtexlua5-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Sep 29 12:13:47 rpmi: zziplib-0.13.69-alt3 p9+240930.100.1.1 1574080033 installed <13>Sep 29 12:13:47 rpmi: liblcms2-2.9-alt1 1516411888 installed <13>Sep 29 12:13:48 rpmi: publicsuffix-list-dafsa-20240701-alt1 p9+352084.100.2.1 1720247829 installed <13>Sep 29 12:13:48 rpmi: libpsl-0.21.1-alt3 p9+308015.200.2.1 1670864661 installed <13>Sep 29 12:13:48 rpmi: libnghttp2-1.41.0-alt1 p9+256449.100.1.1 1597829543 installed <13>Sep 29 12:13:48 rpmi: openldap-common-2.4.59-alt0.p9.1 p9+281540.300.5.1 1629898589 installed <13>Sep 29 12:13:48 rpmi: libbrotlicommon-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed <13>Sep 29 12:13:48 rpmi: libbrotlidec-1.0.7-alt1 sisyphus+226738.100.2.1 1554554565 installed <13>Sep 29 12:13:48 rpmi: poppler-data-0.4.9-alt1 sisyphus.216033.100 1541141723 installed <13>Sep 29 12:13:49 rpmi: libicu64-1:6.4.2-alt3 p9+270873.100.1.1 1619612690 installed <13>Sep 29 12:13:49 rpmi: libxshmfence-1.3-alt1 sisyphus+223149.1000.2.1 1551268594 installed <13>Sep 29 12:13:49 rpmi: libwayland-client-1.18.0-alt1 p9+260591.100.12.1 1606212847 installed <13>Sep 29 12:13:49 rpmi: libpciaccess-1:0.14-alt1 1528969624 installed <13>Sep 29 12:13:49 rpmi: libdrm-1:2.4.105-alt2 p9+271012.100.1.1 1619786664 installed <13>Sep 29 12:13:49 rpmi: libgbm-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed <13>Sep 29 12:13:49 rpmi: t1utils-1.41-alt1 1502978415 installed <13>Sep 29 12:13:49 rpmi: ttf2pt1-3.4.4-alt1.qa1 1366267504 installed <13>Sep 29 12:13:49 rpmi: libqqwing-1.3.4-alt2 1436192940 installed <13>Sep 29 12:13:49 rpmi: qqwing-1.3.4-alt2 1436192940 installed <13>Sep 29 12:13:49 rpmi: python-module-iniconfig-1.0.0-alt1 sisyphus+227494.1100.1.3 1555839106 installed <13>Sep 29 12:13:49 rpmi: python-module-apipkg-1.5-alt1 1531926894 installed <13>Sep 29 12:13:49 rpmi: python-module-imagesize-1.1.0-alt1 sisyphus+229015.100.2.1 1557233756 installed <13>Sep 29 12:13:49 rpmi: python-sphinx-objects.inv-1:2.3.8.20190514-alt1 p9+229421.100.1.1 1557927689 installed <13>Sep 29 12:13:49 rpmi: libxapian-1.4.15-alt1 p9+258827.100.1.1 1601305414 installed <13>Sep 29 12:13:49 rpmi: python-module-google-0.4.2-alt2.1 sisyphus+228356.1500.3.1 1556633038 installed <13>Sep 29 12:13:49 rpmi: python-module-markupsafe-1.1.1-alt1 p9+254838.60.14.1 1602882123 installed <13>Sep 29 12:13:49 rpmi: python-module-enum34-1.1.6-alt3 1527251693 installed <13>Sep 29 12:13:49 rpmi: libnumpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed <13>Sep 29 12:13:49 rpmi: libxblas-1.0.248-alt1.3 sisyphus+229150.100.1.1 1557388758 installed <13>Sep 29 12:13:49 rpmi: liblapack-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed <13>Sep 29 12:13:49 rpmi: python-modules-curses-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:49 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed <13>Sep 29 12:13:49 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed <13>Sep 29 12:13:49 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed <13>Sep 29 12:13:49 rpmi: libdatrie-0.2.9-alt1_6 1511686677 installed <13>Sep 29 12:13:49 rpmi: libthai-0.1.28-alt1_1 sisyphus+226107.100.1.1 1554123079 installed <13>Sep 29 12:13:49 rpmi: libsombok-2.4.0-alt1_8 sisyphus+226104.100.1.1 1554121176 installed <13>Sep 29 12:13:49 rpmi: perl-Unicode-Map-0.112-alt7.1 sisyphus+219907.5000.1.1 1548349925 installed <13>Sep 29 12:13:49 rpmi: perl-Digest-Perl-MD5-1.9-alt1 1394057208 installed <13>Sep 29 12:13:49 rpmi: perl-Crypt-RC4-2.02-alt1 1319549646 installed <13>Sep 29 12:13:49 rpmi: perl-Math-Complex-1.59-alt1 1334229876 installed <13>Sep 29 12:13:49 rpmi: perl-XML-RegExp-0.04-alt1 1348526543 installed <13>Sep 29 12:13:49 rpmi: perl-DBI-1.642-alt1.1 sisyphus+219907.3200.1.1 1548345175 installed <13>Sep 29 12:13:49 rpmi: perl-Package-Stash-XS-0.29-alt1.1 sisyphus+219907.3400.1.1 1548345296 installed <13>Sep 29 12:13:49 rpmi: perl-Package-Stash-0.38-alt1 sisyphus.218845.100 1546250118 installed <13>Sep 29 12:13:49 rpmi: perl-Sub-Identify-0.14-alt1.2 sisyphus+219907.3700.1.1 1548345423 installed <13>Sep 29 12:13:49 rpmi: perl-Variable-Magic-0.62-alt1.2 sisyphus+219907.3600.1.1 1548345381 installed <13>Sep 29 12:13:49 rpmi: perl-B-Hooks-EndOfScope-0.24-alt1 1524680298 installed <13>Sep 29 12:13:49 rpmi: perl-namespace-clean-0.27-alt1 1464272543 installed <13>Sep 29 12:13:49 rpmi: perl-namespace-autoclean-0.28-alt1 1444994071 installed <13>Sep 29 12:13:49 rpmi: perl-Sub-Quote-2.006003-alt1 sisyphus+224895.100.1.1 1552434926 installed <13>Sep 29 12:13:49 rpmi: perl-Role-Tiny-2.000006-alt1 1513709006 installed <13>Sep 29 12:13:49 rpmi: perl-MRO-Compat-0.13-alt2 p9+261964.200.3.1 1606316246 installed <13>Sep 29 12:13:49 rpmi: perl-Class-Data-Inheritable-0.08-alt2 1316996762 installed <13>Sep 29 12:13:49 rpmi: perl-Exception-Class-1.44-alt1 1513614520 installed <13>Sep 29 12:13:49 rpmi: perl-PadWalker-2.3-alt1.2 sisyphus+219907.3500.1.1 1548345336 installed <13>Sep 29 12:13:49 rpmi: perl-Devel-Caller-2.06-alt2.2 sisyphus+219907.4000.1.1 1548345464 installed <13>Sep 29 12:13:49 rpmi: perl-Devel-LexAlias-0.05-alt3_17 sisyphus+219907.4100.1.1 1548345510 installed <13>Sep 29 12:13:49 rpmi: perl-Eval-Closure-0.14-alt1 1465147597 installed <13>Sep 29 12:13:49 rpmi: perl-Params-ValidationCompiler-0.30-alt1 1533170707 installed <13>Sep 29 12:13:49 rpmi: perl-Mail-Sendmail-0.80-alt1 1504118031 installed <13>Sep 29 12:13:49 rpmi: perl-Mail-Sender-1:0.903-alt1 1479576662 installed <13>Sep 29 12:13:49 rpmi: perl-Email-Date-Format-1.005-alt1 1413796337 installed <13>Sep 29 12:13:49 rpmi: ppp-common-0.5.1-alt1 1244040597 installed <13>Sep 29 12:13:49 rpmi: sendmail-common-1.7-alt3 1353029717 installed <13>Sep 29 12:13:49 rpmi: perl-Locale-Maketext-Simple-0.21-alt3 1321333616 installed <13>Sep 29 12:13:49 rpmi: perl-IPC-System-Simple-1.25-alt2_1 1388863478 installed <13>Sep 29 12:13:49 rpmi: perl-Term-Cap-1.17-alt1 1445018869 installed <13>Sep 29 12:13:49 rpmi: perl-Pod-Escapes-1.07-alt1 1418767892 installed <13>Sep 29 12:13:49 rpmi: perl-File-Copy-Recursive-0.44-alt1 1525447381 installed <13>Sep 29 12:13:49 rpmi: perl-Digest-SHA1-2.13-alt5.2 sisyphus+219907.4500.1.1 1548349730 installed <13>Sep 29 12:13:49 rpmi: less-530-alt1 sisyphus+226367.200.2.2 1554151813 installed <13>Sep 29 12:13:49 rpmi: perl-Compress-Raw-Bzip2-2.086-alt1 sisyphus+226394.100.1.2 1554269409 installed <13>Sep 29 12:13:49 rpmi: libdb4.7-devel-4.7.25-alt9 1490438456 installed <13>Sep 29 12:13:49 rpmi: perl-devel-1:5.28.3-alt1 p9+261964.100.3.1 1606316185 installed <13>Sep 29 12:13:49 rpmi: perl-Test-Fatal-0.014-alt1 1418768336 installed <13>Sep 29 12:13:49 rpmi: perl-Specio-0.43-alt1 sisyphus.215861.100 1540964587 installed <13>Sep 29 12:13:49 rpmi: hd2u-1.0.3-alt2 1400842666 installed <13>Sep 29 12:13:49 rpmi: perl-Filter-1.59-alt1.1 sisyphus+219907.400.1.1 1548343225 installed <13>Sep 29 12:13:49 rpmi: perl-Encode-3.01-alt1 sisyphus+224923.100.1.1 1552474113 installed <13>Sep 29 12:13:49 rpmi: perl-URI-1.76-alt1 sisyphus+220243.100.1.1 1548863244 installed <13>Sep 29 12:13:49 rpmi: perl-HTML-Parser-3.72-alt1.2 sisyphus+219907.600.1.1 1548343407 installed <13>Sep 29 12:13:49 rpmi: perl-IO-Compress-2.086-alt1 sisyphus+226399.100.2.1 1554270186 installed <13>Sep 29 12:13:49 rpmi: perl-Net-HTTP-6.18-alt1 1526560501 installed <13>Sep 29 12:13:49 rpmi: perl-Pod-Simple-3.35-alt1 1482098090 installed <13>Sep 29 12:13:49 rpmi: perl-Pod-Usage-1.69-alt1 1464274721 installed <13>Sep 29 12:13:49 rpmi: perl-podlators-4.11-alt1 1525935408 installed <13>Sep 29 12:13:49 rpmi: perl-WWW-RobotRules-6.02-alt1 1329756211 installed <13>Sep 29 12:13:49 rpmi: perl-Encode-Locale-1.05-alt1 1444608613 installed <13>Sep 29 12:13:49 rpmi: perl-IO-HTML-1.001-alt1 1404821752 installed <13>Sep 29 12:13:49 rpmi: perl-HTTP-Message-6.18-alt1 1528288416 installed <13>Sep 29 12:13:49 rpmi: perl-HTTP-Cookies-6.04-alt1 1504116575 installed <13>Sep 29 12:13:49 rpmi: perl-HTTP-Negotiate-6.01-alt1 1329760563 installed <13>Sep 29 12:13:50 rpmi: perl-libwww-6.39-alt1 sisyphus+229237.100.1.1 1557650051 installed <13>Sep 29 12:13:50 rpmi: perl-XML-Parser-2.44-alt2.2 sisyphus+219907.1300.1.1 1548343654 installed <13>Sep 29 12:13:50 rpmi: perl-HTML-Tree-5.07-alt1 1506480309 installed <13>Sep 29 12:13:50 rpmi: perl-HTML-Formatter-2.16-alt1 1482105372 installed <13>Sep 29 12:13:50 rpmi: perl-XML-DOM-1.46-alt1 1474815568 installed <13>Sep 29 12:13:50 rpmi: perl-XML-XPath-1.44-alt1 sisyphus.215541.100 1540451758 installed <13>Sep 29 12:13:50 rpmi: perl-HTML-Form-6.04-alt1 sisyphus+225750.100.1.1 1553678430 installed <13>Sep 29 12:13:50 rpmi: perl-WWW-Mechanize-1.91-alt1 sisyphus+219761.100.1.2 1548132822 installed <13>Sep 29 12:13:50 rpmi: perl-XML-Writer-0.625-alt1 1402417374 installed <13>Sep 29 12:13:50 rpmi: hwinfo-utils-21.23-alt1.1 sisyphus+223919.100.1.1 1551893088 installed <13>Sep 29 12:13:50 rpmi: perl-MIME-Types-2.17-alt1 1517533413 installed <13>Sep 29 12:13:50 rpmi: perl-Text-CSV_XS-1.39-alt1 sisyphus+225184.100.1.2 1552965519 installed <13>Sep 29 12:13:50 rpmi: perl-Spreadsheet-ParseExcel-1:0.65-alt1 1395677487 installed <13>Sep 29 12:13:50 rpmi: perl-MIME-Charset-1.012.2-alt1 1494353584 installed <13>Sep 29 12:13:50 rpmi: perl-Unicode-LineBreak-2019.001-alt1.1 sisyphus+219907.4700.1.1 1548349872 installed <13>Sep 29 12:13:50 rpmi: perl-YAML-Tiny-1.73-alt1 1520430664 installed <13>Sep 29 12:13:50 rpmi: perl-libintl-1.31-alt1.1 sisyphus+219907.6300.1.1 1548352427 installed <13>Sep 29 12:13:50 rpmi: libteckit-2.5.1-alt2.1 1319227424 installed <13>Sep 29 12:13:50 rpmi: libteckit-utils-2.5.1-alt2.1 1319227424 installed <13>Sep 29 12:13:50 rpmi: rgb-1.0.6-alt3 p9+229442.100.1.1 1557941137 installed <13>Sep 29 12:13:50 rpmi: libnetpbm11-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed <13>Sep 29 12:13:50 rpmi: mailx-8.1.2-alt7 1366314831 installed <13>Sep 29 12:13:50 rpmi: sharutils-4.6.3-alt1.1.qa2.1 1449219807 installed <13>Sep 29 12:13:50 rpmi: ncompress-4.2.4.4-alt1 1366160439 installed <13>Sep 29 12:13:50 rpmi: libX11-locales-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed <13>Sep 29 12:13:50 rpmi: libXdmcp-1.1.3-alt1 sisyphus+225206.600.1.2 1552949347 installed <13>Sep 29 12:13:50 rpmi: libxcb-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed <13>Sep 29 12:13:50 rpmi: libX11-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed <13>Sep 29 12:13:50 rpmi: libXext-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed <13>Sep 29 12:13:50 rpmi: libXrender-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed <13>Sep 29 12:13:50 rpmi: libXt-1.1.4-alt1 1369984716 installed <13>Sep 29 12:13:50 rpmi: libXmu-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed <13>Sep 29 12:13:50 rpmi: libXft-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed <13>Sep 29 12:13:50 rpmi: libXfixes-5.0.3-alt1 sisyphus+226736.100.2.2 1554614842 installed <13>Sep 29 12:13:50 rpmi: libXpm-3.5.12-alt1 sisyphus+223149.400.2.1 1551268300 installed <13>Sep 29 12:13:50 rpmi: libXi-1.7.9-alt2 sisyphus+226377.100.1.2 1554260258 installed <13>Sep 29 12:13:50 rpmi: libXcomposite-0.4.5-alt1 sisyphus+225206.300.1.2 1552949136 installed <13>Sep 29 12:13:51 rpmi: libxcb-devel-1.13.1-alt1 sisyphus+226527.100.2.2 1554593799 installed <13>Sep 29 12:13:52 rpmi: libX11-devel-3:1.7.2-alt1 p9+273972.100.2.1 1623924318 installed <13>Sep 29 12:13:52 rpmi: libXrender-devel-0.9.10-alt1 p9+261891.200.2.1 1606149106 installed <13>Sep 29 12:13:52 rpmi: libXext-devel-1.3.4-alt1 sisyphus+225206.700.1.2 1552949422 installed <13>Sep 29 12:13:52 rpmi: libXt-devel-1.1.4-alt1 1369984716 installed <13>Sep 29 12:13:52 rpmi: libXaw-1.0.12-alt1 1391072621 installed <13>Sep 29 12:13:52 rpmi: libgd3-2.2.5-alt3 sisyphus+226800.200.2.1 1554649314 installed <13>Sep 29 12:13:52 rpmi: libXcursor-1.2.0-alt1 sisyphus+225206.400.1.2 1552949214 installed <13>Sep 29 12:13:52 rpmi: perl-Tk-804.034-alt1.2 sisyphus+219907.4300.1.1 1548345831 installed <13>Sep 29 12:13:52 rpmi: libtk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Sep 29 12:13:52 rpmi: tk-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Sep 29 12:13:52 rpmi: xset-1.2.4-alt1 sisyphus.213358.100 1537438593 installed <13>Sep 29 12:13:52 rpmi: libXrandr-1.5.2-alt1 sisyphus+225206.1300.1.2 1552949698 installed <13>Sep 29 12:13:52 rpmi: libXxf86vm-1.1.4-alt2 1527672159 installed <13>Sep 29 12:13:52 rpmi: libGLX-mesa-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed <13>Sep 29 12:13:52 rpmi: libEGL-mesa-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed <13>Sep 29 12:13:52 rpmi: libEGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:52 rpmi: libGLX-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:52 rpmi: libGL-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:52 rpmi: libcairo-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed <13>Sep 29 12:13:52 rpmi: libpango-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed <13>Sep 29 12:13:52 rpmi: libglvnd-devel-7:1.3.2-alt0.p9 p9+265957.240.8.1 1617618104 installed <13>Sep 29 12:13:52 rpmi: libEGL-devel-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed <13>Sep 29 12:13:52 rpmi: libGL-devel-4:21.0.3-alt1 p9+271012.200.3.1 1621244963 installed <13>Sep 29 12:13:52 rpmi: libXinerama-1.1.4-alt1 sisyphus+223149.300.2.1 1551268223 installed <13>Sep 29 12:13:52 rpmi: libXtst-1.2.3-alt1 p9+261891.100.2.1 1606149065 installed <13>Sep 29 12:13:52 rpmi: netpbm-10.85.04-alt1 sisyphus+225727.140.8.1 1553672201 installed <13>Sep 29 12:13:52 rpmi: libXdamage-1.1.5-alt1 sisyphus+225206.500.1.2 1552949282 installed <13>Sep 29 12:13:52 rpmi: xprop-1.2.4-alt1 sisyphus+225764.100.1.1 1553680701 installed <13>Sep 29 12:13:52 rpmi: xdg-utils-1.1.3-alt7 p9+259359.100.1.1 1602061025 installed <13>Sep 29 12:13:52 rpmi: liblz4-1:1.9.2-alt1 p9+238696.500.1.1 1570228072 installed <13>Sep 29 12:13:52 rpmi: libgpg-error-1.36-alt1 p9+261942.140.4.1 1606237682 installed <13>Sep 29 12:13:52 rpmi: libgcrypt20-1.8.5-alt3 p9+261942.200.4.1 1606237844 installed <13>Sep 29 12:13:52 rpmi: libxslt-1.1.34-alt1.p9.1 p9+261811.300.3.1 1605513910 installed <13>Sep 29 12:13:52 rpmi: libsystemd-1:247.13-alt1 p9+313189.100.1.1 1673457063 installed <13>Sep 29 12:13:52 rpmi: libdbus-1.12.16-alt2 p9+240607.100.1.1 1573553670 installed <13>Sep 29 12:13:52 rpmi: libavahi-0.8-alt2 p9+270905.100.1.1 1619639855 installed <13>Sep 29 12:13:52 rpmi: libcups-2.3.3-alt7.op2 p9+289603.100.2.1 1637911367 installed <13>Sep 29 12:13:53 rpmi: libgtk+2-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Sep 29 12:13:53 rpmi: libgail-2.24.32-alt3 sisyphus+227306.100.1.3 1555646039 installed <13>Sep 29 12:13:54 rpmi: libgs-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Sep 29 12:13:54 rpmi: ghostscript-common-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Sep 29 12:13:54 rpmi: ghostscript-classic-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Sep 29 12:13:54 rpmi: ghostscript-module-X-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Sep 29 12:13:54 rpmi: gcc-fortran-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed <13>Sep 29 12:13:54 rpmi: libgfortran8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:55 rpmi: gcc8-fortran-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:55 rpmi: gcc-c++-common-1.4.23-alt1 sisyphus+221902.2500.4.1 1550596716 installed <13>Sep 29 12:13:55 rpmi: libstdc++8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:56 rpmi: gcc8-c++-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:13:56 rpmi: xml-utils-1:2.9.10-alt6.p9.1 p9+314487.100.1.1 1675223837 installed <13>Sep 29 12:13:56 rpmi: rpm-build-gir-0.7.3-alt2 p9+234356.40.2.1 1562933848 installed <13>Sep 29 12:13:56 rpmi: ed-1:0.2-alt10 1449768441 installed <13>Sep 29 12:13:56 rpmi: libdialog-1.3.20171209-alt1 1529583087 installed <13>Sep 29 12:13:56 rpmi: dialog-1.3.20171209-alt1 1529583087 installed <13>Sep 29 12:13:57 rpmi: libruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:13:57 rpmi: libyaml2-0.2.2-alt1 sisyphus+229134.100.1.1 1557342720 installed <13>Sep 29 12:13:57 rpmi: bc-1:1.07.1-alt1 sisyphus+221902.700.4.1 1550587848 installed <13>Sep 29 12:13:57 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Sep 29 12:13:57 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed <13>Sep 29 12:13:57 rpmi: libnss-3.86-alt1 p9+319683.400.4.1 1689082394 installed <13>Sep 29 12:13:57 rpmi: ca-certificates-2021.10.06-alt1 p9+289862.100.1.1 1637033643 installed <13>Sep 29 12:13:57 rpmi: ca-trust-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed <13>Sep 29 12:13:57 rpmi: p11-kit-trust-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed <13>Sep 29 12:13:57 rpmi: libcrypto1.1-1.1.1w-alt0.p9.1 p9+356668.100.1.1 1725304346 installed <13>Sep 29 12:13:57 rpmi: libssl1.1-1.1.1w-alt0.p9.1 p9+356668.100.1.1 1725304346 installed <13>Sep 29 12:13:57 rpmi: libpython3-3.7.17-alt2 p9+350963.100.1.1 1718376947 installed <13>Sep 29 12:13:57 rpmi: python3-3.7.17-alt2 p9+350963.100.1.1 1718376947 installed <13>Sep 29 12:13:58 rpmi: python3-base-3.7.17-alt2 p9+350963.100.1.1 1718376947 installed <86>Sep 29 12:13:58 groupadd[1026634]: group added to /etc/group: name=_keytab, GID=499 <86>Sep 29 12:13:58 groupadd[1026634]: group added to /etc/gshadow: name=_keytab <86>Sep 29 12:13:58 groupadd[1026634]: new group: name=_keytab, GID=499 <13>Sep 29 12:13:58 rpmi: libkrb5-1.17.2-alt5 p9+325691.100.1.1 1690460821 installed <13>Sep 29 12:13:58 rpmi: glib2-devel-2.60.7-alt1 p9+237353.100.2.2 1568372980 installed <13>Sep 29 12:13:58 rpmi: libfreetype-devel-2.10.1-alt1.1.p9.1 p9+260179.200.3.1 1603971391 installed <13>Sep 29 12:13:58 rpmi: libharfbuzz-devel-2.8.1-alt1 p9+319683.500.4.1 1689082543 installed <13>Sep 29 12:13:58 rpmi: fontconfig-devel-2.13.1-alt1 p9+247340.200.3.1 1583400482 installed <13>Sep 29 12:13:58 rpmi: python3-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed <13>Sep 29 12:13:58 rpmi: libXft-devel-2.3.3-alt1 sisyphus+225206.1000.3.2 1552987714 installed <13>Sep 29 12:13:58 rpmi: libcairo-devel-1:1.16.0-alt1 sisyphus+226534.100.2.3 1554515520 installed <13>Sep 29 12:13:58 rpmi: libtirpc-1.0.3-alt1 1532008015 installed <13>Sep 29 12:13:58 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed <13>Sep 29 12:13:58 rpmi: python-modules-encodings-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:58 rpmi: python-modules-compiler-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:58 rpmi: python-modules-email-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:58 rpmi: python-modules-unittest-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:58 rpmi: python-modules-nis-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-xml-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-ctypes-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-module-six-1.12.0-alt1 sisyphus+219665.100.2.1 1548148570 installed <13>Sep 29 12:13:59 rpmi: python-module-pkg_resources-1:40.8.0-alt2 sisyphus+229158.200.2.1 1557735221 installed <13>Sep 29 12:13:59 rpmi: python-modules-multiprocessing-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-logging-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-json-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-module-jinja2-2.11.2-alt1 p9+254838.40.14.1 1602882082 installed <13>Sep 29 12:13:59 rpmi: python-modules-hotshot-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-module-webencodings-0.5.1-alt1.1 1517943573 installed <13>Sep 29 12:13:59 rpmi: python-module-chardet-3.0.4-alt1 sisyphus+227476.1700.1.2 1555756717 installed <13>Sep 29 12:13:59 rpmi: python-tools-2to3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-module-future-0.16.0-alt2 sisyphus+228356.200.3.3 1556645013 installed <13>Sep 29 12:13:59 rpmi: python-module-pyglet-1.3.0-alt4.a1.hg20150730.1.1.1 1460413686 installed <13>Sep 29 12:13:59 rpmi: python-module-whoosh-2.7.4-alt1 1527697941 installed <13>Sep 29 12:13:59 rpmi: python-modules-bsddb-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-strict-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-modules-distutils-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:13:59 rpmi: python-module-numpy-1:1.15.4-alt5 p9+255957.40.47.1 1599835768 installed <13>Sep 29 12:13:59 rpmi: python-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed <13>Sep 29 12:13:59 rpmi: python-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed <13>Sep 29 12:13:59 rpmi: python-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed <13>Sep 29 12:14:00 rpmi: python-module-docutils-0.14-alt2 1535729778 installed <13>Sep 29 12:14:00 rpmi: python-module-idna-2.8-alt1 sisyphus+227494.400.1.3 1555838720 installed <13>Sep 29 12:14:00 rpmi: python-module-pycparser-2.19-alt1 sisyphus+228366.1000.2.3 1556706938 installed <13>Sep 29 12:14:00 rpmi: python-module-cffi-1.12.3-alt1 sisyphus+229040.200.3.1 1557316502 installed <13>Sep 29 12:14:00 rpmi: python-module-asn1crypto-0.24.0-alt1 sisyphus+227473.1300.1.2 1555756512 installed <13>Sep 29 12:14:00 rpmi: python-module-ntlm-1.1.0-alt1.2 sisyphus+228512.100.1.1 1556654575 installed <13>Sep 29 12:14:00 rpmi: python-module-pytz-1:2016.10-alt1 1484291011 installed <13>Sep 29 12:14:00 rpmi: python-module-babel-1:2.6.0-alt1 sisyphus+228351.2400.6.2 1556652168 installed <13>Sep 29 12:14:00 rpmi: python-module-PyStemmer-1.0.1-alt1.2.1 1321387369 installed <13>Sep 29 12:14:00 rpmi: python-module-snowballstemmer-1.2.0-alt2.1 1457859319 installed <13>Sep 29 12:14:00 rpmi: python-module-simplejson-3.15.0-alt1.qa1 sisyphus+225625.16100.91.1 1555293606 installed <13>Sep 29 12:14:00 rpmi: python-module-ipaddress-1.0.18-alt1.1 sisyphus+227494.1700.1.3 1555839523 installed <13>Sep 29 12:14:00 rpmi: python-module-cryptography-2.6.1-alt1 sisyphus+225625.24400.91.1 1555299604 installed <13>Sep 29 12:14:00 rpmi: python-module-OpenSSL-18.0.0-alt1 1532996168 installed <13>Sep 29 12:14:00 rpmi: python-module-ndg-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed <13>Sep 29 12:14:00 rpmi: python-module-ndg-httpsclient-0.4.2-alt1.qa1 sisyphus+227504.1300.1.2 1555853074 installed <13>Sep 29 12:14:00 rpmi: python-module-backports-3.5.0.1-alt1.1.1 1517645428 installed <13>Sep 29 12:14:00 rpmi: python-module-backports.ssl_match_hostname-3.5.0.1-alt1.1.1 1517645428 installed <13>Sep 29 12:14:00 rpmi: python-module-urllib3-2:1.25.6-alt1 p9+250567.200.5.1 1590420860 installed <13>Sep 29 12:14:00 rpmi: python-module-requests-2.23.0-alt1 p9+250567.400.5.1 1590420890 installed <13>Sep 29 12:14:00 rpmi: python-module-typing-3.6.6-alt2 sisyphus+220108.100.1.1 1548749697 installed <13>Sep 29 12:14:00 rpmi: python-modules-sqlite3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed <13>Sep 29 12:14:00 rpmi: python-module-SQLAlchemy-1.2.15-alt1 sisyphus+225625.4500.91.1 1555285684 installed <13>Sep 29 12:14:00 rpmi: python-module-py-1.8.0-alt2 sisyphus+228349.1400.4.1 1556631070 installed <13>Sep 29 12:14:00 rpmi: python-module-mpmath-0.19-alt1.git20150621.1.1.1.1 sisyphus+227503.2100.1.3 1555860908 installed <13>Sep 29 12:14:01 rpmi: python-module-sympy-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed <13>Sep 29 12:14:01 rpmi: python-module-sympy-tests-1:1.1.1-alt1.1.1 sisyphus+228334.100.1.1 1556542452 installed <13>Sep 29 12:14:01 rpmi: python-module-xapian-1.4.15-alt1 p9+258827.200.2.1 1601308059 installed <13>Sep 29 12:14:01 rpmi: python-module-sphinxcontrib-websupport-1.0.1-alt5 p9+247680.340.15.1 1585331199 installed <13>Sep 29 12:14:01 rpmi: python-module-alabaster-0.7.6-alt3 sisyphus+228351.700.4.1 1556637370 installed <13>Sep 29 12:14:01 rpmi: python-module-Pygments-2.4.2-alt3 p9+263160.400.4.1 1607939146 installed <13>Sep 29 12:14:02 rpmi: python-module-sphinx-1:1.6.5-alt8 p9+250806.100.2.1 1588178467 installed <86>Sep 29 12:14:02 groupadd[1038645]: group added to /etc/group: name=sasl, GID=498 <86>Sep 29 12:14:02 groupadd[1038645]: group added to /etc/gshadow: name=sasl <86>Sep 29 12:14:02 groupadd[1038645]: new group: name=sasl, GID=498 <13>Sep 29 12:14:02 rpmi: libsasl2-3-2.1.27-alt2.1 p9+256192.100.1.1 1597226707 installed <13>Sep 29 12:14:02 rpmi: libldap-2.4.59-alt0.p9.1 p9+281540.300.5.1 1629898589 installed <13>Sep 29 12:14:02 rpmi: libcurl-7.79.0-alt2 p9+285689.100.2.1 1632758193 installed <13>Sep 29 12:14:02 rpmi: libpoppler90-0.80.0-alt1 p9+237607.100.1.1 1568643072 installed <13>Sep 29 12:14:02 rpmi: python3-module-genshi-0.7-alt2 sisyphus+229363.100.1.1 1557847321 installed <13>Sep 29 12:14:02 rpmi: python3-module-webencodings-0.5.1-alt1.1 1517943573 installed <13>Sep 29 12:14:02 rpmi: python3-module-html5lib-1:0.999999999-alt4.qa1 sisyphus+227493.600.1.3 1555835341 installed <13>Sep 29 12:14:02 rpmi: python3-module-lxml-4.4.2-alt1 p9+244111.100.1.1 1578758711 installed <13>Sep 29 12:14:02 rpmi: python3-module-cssselect-0.9.1-alt1.2 sisyphus+227479.1100.1.2 1555757152 installed <13>Sep 29 12:14:02 rpmi: python3-module-javapackages-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed <13>Sep 29 12:14:02 rpmi: rpm-build-java-1:5.0.0-alt1_12jpp8.M90P.1 p9+263388.100.2.1 1608141549 installed <13>Sep 29 12:14:02 rpmi: openssl-1.1.1w-alt0.p9.1 p9+356668.100.1.1 1725304346 installed <13>Sep 29 12:14:02 rpmi: ruby-rubygems-update-3.0.4-alt1 p9+247371.35300.135.1 1590436206 installed <13>Sep 29 12:14:02 rpmi: gem-did-you-mean-1.3.0-alt2.1 p9+247371.40400.161.1 1591376055 installed <13>Sep 29 12:14:02 rpmi: gem-minitest-5.14.0-alt1.1 p9+247371.67710.170.1 1592235999 installed <13>Sep 29 12:14:02 rpmi: ruby-net-telnet-0.2.0-alt1 sisyphus+219345.2700.8.1 1547631566 installed <13>Sep 29 12:14:02 rpmi: gem-rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed <13>Sep 29 12:14:02 rpmi: ruby-xmlrpc-0.3.0-alt1 sisyphus+219345.3300.8.1 1547631818 installed <13>Sep 29 12:14:02 rpmi: gem-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:14:02 rpmi: ri-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Sep 29 12:14:02 rpmi: rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Sep 29 12:14:02 rpmi: ruby-rdoc-6.1.1-alt3 sisyphus+220149.7500.44.1 1552167568 installed <13>Sep 29 12:14:02 rpmi: rake-13.0.1-alt1 p9+247371.77140.170.1 1592237858 installed <13>Sep 29 12:14:02 rpmi: erb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:14:02 rpmi: irb-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:14:03 rpmi: gem-bundler-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed <13>Sep 29 12:14:03 rpmi: gem-test-unit-3.3.5-alt0.1 p9+247371.60440.162.1 1591424158 installed <13>Sep 29 12:14:03 rpmi: gem-power-assert-1.1.7-alt1 p9+247371.60200.162.1 1591424056 installed <13>Sep 29 12:14:04 rpmi: ruby-stdlibs-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:14:04 rpmi: bundle-2.1.4-alt1 p9+247371.33100.135.1 1590435793 installed <13>Sep 29 12:14:04 rpmi: ruby-2.5.9-alt1 p9+261867.500.5.1 1606313941 installed <13>Sep 29 12:14:04 rpmi: perl-Net-SSLeay-1.86_09-alt2 sisyphus+227568.100.1.1 1555676534 installed <13>Sep 29 12:14:04 rpmi: perl-IO-Socket-SSL-2.066-alt1 sisyphus+223890.100.1.1 1551873760 installed <13>Sep 29 12:14:04 rpmi: perl-Net-HTTPS-6.18-alt1 1526560501 installed <13>Sep 29 12:14:04 rpmi: perl-LWP-Protocol-https-6.07-alt1 1494527383 installed <13>Sep 29 12:14:04 rpmi: perl-Net-SMTP-SSL-1.04-alt1 1479470835 installed <13>Sep 29 12:14:04 rpmi: perl-MailTools-2.20-alt1 1517533205 installed <13>Sep 29 12:14:04 rpmi: perl-MIME-Lite-3.030-alt1 1383865152 installed <13>Sep 29 12:14:04 rpmi: perl-Log-Dispatch-2.68-alt2 sisyphus.218872.100 1546338428 installed <13>Sep 29 12:14:04 rpmi: perl-Log-Log4perl-1.49-alt1 1489613295 installed <13>Sep 29 12:14:04 rpmi: ca-trust-java-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed <13>Sep 29 12:14:06 rpmi: java-1.8.0-openjdk-headless-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Sep 29 12:14:08 rpmi: gambit-4.9.3-alt1 sisyphus+220998.100.1.4 1549742897 installed <13>Sep 29 12:14:08 rpmi: foomatic-db-engine-4.0.12-alt1 1449527980 installed <13>Sep 29 12:14:08 rpmi: ghostscript-utils-9.27-alt1.M90P.1 p9+258832.300.4.1 1601632175 installed <13>Sep 29 12:14:09 rpmi: texlive-2019-alt1_2 p9+238369.100.3.1 1569961493 installed <13>Sep 29 12:14:20 rpmi: texlive-collection-basic-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Sep 29 12:14:20 rpmi: texlive-texmf-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Sep 29 12:15:17 rpmi: texlive-dist-2018-alt1_5 sisyphus+226263.100.1.1 1554169804 installed <13>Sep 29 12:15:17 rpmi: java-stub-javadoc-0.1-alt1 1229813340 installed <13>Sep 29 12:15:17 rpmi: alsa-ucm-conf-1.2.4-alt1 p9+250722.2300.14.1 1614269485 installed <13>Sep 29 12:15:17 rpmi: alsa-topology-conf-1.2.4-alt1 p9+250722.2200.14.1 1614269467 installed <13>Sep 29 12:15:17 rpmi: libalsa-1:1.2.4-alt1 p9+250722.2400.14.1 1614269549 installed <13>Sep 29 12:15:17 rpmi: java-1.8.0-openjdk-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Sep 29 12:15:18 rpmi: java-1.8.0-openjdk-devel-0:1.8.0.212.b04-alt2_0jpp8 p9+234508.100.3.1 1563175554 installed <13>Sep 29 12:15:18 rpmi: java-devel-default-1.7.0-alt1 1454012839 installed <13>Sep 29 12:15:18 rpmi: libcurl-devel-7.79.0-alt2 p9+285689.100.2.1 1632758193 installed <13>Sep 29 12:15:18 rpmi: libpango-devel-1.44.6-alt1 p9+237353.700.2.2 1568373865 installed <13>Sep 29 12:15:18 rpmi: gcc-c++-8-alt2 p9+246536.100.3.1 1582643803 installed <13>Sep 29 12:15:18 rpmi: gcc-fortran-8-alt2 p9+246536.100.3.1 1582643803 installed <13>Sep 29 12:15:18 rpmi: tk-devel-8.6.9-alt1 sisyphus+227145.200.1.2 1555606663 installed <13>Sep 29 12:15:18 rpmi: libXmu-devel-1.1.3-alt1 sisyphus+225206.1200.1.2 1552949629 installed <13>Sep 29 12:15:18 rpmi: makeinfo-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Sep 29 12:15:18 rpmi: liblapack-devel-1:3.8.0-alt3 sisyphus+221521.100.1.1 1550134909 installed <13>Sep 29 12:15:18 rpmi: libgomp8-devel-8.4.1-alt0.p9.1 p9+247559.100.2.1 1585587756 installed <13>Sep 29 12:15:18 rpmi: libpcre-devel-8.44-alt1 p9+249555.100.1.1 1586300287 installed <13>Sep 29 12:15:18 rpmi: libtre-devel-0.8.0-alt2.1 1334590818 installed <13>Sep 29 12:15:18 rpmi: libtiff-devel-4.0.10.0.57.f9fc01c3-alt1 sisyphus+226958.100.1.1 1554850937 installed <13>Sep 29 12:15:18 rpmi: texi2dvi-6.5-alt2 sisyphus+220294.200.2.1 1548933637 installed <13>Sep 29 12:15:18 rpmi: libjpeg-devel-2:2.0.2-alt1 sisyphus+226996.100.1.1 1554902884 installed <13>Sep 29 12:15:18 rpmi: libreadline-devel-7.0.3-alt3 sisyphus+222164.300.1.1 1550686325 installed <13>Sep 29 12:15:18 rpmi: liblzma-devel-5.2.5-alt1 p9+268339.40.3.1 1616664413 installed <13>Sep 29 12:15:18 rpmi: bzlib-devel-1:1.0.8-alt1 p9+261810.100.1.1 1605510817 installed Building target platforms: x86_64 Building for target x86_64 Wrote: /usr/src/in/nosrpm/R-base-3.6.1-alt1.nosrc.rpm (w1.gzdio) Installing R-base-3.6.1-alt1.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /usr/src/tmp/rpm-tmp.6019 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + rm -rf R-3.6.1 + echo 'Source #0 (R-3.6.1.tar):' Source #0 (R-3.6.1.tar): + /bin/tar -xf /usr/src/RPM/SOURCES/R-3.6.1.tar + cd R-3.6.1 + /bin/chmod -c -Rf u+rwX,go-w . + echo 'Patch #0 (R-3.6.1-alt1.patch):' Patch #0 (R-3.6.1-alt1.patch): + /usr/bin/patch -p1 patching file .gear/rules patching file .gear/tags/15fa18936deccebb8baa76357c7a902b06205ce0 patching file .gear/tags/1af743c7e25d963067c0a7736c2f362bc1a54087 patching file .gear/tags/2c68f436cffd98cb9581510d928bea5942555c48 patching file .gear/tags/70ae5201e8ecc68e51ed59c0bedcfa01dbb4b579 patching file .gear/tags/890191223501f9206c89761358c534357f6c76b8 patching file .gear/tags/9bcb4bdb4dd1185d3f43ac2d1ba0d8a70921a4e0 patching file .gear/tags/a267957eb382565da32225335ac89fb8c75df0da patching file .gear/tags/a3506a8419eb2903e6d3ce37c465295a254fd1d5 patching file .gear/tags/a8802667f7d1597d2cd5442d00d4d4773505446e patching file .gear/tags/c7dc0028771e7098f72fe8ac9e9575451d4fb020 patching file .gear/tags/dbe24e8137437d3688e1d77cf1b67279d3099cea patching file .gear/tags/e6f3c8b737583c5e27038507647866d029bfb5e4 patching file .gear/tags/ebdb5ee7ba9a5499c21aadcfee3318a7d6d52061 patching file .gear/tags/eef29626bf3bf68c9462ce5f0594fedd5a80168b patching file .gear/tags/f600e7641c9fbf40a0abc5b1cdd67c703376e847 patching file .gear/tags/fdd01de5a3b9e7e6d41e1f4f9db33a99b6973818 patching file .gear/tags/list patching file R-base.spec patching file src/extra/blas/Makefile.in patching file src/extra/xdr/Makefile.in patching file tests/reg-tests-1c.R patching file tests/reg-tests-1d.R + rm src/extra/blas/blas.f src/extra/blas/cmplxblas.f src/modules/lapack/cmplx.f src/modules/lapack/dlamch.f src/modules/lapack/dlapack.f src/modules/lapack/vecLibg95f.f + exit 0 Executing(%build): /bin/sh -e /usr/src/tmp/rpm-tmp.6019 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.6.1 + export lt_cv_prog_cc_static_works=no ac_cv_path_R_ZIPCMD=zip ac_cv_path_R_UNZIPCMD=unzip ac_cv_path_R_BROWSER=firefox ac_cv_path_R_PDFVIEWER=evince 'ac_cv_path_PAGER=less -isR' ac_cv_prog_R_PRINTCMD=lpr + lt_cv_prog_cc_static_works=no + ac_cv_path_R_ZIPCMD=zip + ac_cv_path_R_UNZIPCMD=unzip + ac_cv_path_R_BROWSER=firefox + ac_cv_path_R_PDFVIEWER=evince + ac_cv_path_PAGER='less -isR' + ac_cv_prog_R_PRINTCMD=lpr + CFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' + export CFLAGS + CXXFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' + export CXXFLAGS + FFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' + export FFLAGS + FCFLAGS='-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' + export FCFLAGS + '[' -n '' ']' ++ printf %s '-pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing' ++ sed -r 's/(^|[[:space:]]+)-[^m][^[:space:]]*//g' + ASFLAGS= + export ASFLAGS + export lt_cv_deplibs_check_method=pass_all + lt_cv_deplibs_check_method=pass_all + sort -u + readlink -e -- ./configure + xargs -rn1 install -pm755 -- /usr/share/gnu-config/config.sub /usr/share/gnu-config/config.guess + xargs -ri dirname -- '{}' + xargs -ri find '{}' -type f '(' -name config.sub -or -name config.guess ')' -printf '%h/\n' + ./configure --build=x86_64-alt-linux --host=x86_64-alt-linux --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/lib --localstatedir=/var/lib --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-dependency-tracking --disable-silent-rules --without-included-gettext --enable-prebuilt-html --enable-R-shlib --with-x --disable-rpath --with-system-tre --with-gnu-ld --with-blas=openblas --with-lapack=lapack --with-tcl-config=/usr/lib64/tclConfig.sh --with-tk-config=/usr/lib64/tkConfig.sh '--libdir=${prefix}/lib64' 'rincludedir=${prefix}/include/R' 'rdocdir=${prefix}/share/doc/R-3.6' configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules checking build system type... x86_64-alt-linux-gnu checking host system type... x86_64-alt-linux-gnu loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking whether ln -s works... yes checking for ar... ar checking for a BSD-compatible install... /bin/install -c checking for sed... /bin/sed checking for which... /usr/bin/which checking for less... (cached) less -isR checking for gtar... /usr/bin/gtar checking for tex... /usr/bin/tex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeindex... /usr/bin/makeindex checking for texi2any... /usr/bin/texi2any checking whether texi2any version is at least 5.1... yes checking for ginstall-info... no checking for install-info... no checking for texi2dvi... /usr/bin/texi2dvi checking for kpsewhich... /usr/bin/kpsewhich checking for latex inconsolata package... missing configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally checking for unzip... (cached) unzip checking for zip... (cached) zip checking for gzip... /bin/gzip checking for bzip2... /bin/bzip2 checking for firefox... (cached) firefox using default browser ... firefox checking for acroread... (cached) evince checking for working aclocal... found checking for working autoconf... found checking for working autoheader... found checking for bison... bison -y checking for notangle... false checking for realpath... /usr/bin/realpath checking for x86_64-alt-linux-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-alt-linux-gcc accepts -g... yes checking for x86_64-alt-linux-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-alt-linux-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether x86_64-alt-linux-gcc needs -traditional... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking how to run the C preprocessor... x86_64-alt-linux-gcc -E looking for a modern Fortran compiler checking for x86_64-alt-linux-gfortran... x86_64-alt-linux-gfortran checking whether we are using the GNU Fortran compiler... yes checking whether x86_64-alt-linux-gfortran accepts -g... yes checking for x86_64-alt-linux-g++... x86_64-alt-linux-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-alt-linux-g++ accepts -g... yes checking whether x86_64-alt-linux-g++ -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing can compile C++ code... yes checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking whether __attribute__((visibility())) is supported... yes checking whether x86_64-alt-linux-gcc accepts -fvisibility... yes checking whether x86_64-alt-linux-g++ accepts -fvisibility... yes checking whether x86_64-alt-linux-gfortran accepts -fvisibility... yes checking for x86_64-alt-linux-gcc... x86_64-alt-linux-gcc checking whether we are using the GNU Objective C compiler... no checking whether x86_64-alt-linux-gcc accepts -g... no checking whether x86_64-alt-linux-g++ can compile ObjC++... no checking for Objective C++ compiler... no working ObjC++ compiler found checking how to print strings... printf checking for a sed that does not truncate output... (cached) /bin/sed checking for fgrep... /bin/grep -F checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-alt-linux-gnu file names to x86_64-alt-linux-gnu format... func_convert_file_noop checking how to convert x86_64-alt-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-alt-linux-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... (cached) pass_all checking for x86_64-alt-linux-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-alt-linux-ar... (cached) ar checking for archiver @FILE support... @ checking for x86_64-alt-linux-strip... no checking for strip... strip checking for x86_64-alt-linux-ranlib... no checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from x86_64-alt-linux-gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for x86_64-alt-linux-mt... no checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-alt-linux-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-alt-linux-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-gcc static flag -static works... no checking if x86_64-alt-linux-gcc supports -c -o file.o... yes checking if x86_64-alt-linux-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... x86_64-alt-linux-g++ -E checking for ld used by x86_64-alt-linux-g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-alt-linux-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-alt-linux-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-alt-linux-g++ static flag -static works... no checking if x86_64-alt-linux-g++ supports -c -o file.o... yes checking if x86_64-alt-linux-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-alt-linux-gfortran option to produce PIC... -fPIC checking if x86_64-alt-linux-gfortran PIC flag -fPIC works... yes checking if x86_64-alt-linux-gfortran static flag -static works... no checking if x86_64-alt-linux-gfortran supports -c -o file.o... yes checking if x86_64-alt-linux-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-alt-linux-gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... yes checking readline/history.h presence... yes checking for readline/history.h... yes checking readline/readline.h usability... yes checking readline/readline.h presence... yes checking for readline/readline.h... yes checking for rl_callback_read_char in -lreadline... yes checking for history_truncate_file... yes checking for tilde_expand_word... yes checking whether rl_callback_sigcleanup exists and is declared... yes checking whether rl_completion_matches exists and is declared... yes checking whether rl_resize_terminal exists and is declared... yes checking whether rl_sort_completion_matches exists and is declared... yes checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for sys/wait.h that is POSIX.1 compatible... yes checking for dlfcn.h... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking glob.h usability... yes checking glob.h presence... yes checking for glob.h... yes checking grp.h usability... yes checking grp.h presence... yes checking for grp.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for strings.h... (cached) yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/stat.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking sys/utsname.h usability... yes checking sys/utsname.h presence... yes checking for sys/utsname.h... yes checking for unistd.h... (cached) yes checking utime.h usability... yes checking utime.h presence... yes checking for utime.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking floatingpoint.h usability... no checking floatingpoint.h presence... no checking for floatingpoint.h... no checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking stdalign.h usability... yes checking stdalign.h presence... yes checking for stdalign.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking for stdint.h... (cached) yes checking for string.h... (cached) yes checking whether setjmp.h is POSIX.1 compatible... yes checking whether sigsetjmp is declared... yes checking whether siglongjmp is declared... yes checking for GNU C library with version >= 2... yes checking return type of signal handlers... void checking for uint64_t... yes checking for int64_t... yes checking for int_fast64_t... yes checking for pid_t... yes checking for size_t... yes checking whether SIZE_MAX is declared... yes checking for blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for x86_64-alt-linux-gcc option to accept ISO C99... none needed checking for x86_64-alt-linux-gcc option to accept ISO Standard C... (cached) none needed checking for inline... inline checking size of int... 4 checking size of long... 8 checking size of long long... 8 checking size of double... 8 checking size of size_t... 8 checking size of long double... 16 checking whether we can compute C Make dependencies... yes, using $(CC) -MM checking whether x86_64-alt-linux-gcc supports -c -o FILE.lo... yes checking for x86_64-alt-linux-gcc option to support OpenMP... -fopenmp checking how to get verbose linking output from x86_64-alt-linux-gfortran... -v checking for Fortran libraries of x86_64-alt-linux-gfortran... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from x86_64-alt-linux-gcc... -v checking for C libraries of x86_64-alt-linux-gcc... -L/usr/local/lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-alt-linux/8/../../.. -lgcc_s checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking whether x86_64-alt-linux-gfortran appends underscores to external names... yes checking whether x86_64-alt-linux-gfortran appends extra underscores to external names... no checking whether mixed C/Fortran code can be run... yes checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on int and double... yes checking whether x86_64-alt-linux-gfortran and x86_64-alt-linux-gcc agree on double complex... yes checking for x86_64-alt-linux-gfortran option to support OpenMP... -fopenmp checking whether x86_64-alt-linux-g++ accepts -M for generating dependencies... yes checking whether we can compute ObjC Make dependencies... no checking for ObjC runtime library... checking whether x86_64-alt-linux-gcc accepts -fobjc-exceptions... no checking if need -fno-optimize-sibling-calls for gfortran... yes checking for xmkmf... no checking whether x86_64-alt-linux-g++ supports C++98 features with -std=gnu++98... yes checking whether x86_64-alt-linux-g++ supports C++11 features with -std=gnu++11... yes checking whether x86_64-alt-linux-g++ supports C++14 features with -std=gnu++14... yes checking whether x86_64-alt-linux-g++ supports C++17 features with -std=gnu++17... yes checking for x86_64-alt-linux-g++ -std=gnu++11 option to support OpenMP... -fopenmp checking for option providing pthread_kill... none required checking whether POSIX threads are supported... yes checking for off_t... yes checking for working alloca.h... yes checking for alloca... yes checking whether alloca is declared... yes checking whether expm1 exists and is declared... yes checking whether hypot exists and is declared... yes checking whether log1p exists and is declared... yes checking whether log1pl exists and is declared... yes checking whether log2 exists and is declared... yes checking whether log10 exists and is declared... yes checking whether nearbyint exists and is declared... yes checking whether nearbyintl exists and is declared... yes checking whether powl exists and is declared... yes checking whether rintl exists and is declared... yes checking whether va_copy exists and is declared... yes checking for isblank... yes checking sunmath.h usability... no checking sunmath.h presence... no checking for sunmath.h... no checking for cospi in -lsunmath... no checking for atanpi... no checking for atan2pi... no checking for cospi... no checking for exp10... yes checking for pown... no checking for sinpi... no checking for tanpi... no checking for __cospi... no checking for __sinpi... no checking for __tanpi... no checking for fseeko... yes checking for ftello... yes checking for matherr... no checking whether fcntl exists and is declared... yes checking whether getgrgid exists and is declared... yes checking whether getpwuid exists and is declared... yes checking whether kill exists and is declared... yes checking whether sigaction exists and is declared... yes checking whether sigaltstack exists and is declared... yes checking whether sigemptyset exists and is declared... yes checking whether fdopen exists and is declared... yes checking whether popen exists and is declared... yes checking whether getline exists and is declared... yes checking whether select exists and is declared... yes checking whether setenv exists and is declared... yes checking whether unsetenv exists and is declared... yes checking whether getrlimit exists and is declared... yes checking whether setrlimit exists and is declared... yes checking whether getrusage exists and is declared... yes checking whether getpriority exists and is declared... yes checking whether chmod exists and is declared... yes checking whether mkfifo exists and is declared... yes checking whether stat exists and is declared... yes checking whether umask exists and is declared... yes checking whether gettimeofday exists and is declared... yes checking whether utimes exists and is declared... yes checking whether times exists and is declared... yes checking whether gmtime_r exists and is declared... yes checking whether localtime_r exists and is declared... yes checking whether nl_langinfo exists and is declared... yes checking whether access exists and is declared... yes checking whether chdir exists and is declared... yes checking whether execv exists and is declared... yes checking whether ftruncate exists and is declared... yes checking whether getcwd exists and is declared... yes checking whether geteuid exists and is declared... yes checking whether getuid exists and is declared... yes checking whether link exists and is declared... yes checking whether readlink exists and is declared... yes checking whether symlink exists and is declared... yes checking whether sysconf exists and is declared... yes checking whether sched_setaffinity exists and is declared... yes checking whether sched_getaffinity exists and is declared... yes checking whether utime exists and is declared... yes checking whether utimensat exists and is declared... yes checking for clock_gettime in -lrt... yes checking whether clock_gettime exists and is declared... yes checking whether timespec_get exists and is declared... yes checking for putenv... yes checking whether putenv is declared... yes checking for vasprintf... yes checking whether vasprintf is declared... yes checking for mempcpy... yes checking for realpath... yes checking whether realpath is declared... yes checking whether glob exists and is declared... yes checking for dladdr... yes checking for dlsym... yes checking whether dladdr is declared... yes checking whether dlsym is declared... yes checking whether RTLD_DEFAULT is declared... yes checking whether RTLD_NEXT is declared... yes checking thread.h usability... no checking thread.h presence... no checking for thread.h... no checking whether thr_stksegment exists and is declared... no checking for isnan... yes checking whether isfinite is declared... yes checking whether isnan is declared... yes checking whether you have IEEE 754 floating-point arithmetic... yes checking whether putenv("FOO") can unset an environment variable... yes checking whether putenv("FOO=") can unset an environment variable... no checking for nl_langinfo and CODESET... yes checking for mkdtemp... yes checking for strdup... yes checking for strncasecmp... yes checking whether mkdtemp is declared... yes checking whether strdup is declared... yes checking whether strncasecmp is declared... yes checking for library containing connect... none required checking for library containing gethostbyname... none required checking for library containing xdr_string... none required checking for working calloc... yes checking for working isfinite... yes checking for working log1p... yes checking whether ftell works correctly on files opened for append... yes checking for working sigaction... yes checking whether mktime sets errno... yes checking whether mktime works correctly outside 1902-2037... yes checking complex.h usability... yes checking complex.h presence... yes checking for complex.h... yes checking for double complex... yes checking whether C99 double complex is supported... yes checking whether cabs exists and is declared... yes checking whether carg exists and is declared... yes checking whether cexp exists and is declared... yes checking whether clog exists and is declared... yes checking whether csqrt exists and is declared... yes checking whether cpow exists and is declared... yes checking whether ccos exists and is declared... yes checking whether csin exists and is declared... yes checking whether ctan exists and is declared... yes checking whether cacos exists and is declared... yes checking whether casin exists and is declared... yes checking whether catan exists and is declared... yes checking whether ccosh exists and is declared... yes checking whether csinh exists and is declared... yes checking whether ctanh exists and is declared... yes checking for working ctanh... yes checking whether 'struct tm' includes tm_zone... yes checking whether 'struct tm' includes tm_gmtoff... yes checking for dgemm_ in -lopenblas... yes checking whether double complex BLAS can be used... yes checking whether the BLAS is complete... yes checking for dpstrf_... no checking for dpstrf_ in -llapack... yes checking iconv.h usability... yes checking iconv.h presence... yes checking for iconv.h... yes checking for iconv... yes checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes checking whether iconv accepts "CP1252"... yes checking for iconvlist... no checking for iconv... yes checking for iconv declaration... extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether wcstod exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... yes checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes checking for wctrans_t... yes checking for mbstate_t... yes checking for ICU... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for XtToolkitInitialize in -lXt... yes using X11 ... yes checking for KeySym... yes checking X11/Xmu/Atoms.h usability... yes checking X11/Xmu/Atoms.h presence... yes checking for X11/Xmu/Atoms.h... yes checking for XmuInternAtom in -lXmu... yes checking whether pkg-config knows about cairo and pango... yes checking whether cairo including pango is >= 1.2 and works... yes checking for /usr/lib64/tclConfig.sh... /usr/lib64/tclConfig.sh checking for /usr/lib64/tkConfig.sh... /usr/lib64/tkConfig.sh checking tcl.h usability... yes checking tcl.h presence... yes checking for tcl.h... yes checking tk.h usability... yes checking tk.h presence... yes checking for tk.h... yes checking whether compiling/linking Tcl/Tk code works... yes checking for BSD networking... yes checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking for XDR support... yes checking for inflateInit2_ in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.2.5... yes checking whether zlib support suffices... yes checking mmap support for zlib... yes checking for BZ2_bzlibVersion in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking if bzip2 version >= 1.0.6... yes checking whether bzip2 support suffices... yes checking for lzma_version_number in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking if lzma version >= 5.0.3... yes checking for pcre_fullinfo in -lpcre... yes checking pcre.h usability... no checking pcre.h presence... no checking for pcre.h... no checking pcre/pcre.h usability... yes checking pcre/pcre.h presence... yes checking for pcre/pcre.h... yes checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes checking if PCRE version >= 8.32... yes checking whether PCRE support suffices... yes checking for pcre2-config... no checking for tre_regncompb in -ltre... no checking for curl-config... /usr/bin/curl-config checking libcurl version ... 7.79.0 checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking if libcurl is version 7 and >= 7.22.0... yes checking if libcurl supports https... yes checking if jpeglib version >= 6b... yes checking for jpeg_destroy_compress in -ljpeg... yes checking if libpng version >= 1.2.7... yes checking for png_create_write_struct in -lpng... yes checking tiffio.h usability... yes checking tiffio.h presence... yes checking for tiffio.h... yes checking for TIFFOpen in -ltiff... yes checking whether leap seconds are treated according to POSIX... yes checking for inline... inline checking for sys/time.h... 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(cached) -fopenmp checking for recommended packages... yes checking whether NLS is requested... yes Configuring src/extra/intl directory checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether we are using the GNU C Library 2 or newer... yes checking for x86_64-alt-linux-ranlib... ranlib checking for simple visibility declarations... yes checking for stdint.h... yes checking for getpagesize... yes checking for working mmap... yes checking whether integer division by zero raises SIGFPE... yes checking for inttypes.h... yes checking for unsigned long long int... yes checking for inttypes.h... (cached) yes checking whether the inttypes.h PRIxNN macros are broken... no checking for ld used by x86_64-alt-linux-gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking whether imported symbols can be declared weak... yes checking for multithread API to use... none checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for inttypes.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... (cached) yes checking for munmap... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for argz_count... yes checking for argz_stringify... yes checking for argz_next... yes checking for __fsetlocking... yes checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... yes checking for iconv... (cached) yes checking for iconv declaration... (cached) extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft); checking for NL_LOCALE_NAME macro... yes checking for bison... bison checking version of bison... 3.0.5, ok checking for long long int... yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking for stdint.h... (cached) yes checking for SIZE_MAX... yes checking for stdint.h... (cached) yes checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for ptrdiff_t... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... yes checking for wcslen... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether getc_unlocked is declared... yes checking for nl_langinfo and CODESET... (cached) yes checking for LC_MESSAGES... yes checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands configure: WARNING: unrecognized options: --disable-dependency-tracking, --disable-silent-rules R is now configured for x86_64-alt-linux-gnu Source directory: . Installation directory: /usr C compiler: x86_64-alt-linux-gcc -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Fortran fixed-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Default C++ compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing C++98 compiler: x86_64-alt-linux-g++ -std=gnu++98 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing C++11 compiler: x86_64-alt-linux-g++ -std=gnu++11 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing C++14 compiler: x86_64-alt-linux-g++ -std=gnu++14 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing C++17 compiler: x86_64-alt-linux-g++ -std=gnu++17 -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Fortran free-form compiler: x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing Obj-C compiler: x86_64-alt-linux-gcc Interfaces supported: X11, tcltk External libraries: readline, BLAS(OpenBLAS), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling, static HTML Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally + make -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-3.6.1/src/scripts' creating src/scripts/R.fe make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts' mkdir -p -- ../../bin make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/scripts' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/include' mkdir -p -- ../../include make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/include' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/include/R_ext' mkdir -p -- ../../../include/R_ext make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/include/R_ext' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making regerror.d from regerror.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making regexec.d from regexec.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-ast.d from tre-ast.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making regcomp.d from regcomp.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-match-approx.d from tre-match-approx.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-compile.d from tre-compile.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-match-backtrack.d from tre-match-backtrack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-match-parallel.d from tre-match-parallel.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-mem.d from tre-mem.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-parse.d from tre-parse.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making tre-stack.d from tre-stack.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' making xmalloc.d from xmalloc.c make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c xmalloc.c -o xmalloc.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' x86_64-alt-linux-gcc -I. -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/extra/tre' 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-3.6.1/src/extra/tre' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making interv.d from interv.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making maxcol.d from maxcol.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making integrate.d from integrate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making uncmin.d from uncmin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making pretty.d from pretty.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' making optim.d from optim.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c maxcol.c -o maxcol.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbfa.f -o dpbfa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpbsl.f -o dpbsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c interv.c -o interv.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pretty.c -o pretty.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpodi.f -o dpodi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpoco.f -o dpoco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dchdc.f -o dchdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpofa.f -o dpofa.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dposl.f -o dposl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrls.f -o dqrls.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrutl.f -o dqrutl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrco.f -o dtrco.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc2.f -o dqrdc2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrsl.f -o dqrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dqrdc.f -o dqrdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrsl.f -o dtrsl.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dsvdc.f -o dsvdc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c uncmin.c -o uncmin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o ranlib libappl.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/appl' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making mlutils.d from mlutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making d1mach.d from d1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making i1mach.d from i1mach.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making fmax2.d from fmax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making fmin2.d from fmin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making fprec.d from fprec.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making fround.d from fround.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making ftrunc.d from ftrunc.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making fsign.d from fsign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making sign.d from sign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making imax2.d from imax2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making imin2.d from imin2.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making lgammacor.d from lgammacor.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making chebyshev.d from chebyshev.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making log1p.d from log1p.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making gammalims.d from gammalims.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making stirlerr.d from stirlerr.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making bd0.d from bd0.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making gamma.d from gamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making lgamma.d from lgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making gamma_cody.d from gamma_cody.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making beta.d from beta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making lbeta.d from lbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making polygamma.d from polygamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making cospi.d from cospi.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making bessel_i.d from bessel_i.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making bessel_k.d from bessel_k.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making bessel_j.d from bessel_j.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making bessel_y.d from bessel_y.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making choose.d from choose.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making sexp.d from sexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making snorm.d from snorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dgamma.d from dgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pgamma.d from pgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qgamma.d from qgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dbeta.d from dbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rgamma.d from rgamma.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pbeta.d from pbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qbeta.d from qbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rbeta.d from rbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dunif.d from dunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making punif.d from punif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making runif.d from runif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qunif.d from qunif.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnorm.d from dnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnorm.d from pnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnorm.d from qnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rnorm.d from rnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dlnorm.d from dlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making plnorm.d from plnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qlnorm.d from qlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rlnorm.d from rlnorm.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making df.d from df.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qf.d from qf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pf.d from pf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rf.d from rf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnf.d from dnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dt.d from dt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pt.d from pt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qt.d from qt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rt.d from rt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnt.d from dnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dchisq.d from dchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pchisq.d from pchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qchisq.d from qchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rchisq.d from rchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rnchisq.d from rnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dbinom.d from dbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pbinom.d from pbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qbinom.d from qbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rbinom.d from rbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rmultinom.d from rmultinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dcauchy.d from dcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rcauchy.d from rcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dexp.d from dexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pexp.d from pexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pcauchy.d from pcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qcauchy.d from qcauchy.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qexp.d from qexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rexp.d from rexp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dgeom.d from dgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pgeom.d from pgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qgeom.d from qgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dhyper.d from dhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rgeom.d from rgeom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making phyper.d from phyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qhyper.d from qhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rhyper.d from rhyper.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnbinom.d from dnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnbinom.d from pnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnbinom.d from qnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rnbinom.d from rnbinom.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dpois.d from dpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making ppois.d from ppois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qpois.d from qpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dweibull.d from dweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rpois.d from rpois.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qweibull.d from qweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pweibull.d from pweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rweibull.d from rweibull.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dlogis.d from dlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qlogis.d from qlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making plogis.d from plogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making rlogis.d from rlogis.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnchisq.d from dnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnchisq.d from pnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnchisq.d from qnchisq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making dnbeta.d from dnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnbeta.d from pnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnbeta.d from qnbeta.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnf.d from pnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnf.d from qnf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making pnt.d from pnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qnt.d from qnt.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making ptukey.d from ptukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making toms708.d from toms708.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making qtukey.d from qtukey.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making wilcox.d from wilcox.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' making signrank.d from signrank.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mlutils.c -o mlutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c i1mach.c -o i1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ftrunc.c -o ftrunc.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d1mach.c -o d1mach.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmax2.c -o fmax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fmin2.c -o fmin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fround.c -o fround.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fsign.c -o fsign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sign.c -o sign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c imax2.c -o imax2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fprec.c -o fprec.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c imin2.c -o imin2.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c log1p.c -o log1p.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gammalims.c -o gammalims.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgammacor.c -o lgammacor.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chebyshev.c -o chebyshev.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stirlerr.c -o stirlerr.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bd0.c -o bd0.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gamma.c -o gamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgamma.c -o lgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c beta.c -o beta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lbeta.c -o lbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cospi.c -o cospi.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sexp.c -o sexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c choose.c -o choose.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c snorm.c -o snorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgamma.c -o dgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_j.c -o bessel_j.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_i.c -o bessel_i.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_k.c -o bessel_k.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bessel_y.c -o bessel_y.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c polygamma.c -o polygamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rgamma.c -o rgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbeta.c -o rbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pbeta.c -o pbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dunif.c -o dunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbeta.c -o dbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c punif.c -o punif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qgamma.c -o qgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qunif.c -o qunif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c runif.c -o runif.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnorm.c -o dnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plnorm.c -o plnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pgamma.c -o pgamma.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnorm.c -o rnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qlnorm.c -o qlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dlnorm.c -o dlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pf.c -o pf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnorm.c -o qnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c df.c -o df.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnorm.c -o pnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnf.c -o dnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlnorm.c -o rlnorm.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rf.c -o rf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qf.c -o qf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dt.c -o dt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qbeta.c -o qbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rt.c -o rt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pt.c -o pt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pchisq.c -o pchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnt.c -o dnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dchisq.c -o dchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qchisq.c -o qchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rchisq.c -o rchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnchisq.c -o rnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pbinom.c -o pbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qt.c -o qt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pcauchy.c -o pcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rmultinom.c -o rmultinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbinom.c -o dbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qbinom.c -o qbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dcauchy.c -o dcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rcauchy.c -o rcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qcauchy.c -o qcauchy.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rbinom.c -o rbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dexp.c -o dexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pexp.c -o pexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgeom.c -o dgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rgeom.c -o rgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qexp.c -o qexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rexp.c -o rexp.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pgeom.c -o pgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qgeom.c -o qgeom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dhyper.c -o dhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rnbinom.c -o rnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c phyper.c -o phyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qhyper.c -o qhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnbinom.c -o pnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnbinom.c -o qnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ppois.c -o ppois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnbinom.c -o dnbinom.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpois.c -o dpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dweibull.c -o dweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qpois.c -o qpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rweibull.c -o rweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dlogis.c -o dlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pweibull.c -o pweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qweibull.c -o qweibull.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qlogis.c -o qlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plogis.c -o plogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rhyper.c -o rhyper.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlogis.c -o rlogis.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpois.c -o rpois.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnchisq.c -o qnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnchisq.c -o dnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dnbeta.c -o dnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnf.c -o pnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnbeta.c -o qnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnt.c -o pnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnf.c -o qnf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnbeta.c -o pnbeta.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pnchisq.c -o pnchisq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qnt.c -o qnt.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qtukey.c -o qtukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ptukey.c -o ptukey.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c signrank.c -o signrank.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c wilcox.c -o wilcox.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c toms708.c -o toms708.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o ranlib libnmath.a make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/nmath' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' config.status: creating src/unix/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making Rembedded.d from Rembedded.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making dynload.d from dynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making system.d from system.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making X11.d from X11.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making sys-unix.d from sys-unix.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' making sys-std.d from sys-std.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rembedded.c -o Rembedded.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dynload.c -o dynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c X11.c -o X11.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c system.c -o system.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-unix.c -o sys-unix.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sys-std.c -o sys-std.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/unix' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' x86_64-alt-linux-gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -L/usr/local/lib64 -DR_HOME='"/usr/src/RPM/BUILD/R-3.6.1"' \ -o Rscript ./Rscript.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/unix' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' config.status: creating src/main/Makefile make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making CommandLineArgs.d from CommandLineArgs.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making Rdynload.d from Rdynload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making RNG.d from RNG.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making Renviron.d from Renviron.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making agrep.d from agrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making altrep.d from altrep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making apply.d from apply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making array.d from array.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making builtin.d from builtin.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making arithmetic.d from arithmetic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making attrib.d from attrib.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making bind.d from bind.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making character.d from character.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making altclasses.d from altclasses.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making colors.d from colors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making coerce.d from coerce.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making connections.d from connections.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making complex.d from complex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making cum.d from cum.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making deparse.d from deparse.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making context.d from context.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making devices.d from devices.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making dcf.d from dcf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making datetime.d from datetime.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making debug.d from debug.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making dotcode.d from dotcode.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making dounzip.d from dounzip.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making dstruct.d from dstruct.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making edit.d from edit.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making engine.d from engine.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making duplicate.d from duplicate.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making envir.d from envir.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making eval.d from eval.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making errors.d from errors.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making format.d from format.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making gevents.d from gevents.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making gram.d from gram.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making grep.d from grep.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making identical.d from identical.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making graphics.d from graphics.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making inlined.d from inlined.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making internet.d from internet.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making inspect.d from inspect.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making gram-ex.d from gram-ex.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making iosupport.d from iosupport.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making lapack.d from lapack.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making localecharset.d from localecharset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making list.d from list.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making logic.d from logic.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making main.d from main.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making mapply.d from mapply.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making memory.d from memory.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making match.d from match.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making names.d from names.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making options.d from options.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making objects.d from objects.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making paste.d from paste.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making plot.d from plot.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making plot3d.d from plot3d.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making plotmath.d from plotmath.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making platform.d from platform.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making printarray.d from printarray.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making print.d from print.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making printvector.d from printvector.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making printutils.d from printutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making radixsort.d from radixsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making random.d from random.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making qsort.d from qsort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making raw.d from raw.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making registration.d from registration.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making rlocale.d from rlocale.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making relop.d from relop.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making saveload.d from saveload.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making scan.d from scan.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making seq.d from seq.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making serialize.d from serialize.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making sort.d from sort.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making sprintf.d from sprintf.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making source.d from source.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making startup.d from startup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making subscript.d from subscript.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making split.d from split.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making subassign.d from subassign.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making subset.d from subset.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making summary.d from summary.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making times.d from times.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making g_alab_her.d from g_alab_her.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making util.d from util.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making version.d from version.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making sysutils.d from sysutils.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making g_cntrlify.d from g_cntrlify.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making unique.d from unique.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making g_fontdb.d from g_fontdb.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making Rmain.d from Rmain.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making alloca.d from alloca.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making strdup.d from strdup.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making mkdtemp.d from mkdtemp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making strncasecmp.d from strncasecmp.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' making g_her_glyph.d from g_her_glyph.c make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Renviron.c -o Renviron.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c altrep.c -o altrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c RNG.c -o RNG.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c apply.c -o apply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdynload.c -o Rdynload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agrep.c -o agrep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c altclasses.c -o altclasses.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colors.c -o colors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c builtin.c -o builtin.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c complex.c -o complex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c character.c -o character.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c attrib.c -o attrib.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cum.c -o cum.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c array.c -o array.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c context.c -o context.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bind.c -o bind.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dcf.c -o dcf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c debug.c -o debug.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c devices.c -o devices.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dstruct.c -o dstruct.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dounzip.c -o dounzip.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c arithmetic.c -o arithmetic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coerce.c -o coerce.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c edit.c -o edit.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c duplicate.c -o duplicate.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c deparse.c -o deparse.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c datetime.c -o datetime.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dotcode.c -o dotcode.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gram-ex.c -o gram-ex.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gevents.c -o gevents.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graphics.c -o graphics.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c identical.c -o identical.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c errors.c -o errors.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c engine.c -o engine.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c inlined.c -o inlined.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c inspect.c -o inspect.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c internet.c -o internet.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c iosupport.c -o iosupport.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lapack.c -o lapack.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c connections.c -o connections.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c localecharset.c -o localecharset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c list.c -o list.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mapply.c -o mapply.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c match.c -o match.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c main.c -o main.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c logic.c -o logic.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c names.c -o names.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c envir.c -o envir.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gram.c -o gram.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c options.c -o options.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c paste.c -o paste.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plot.c -o plot.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c objects.c -o objects.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plot3d.c -o plot3d.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c grep.c -o grep.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c printvector.c -o printvector.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c printarray.c -o printarray.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c print.c -o print.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c platform.c -o platform.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c printutils.c -o printutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c registration.c -o registration.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qsort.c -o qsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlocale.c -o rlocale.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c raw.c -o raw.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c memory.c -o memory.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c plotmath.c -o plotmath.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c radixsort.c -o radixsort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c source.c -o source.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c scan.c -o scan.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c relop.c -o relop.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c saveload.c -o saveload.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c split.c -o split.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c startup.c -o startup.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sprintf.c -o sprintf.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c seq.c -o seq.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c serialize.c -o serialize.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sort.c -o sort.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c times.c -o times.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subscript.c -o subscript.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c version.c -o version.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sysutils.c -o sysutils.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c summary.c -o summary.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subset.c -o subset.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -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-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unique.c -o unique.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c subassign.c -o subassign.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c eval.c -o eval.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a -lopenblas -lgfortran -lm -lquadmath -lreadline -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-3.6.1/bin/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' mkdir -p -- /usr/src/RPM/BUILD/R-3.6.1/lib make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -I../../src/extra -I. -I../../src/include -I../../src/include -I/usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rmain.c -o Rmain.o make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' x86_64-alt-linux-gcc -Wl,--export-dynamic -fopenmp -L"../../lib" -L/usr/local/lib64 -o R.bin Rmain.o -lR make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/main' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' making rbitmap.d from rbitmap.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making Rhttpd.d from Rhttpd.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making Rsock.d from Rsock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack' making Lapack.d from Lapack.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making libcurl.d from libcurl.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making internet.d from internet.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' making rotated.d from rotated.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making sock.d from sock.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making nanohttp.d from nanohttp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making nanoftp.d from nanoftp.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' making sockconn.d from sockconn.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' making devX11.d from devX11.c make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanoftp.c -o nanoftp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c nanohttp.c -o nanohttp.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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 -fopenmp -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-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/modules/internet' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' mkdir -p -- /usr/src/RPM/BUILD/R-3.6.1/modules make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/internet' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack' x86_64-alt-linux-gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Lapack.c -o Lapack.o make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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 -fopenmp -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-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/modules/lapack' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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 -fopenmp -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-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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 -fopenmp -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-3.6.1/src/modules/X11' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/modules/X11' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library' mkdir -p -- ../../library make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/profile' building system startup profile mkdir -p -- ../../../library/base/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/profile' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/translations' building package 'translations' mkdir -p -- ../../../library/translations make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/translations' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' building package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' mkdir -p -- ../../../library/base/demo make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' building package 'tools' mkdir -p -- ../../../library/tools make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' mkdir -p -- ../../../library/tools/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making md5.d from md5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making text.d from text.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making Rmd5.d from Rmd5.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making signals.d from signals.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making getfmts.d from getfmts.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making install.d from install.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making http.d from http.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making gramLatex.d from gramLatex.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' making gramRd.d from gramRd.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/tools/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' mkdir -p -- ../../../library/compiler/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' byte-compiling package 'compiler' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/compiler' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' byte-compiling package 'base' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/base' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' byte-compiling package 'tools' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tools' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' building package 'utils' mkdir -p -- ../../../library/utils mkdir -p -- ../../../library/utils/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' mkdir -p -- ../../../library/utils/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' mkdir -p -- ../../../library/utils/Sweave mkdir -p -- ../../../library/utils/misc make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making io.d from io.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making size.d from size.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making sock.d from sock.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/utils/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' mkdir -p -- ../../../../library/utils/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' installing 'sysdata.rda' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' byte-compiling package 'utils' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/utils' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' building package 'grDevices' mkdir -p -- ../../../library/grDevices make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' mkdir -p -- ../../../library/grDevices/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making chull.d from chull.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making axis_scales.d from axis_scales.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making devices.d from devices.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making stubs.d from stubs.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making devCairo.d from devCairo.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making colors.d from colors.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making devPicTeX.d from devPicTeX.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making devPS.d from devPS.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' making devQuartz.d from devQuartz.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' mkdir -p -- ../../../../library/grDevices/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src' make[7]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c make[7]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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 -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cairoBM.c -o cairoBM.o make[9]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices/src/cairo' make[9]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/grDevices/src/cairo' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' byte-compiling package 'grDevices' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grDevices' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' building package 'graphics' mkdir -p -- ../../../library/graphics make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' mkdir -p -- ../../../library/graphics/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making base.d from base.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making graphics.d from graphics.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making plot3d.d from plot3d.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making par.d from par.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making plot.d from plot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' making stem.d from stem.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/src/library/graphics/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' mkdir -p -- ../../../../library/graphics/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' byte-compiling package 'graphics' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/graphics' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' building package 'stats' mkdir -p -- ../../../library/stats make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' mkdir -p -- ../../../library/stats/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making kmeans.d from kmeans.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making chisqsim.d from chisqsim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making bandwidths.d from bandwidths.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making d2x2xk.d from d2x2xk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making ansari.d from ansari.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making fexact.d from fexact.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making kendall.d from kendall.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making ks.d from ks.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making line.d from line.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making smooth.d from smooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making prho.d from prho.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making swilk.d from swilk.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making monoSpl.d from monoSpl.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making ksmooth.d from ksmooth.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making loessc.d from loessc.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making isoreg.d from isoreg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making Srunmed.d from Srunmed.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making dblcen.d from dblcen.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making hclust-utils.d from hclust-utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making distance.d from distance.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making nls.d from nls.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making rWishart.d from rWishart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making HoltWinters.d from HoltWinters.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making PPsum.d from PPsum.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making arima.d from arima.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making burg.d from burg.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making filter.d from filter.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making mAR.d from mAR.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making starma.d from starma.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making pacf.d from pacf.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making family.d from family.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making port.d from port.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making sbart.d from sbart.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making approx.d from approx.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making loglin.d from loglin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making lowess.d from lowess.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making massdist.d from massdist.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making lm.d from lm.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making complete_cases.d from complete_cases.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making cov.d from cov.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making deriv.d from deriv.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making fft.d from fft.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making fourier.d from fourier.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making model.d from model.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making optim.d from optim.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making optimize.d from optimize.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making integrate.d from integrate.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making random.d from random.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making distn.d from distn.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making zeroin.d from zeroin.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making rcont.d from rcont.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' making influence.d from influence.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kendall.c -o kendall.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chisqsim.c -o chisqsim.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ansari.c -o ansari.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bandwidths.c -o bandwidths.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kmeans.c -o kmeans.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c prho.c -o prho.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ks.c -o ks.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c line.c -o line.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ksmooth.c -o ksmooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c smooth.c -o smooth.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c swilk.c -o swilk.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c isoreg.c -o isoreg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dblcen.c -o dblcen.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c monoSpl.c -o monoSpl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessc.c -o loessc.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c HoltWinters.c -o HoltWinters.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c hclust-utils.c -o hclust-utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rWishart.c -o rWishart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nls.c -o nls.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Srunmed.c -o Srunmed.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c PPsum.c -o PPsum.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c distance.c -o distance.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c burg.c -o burg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c filter.c -o filter.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c family.c -o family.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c approx.c -o approx.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c port.c -o port.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sbart.c -o sbart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c massdist.c -o massdist.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pacf.c -o pacf.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lowess.c -o lowess.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loglin.c -o loglin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lm.c -o lm.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c starma.c -o starma.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c complete_cases.c -o complete_cases.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fexact.c -o fexact.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fft.c -o fft.o fft.c: In function 'fft_work': fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] nfac--;/*the global one!*/ ~~~~^~ fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] fft.c:148:9: warning: array subscript -1 is below array bounds of 'int[20]' [-Warray-bounds] make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fourier.c -o fourier.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c arima.c -o arima.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c integrate.c -o integrate.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mAR.c -o mAR.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c zeroin.c -o zeroin.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rcont.c -o rcont.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c optim.c -o optim.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c optimize.c -o optimize.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c influence.c -o influence.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bsplvd.f -o bsplvd.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bvalus.f -o bvalus.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bvalue.f -o bvalue.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c qsbart.f -o qsbart.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c deriv.c -o deriv.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cov.c -o cov.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sinerp.f -o sinerp.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sgram.f -o sgram.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stxwx.f -o stxwx.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sslvrg.f -o sslvrg.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c eureka.f -o eureka.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c hclust.f -o hclust.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c distn.c -o distn.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c kmns.f -o kmns.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lminfl.f -o lminfl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stl.f -o stl.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c random.c -o random.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ppr.f -o ppr.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c loessf.f -o loessf.o loessf.f:60:14: j=DBLE(j)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1894:14: m=DBLE(l+u)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1399:20: i=phi(pi(ii)) 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:928:12: lg=DBLE(lg)/2.D0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:523:22: if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1205:13: ifloor=x 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:835:22: if(deg.eq.2) dk=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:1583:18: i1=dble((d+2)*(d+1))/2.d0 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] loessf.f:473:25: subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) 1 Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument] loessf.f:473:39: subroutine ehg133(n,d,vc,nvmax,nc,ncmax,a,c,hi,lo,v,vval,xi,m,z,s) 1 Warning: Unused dummy argument 'nc' at (1) [-Wunused-dummy-argument] loessf.f:828:31: subroutine ehg197(deg,tau,d,f,dk,trl) 1 Warning: Unused dummy argument 'tau' at (1) [-Wunused-dummy-argument] loessf.f:1985:31: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'kappa' at (1) [-Wunused-dummy-argument] loessf.f:1985:47: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'nv' at (1) [-Wunused-dummy-argument] loessf.f:1985:53: subroutine ehg137(z,kappa,leaf,nleaf,d,nv,nvmax,ncmax,a,xi,lo,hi) 1 Warning: Unused dummy argument 'nvmax' at (1) [-Wunused-dummy-argument] loessf.f:1498:50: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1498:53: subroutine lowesb(xx,yy,ww,diagl,infl,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1649:30: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1649:33: subroutine lowese(iv,liv,lv,wv,m,z,s) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1668:39: subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1668:42: subroutine lowesf(xx,yy,ww,iv,liv,lv,wv,m,z,l,ihat,s) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1700:30: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1700:33: subroutine lowesl(iv,liv,lv,wv,m,z,l) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] loessf.f:1722:33: subroutine lowesr(yy,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'liv' at (1) [-Wunused-dummy-argument] loessf.f:1722:36: subroutine lowesr(yy,iv,liv,lv,wv) 1 Warning: Unused dummy argument 'lv' at (1) [-Wunused-dummy-argument] make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fopenmp -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c model.c -o model.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gfortran -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o portsrc.f:6658:0: NCOMP = NCOMP + 1 Warning: 'ncomp' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:6569:0: INTEGER DEG,HEAD,IC,IP,IPL,IPU,IR,JCOL,JP,JPL,JPU,L,MAXINC, Warning: 'jcol' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5516:0: IF (ALPHAK .LE. ZERO .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:5653:0: IF (ALPHAK .GE. TWOPSI*PSIFAC) GO TO 310 Warning: 'psifac' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10407:0: V(PREDUC) = HALF * (DABS(ALPHAK)*DST*DST + GTSTA) Warning: 'gtsta' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10324:0: IF (-V(DST0) .GE. ALPHAK .OR. ALPHAK .LT. LK .OR. ALPHAK .GE. UK) Warning: 'alphak' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10319:0: LK = DMAX1(LK, PHI*W(PHIPIN)) Warning: 'phi' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:10461:0: IF (KA .GE. KAMIN) GO TO 340 Warning: 'kamin' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12238:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12241:0: V(DST0) = DNWTST Warning: 'dnwtst' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2510:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:2509:0: 60 V(DST0) = DS0 Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8169:0: V(NREDUC) = NRED Warning: 'nred' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8168:0: 90 V(DST0) = DS0 Warning: 'ds0' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:8647:0: 210 IV(FDH) = HES Warning: 'hes' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:3582:0: IF (LIV .LT. MIV2) GO TO 300 Warning: 'miv2' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:12074:0: 270 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] portsrc.f:453:0: 300 CALL DITSUM(D, V(G1), IV, LIV, LV, P, V, X) Warning: 'g1' may be used uninitialized in this function [-Wmaybe-uninitialized] make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -llapack -lopenblas -lgfortran -lm -lquadmath -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' mkdir -p -- ../../../../library/stats/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' byte-compiling package 'stats' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets' building package 'datasets' mkdir -p -- ../../../library/datasets make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets' mkdir -p -- ../../../library/datasets/data make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/datasets' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' building package 'methods' mkdir -p -- ../../../library/methods make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' mkdir -p -- ../../../library/methods/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making slot.d from slot.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making class_support.d from class_support.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making tests.d from tests.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making utils.d from utils.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making init.d from init.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' making methods_list_dispatch.d from methods_list_dispatch.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tests.c -o tests.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c slot.c -o slot.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c class_support.c -o class_support.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c utils.c -o utils.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' mkdir -p -- ../../../../library/methods/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' byte-compiling 'methods' initializing class and method definitions ... done make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/methods' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' building package 'grid' mkdir -p -- ../../../library/grid mkdir -p -- ../../../library/grid/doc make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' mkdir -p -- ../../../library/grid/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making gpar.d from gpar.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making grid.d from grid.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making just.d from just.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making layout.d from layout.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making matrix.d from matrix.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making register.d from register.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making state.d from state.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making unit.d from unit.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making viewport.d from viewport.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' making util.d from util.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c just.c -o just.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c register.c -o register.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c state.c -o state.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gpar.c -o gpar.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c util.c -o util.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c viewport.c -o viewport.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c layout.c -o layout.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c unit.c -o unit.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c grid.c -o grid.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o grid.so gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' mkdir -p -- ../../../../library/grid/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' byte-compiling package 'grid' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/grid' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' building package 'splines' mkdir -p -- ../../../library/splines make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' mkdir -p -- ../../../library/splines/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' making splines.d from splines.c make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' x86_64-alt-linux-gcc -I"../../../../include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c splines.c -o splines.o make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' make[5]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' x86_64-alt-linux-gcc -shared -L../../../../lib -L/usr/local/lib64 -o splines.so splines.o -L../../../../lib -lR make[5]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' make[6]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' mkdir -p -- ../../../../library/splines/libs make[6]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines/src' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' byte-compiling package 'splines' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/splines' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' building package 'stats4' mkdir -p -- ../../../library/stats4 make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' mkdir -p -- ../../../library/stats4/R make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' byte-compiling package 'stats4' make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/stats4' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tcltk' building package 'tcltk' mkdir -p -- ../../../library/tcltk/R make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tcltk' mkdir -p -- ../../../library/tcltk/exec make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tcltk' make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/tcltk/src' making init.d from init.c make[4]: Leaving directory 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file.edit html filetest html findLineNum html fix html flush.console html format html getAnywhere html getFromNamespace html getParseData html getS3method html getWindowsHandle html getWindowsHandles html glob2rx html globalVariables html hasName html head html help html help.request html help.search html help.start html hsearch-utils html install.packages html installed.packages html isS3method html isS3stdGen html localeToCharset html ls_str html maintainer html make.packages.html html make.socket html memory.size html menu html methods html mirrorAdmin html modifyList html news html nsl html object.size html package.skeleton html packageDescription html packageName html packageStatus html page html person html process.events html prompt html promptData html promptPackage html rcompgen html read.DIF html read.fortran html read.fwf html read.socket html read.table html readRegistry html recover html relist html remove.packages html removeSource html roman html rtags html savehistory html select.list html sessionInfo html setRepositories html setWindowTitle html shortPathName html sourceutils html stack html str html strcapture html summaryRprof html tar html toLatex html txtProgressBar html type.convert html untar html unzip html update.packages html url.show html utils-defunct html utils-deprecated html utils-package html vignette html warnErrList html winDialog html winMenus html winProgressBar html winextras html write.table html zip html converting help for package 'grDevices' Devices html Hershey html Japanese html Type1Font html adjustcolor html as.graphicsAnnot html as.raster html axisTicks html boxplot.stats html bringToTop html cairo html check.options html chull html cm html col2rgb html colorRamp html colors html contourLines html convertColor html densCols html dev html dev.capabilities html dev.capture html dev.flush html dev.interactive html dev.size html dev2 html dev2bitmap html devAskNewPage html embedFonts html extendrange html getGraphicsEvent html grDevices-package html grSoftVersion html gray html gray.colors html hcl html hsv html make.rgb html msgWindow html n2mfrow html nclass html palette html palettes html pdf html pdf.options html pictex html plotmath html postscript html postscriptFonts html pretty.Date html ps.options html quartz html quartzFonts html recordGraphics html recordplot html rgb html rgb2hsv html trans3d html windows html windows.options html windowsFonts html x11 html x11Fonts html xfig html xy.coords html xyTable html xyz.coords html png html savePlot html converting help for package 'graphics' abline html arrows html assocplot html axTicks html axis.POSIXct html axis html barplot html box html boxplot html boxplot.matrix html bxp html cdplot html clip html contour html convertXY html coplot html curve html dotchart html filled.contour html fourfoldplot html frame html graphics-defunct html graphics-package html grid html hist.POSIXt html hist html identify html image html layout html legend html lines html locator html matplot html mosaicplot html mtext html pairs html panel.smooth html par html persp html pie html plot html plot.dataframe html plot.default html plot.design html plot.factor html plot.formula html plot.raster html plot.table html plot.window html plot.xy html plothistogram html points html polygon html polypath html rasterImage html rect html rug html screen html segments html smoothScatter html spineplot html stars html stem html stripchart html strwidth html sunflowerplot html symbols html text html title html units html xspline html zAxis html converting help for package 'stats' AIC html ARMAacf html ARMAtoMA html Beta html Binomial html Cauchy html Chisquare html Distributions html Exponential html Fdist html GammaDist html Geometric html HoltWinters html Hypergeometric html IQR html KalmanLike html Logistic html Lognormal html Multinom html NLSstAsymptotic html NLSstClosestX html NLSstLfAsymptote html NLSstRtAsymptote html NegBinomial html Normal html Poisson html SSD html SSasymp html SSasympOff html SSasympOrig html SSbiexp html SSfol html SSfpl html SSgompertz html SSlogis html SSmicmen html SSweibull html SignRank html StructTS html TDist html Tukey html TukeyHSD html Uniform html Weibull html Wilcoxon html acf html acf2AR html add1 html addmargins html aggregate html alias html anova html anova.glm html anova.lm html anova.mlm html ansari.test html aov html approxfun html ar html ar.ols html arima html arima.sim html arima0 html as.hclust html asOneSidedFormula html ave html bandwidth html bartlett.test html binom.test html biplot html biplot.princomp html birthday html box.test html cancor html case.names html checkMFClasses html chisq.test html cmdscale html coef html complete.cases html confint html constrOptim html contrast html contrasts html convolve html cophenetic html cor html cor.test html cov.wt html cpgram html cutree html decompose html delete.response html dendrapply html dendrogram html density html deriv html deviance html df.residual html diffinv html dist html dummy.coef html ecdf html eff.aovlist html effects html embed html expand.model.frame html extractAIC html factanal html factor.scope html family html fft html filter html fisher.test html fitted.values html fivenum html fligner.test html formula html formula.nls html friedman.test html ftable html ftable.formula html getInitial html glm html glm.control html glm.summaries html hclust html heatmap html identify.hclust html influence.measures html integrate html interaction.plot html is.empty html isoreg html kernapply html kernel html kmeans html kruskal.test html ks.test html ksmooth html lag html lag.plot html line html listof html lm html lm.influence html lm.summaries html lmfit html loadings html loess html loess.control html logLik html loglin html lowess html ls.diag html ls.print html lsfit html mad html mahalanobis html make.link html makepredictcall html manova html mantelhaen.test html mauchly.test html mcnemar.test html median html medpolish html model.extract html model.frame html model.matrix html model.tables html monthplot html mood.test html na.action html na.contiguous html na.fail html nafns html naprint html nextn html nlm html nlminb html nls html nls.control html nobs html numericDeriv html offset html oneway.test html optim html optimize html order.dendrogram html p.adjust html pairwise.prop.test html pairwise.t.test html pairwise.table html pairwise.wilcox.test html plot.HoltWinters html plot.acf html plot.density html plot.isoreg html plot.lm html plot.ppr html plot.profile.nls html plot.spec html plot.stepfun html plot.ts html poisson.test html poly html power html power.anova.test html power.prop.test html power.t.test html pp.test html ppoints html ppr html prcomp html predict.HoltWinters html predict html predict.arima html predict.glm html predict.lm html predict.loess html predict.nls html predict.smooth.spline html preplot html princomp html print.power.htest html print.ts html printCoefmat html profile html profile.nls html proj html prop.test html prop.trend.test html qqnorm html quade.test html quantile html r2dtable html rWishart html read.ftable html rect.hclust html relevel html reorder.dendrogram html reorder.factor html replications html reshape html residuals html runmed html scatter.smooth html screeplot html sd html se.contrast html selfStart html setNames html shapiro.test html sigma html simulate html smooth html smooth.spline html smoothEnds html sortedXyData html spec.ar html spec.pgram html spec.taper html spectrum html splinefun html start html stat.anova html stats-defunct html stats-deprecated html stats-package html step html stepfun html stl html stlmethods html summary.aov html summary.glm html summary.lm html summary.manova html summary.nls html summary.princomp html supsmu html symnum html t.test html termplot html terms html terms.formula html terms.object html time html toeplitz html ts-methods html ts html ts.plot html ts.union html tsSmooth html tsdiag html tsp html uniroot html update html update.formula html var.test html varimax html vcov html weighted.mean html weighted.residuals html weights html wilcox.test html window html xtabs html zC html converting help for package 'datasets' AirPassengers html BJsales html BOD html ChickWeight html DNase html EuStockMarkets html Formaldehyde html HairEyeColor html Harman23.cor html Harman74.cor html Indometh html InsectSprays html JohnsonJohnson html LakeHuron html LifeCycleSavings html Loblolly html Nile html Orange html OrchardSprays html PlantGrowth html Puromycin html Theoph html Titanic html ToothGrowth html UCBAdmissions html UKDriverDeaths html UKLungDeaths html UKgas html USAccDeaths html USArrests html USJudgeRatings html USPersonalExpenditure html VADeaths html WWWusage html WorldPhones html ability.cov html airmiles html airquality html anscombe html attenu html attitude html austres html beavers html cars html chickwts html co2 html crimtab html datasets-package html discoveries html esoph html euro html eurodist html faithful html freeny html infert html iris html islands html lh html longley html lynx html morley html mtcars html nhtemp html nottem html npk html occupationalStatus html precip html presidents html pressure html quakes html randu html rivers html rock html sleep html stackloss html state html sunspot.month html sunspot.year html sunspots html swiss html treering html trees html uspop html volcano html warpbreaks html women html zCO2 html converting help for package 'methods' BasicClasses html Classes html Classes_Details html Documentation html EmptyMethodsList-class html EnvironmentClass html GenericFunctions html Introduction html LanguageClasses html LinearMethodsList-class html MethodDefinition-class html MethodSupport html MethodWithNext-class html Methods html MethodsList-class html MethodsList html Methods_Details html Methods_for_Nongenerics html Methods_for_S3 html NextMethod html ObjectsWithPackage-class html RClassUtils html RMethodUtils html S3Part html S4groupGeneric html SClassExtension-class html StructureClasses html TraceClasses html as html callGeneric html canCoerce html cbind2 html className html classRepresentation-class html classesToAM html dotsMethods html evalSource html findClass html findMethods html fixPrevious html genericFunction-class html getClass html getMethod html getPackageName html hasArg html implicitGeneric html inheritedSlotNames html initialize-methods html is html isSealedMethod html languageEl html localRefClass html method.skeleton html methodUtilities html methods-defunct html methods-deprecated html methods-package html new html nonStructure-class html promptClass html promptMethods html refClass html removeMethod html representation html selectSuperClasses html setAs html setClass html setClassUnion html setGeneric html setGroupGeneric html setIs html setLoadActions html setMethod html setOldClass html setSClass html show html showMethods html signature-class html slot html stdRefClass html substituteDirect html testInheritedMethods html validObject html zBasicFunsList html converting help for package 'grid' Grid html absolute.size html arrow html calcStringMetric html current.viewport html dataViewport html depth html deviceLoc html drawDetails html editDetails html explode html gEdit html gPath html getNames html gpar html grid-defunct html grid-internal html grid-package html grid.DLapply html grid.add html grid.bezier html grid.cap html grid.circle html grid.clip html grid.convert html grid.copy html grid.curve html grid.delay html grid.display.list html grid.draw html grid.edit html grid.force html grid.frame html grid.function html grid.get html grid.grab html grid.grep html grid.grill html grid.grob html grid.layout html grid.lines html grid.locator html grid.ls html grid.move.to html grid.newpage html grid.null html grid.pack html grid.path html grid.place html grid.plot.and.legend html grid.points html grid.polygon html grid.pretty html grid.raster html grid.record html grid.rect html grid.refresh html grid.remove html grid.reorder html grid.roundrect html grid.segments html grid.set html grid.show.layout html grid.show.viewport html grid.text html grid.xaxis html grid.xspline html grid.yaxis html grobCoords html grobName html grobWidth html grobX html legendGrob html makeContent html plotViewport html resolveRasterSize html showGrob html showViewport html stringWidth html unit html unit.c html unit.length html unit.pmin html unit.rep html 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-3.6.1/src/library' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package MASS make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package codetools make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package lattice make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package rpart make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package foreign make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package KernSmooth make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package nnet make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package spatial make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'codetools' ... ** package 'codetools' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'codetools' finding HTML links ... done checkUsage html codetools html findGlobals html showTree html ** building package indices ** testing if installed package can be loaded * DONE (codetools) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'nnet' ... ** package 'nnet' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpROR1Qg/R.INSTALL15f3bf1183e99a/nnet/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nnet.c -o nnet.o make[3]: Leaving directory '/usr/src/tmp/RtmpROR1Qg/R.INSTALL15f3bf1183e99a/nnet/src' make[3]: Entering directory '/usr/src/tmp/RtmpROR1Qg/R.INSTALL15f3bf1183e99a/nnet/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o nnet.so nnet.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpROR1Qg/R.INSTALL15f3bf1183e99a/nnet/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nnet' finding HTML links ... done class.ind html multinom html nnet.Hess html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'spatial' ... ** package 'spatial' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c krc.c -o krc.o make[3]: Leaving directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pps.c -o pps.o make[3]: Leaving directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' make[3]: Entering directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o spatial.so init.o krc.o pps.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpNrywkj/R.INSTALL15f3cd6b9802b6/spatial/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'spatial' finding HTML links ... done Kaver html Kenvl html Kfn html Psim html SSI html Strauss html anova.trls html correlogram html expcov html ppgetregion html ppinit html pplik html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'KernSmooth' ... ** package 'KernSmooth' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c blkest.f -o blkest.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cp.f -o cp.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgedi.f -o dgedi.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgefa.f -o dgefa.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgesl.f -o dgesl.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin.f -o linbin.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c linbin2D.f -o linbin2D.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c locpoly.f -o locpoly.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rlbin.f -o rlbin.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sdiag.f -o sdiag.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sstdiag.f -o sstdiag.o make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' make[3]: Entering directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lopenblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmp3deHkf/R.INSTALL15f3b94e64a68a/KernSmooth/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'KernSmooth' finding HTML links ... done bkde html bkde2D html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'foreign' ... ** package 'foreign' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c R_systat.c -o R_systat.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c SASxport.c -o SASxport.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c avl.c -o avl.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dbfopen.c -o dbfopen.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c file-handle.c -o file-handle.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c format.c -o format.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c minitab.c -o minitab.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pfm-read.c -o pfm-read.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c spss.c -o spss.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sfm-read.c -o sfm-read.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c stataread.c -o stataread.o make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' make[3]: Entering directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpH66cZg/R.INSTALL15f3bd2c5309ba/foreign/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'foreign' finding HTML links ... done lookup.xport html read.S html read.arff html read.dbf html read.dta html read.epiinfo html read.mtp html read.octave html read.spss html read.ssd html read.systat html read.xport html write.arff html write.dbf html write.dta html write.foreign html ** building package indices ** testing if installed package can be loaded * DONE (foreign) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'rpart' ... ** package 'rpart' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c anova.c -o anova.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c anovapred.c -o anovapred.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c branch.c -o branch.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c bsplit.c -o bsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c choose_surg.c -o choose_surg.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fix_cp.c -o fix_cp.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c free_tree.c -o free_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gini.c -o gini.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c graycode.c -o graycode.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c insert_split.c -o insert_split.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mysort.c -o mysort.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nodesplit.c -o nodesplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c partition.c -o partition.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c poisson.c -o poisson.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c print_tree.c -o print_tree.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpart.c -o rpart.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpartexp.c -o rpartexp.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpcountup.c -o rpcountup.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown2.c -o rundown2.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rundown.c -o rundown.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c surrogate.c -o surrogate.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c usersplit.c -o usersplit.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xpred.c -o xpred.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c xval.c -o xval.o make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' make[3]: Entering directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpwfACA7/R.INSTALL15f38c5ea30e52/rpart/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rpart' finding HTML links ... done car.test.frame html car90 html cu.summary html kyphosis html labels.rpart html meanvar.rpart html na.rpart html path.rpart html plot.rpart html plotcp html post.rpart html predict.rpart html print.rpart html printcp html prune.rpart html residuals.rpart html rpart-internal html rpart html rpart.control html rpart.exp html rpart.object html rsq.rpart html snip.rpart html solder.balance html stagec html summary.rpart html text.rpart html xpred.rpart html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'MASS' ... ** package 'MASS' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c MASS.c -o MASS.o make[3]: Leaving directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' make[3]: Entering directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lqs.c -o lqs.o make[3]: Leaving directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' make[3]: Entering directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o MASS.so MASS.o lqs.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/Rtmpea0KMa/R.INSTALL15f3947cc689dd/MASS/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'MASS' finding HTML links ... done Aids2 html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package cluster make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package class make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'class' ... ** package 'class' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpbjyKLS/R.INSTALL1608ea4cb28326/class/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c class.c -o class.o make[3]: Leaving directory '/usr/src/tmp/RtmpbjyKLS/R.INSTALL1608ea4cb28326/class/src' make[3]: Entering directory '/usr/src/tmp/RtmpbjyKLS/R.INSTALL1608ea4cb28326/class/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o class.so class.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpbjyKLS/R.INSTALL1608ea4cb28326/class/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'class' finding HTML links ... done SOM html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'lattice' ... ** package 'lattice' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c threeDplot.c -o threeDplot.o make[3]: Leaving directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' make[3]: Entering directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o lattice.so init.o threeDplot.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpKvYYe5/R.INSTALL15f38a2aae2886/lattice/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'lattice' 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package Matrix make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package nlme make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'cluster' ... ** package 'cluster' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dysta.f -o dysta.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c daisy.f -o daisy.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sildist.c -o sildist.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c mona.c -o mona.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c spannel.c -o spannel.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c fanny.c -o fanny.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c clara.c -o clara.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c twins.c -o twins.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pam.c -o pam.o make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' make[3]: Entering directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/cluster/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'cluster' finding HTML links ... done agnes html 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/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/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/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/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/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/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/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/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/RtmpSbQc2Q/R.INSTALL1608dd808bdc2/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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chol.f -o chol.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c corStruct.c -o corStruct.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gnls.c -o gnls.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c matrix.c -o matrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pythag.c -o pythag.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pdMat.c -o pdMat.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlme.c -o nlme.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gfortran -fno-optimize-sibling-calls -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c rs.f -o rs.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c nlmefit.c -o nlmefit.o make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' make[3]: Entering directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'nlme' finding HTML links ... done ACF html ACF.gls html 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 Rd warning: /usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic plot.lmList html plot.lme html plot.nffGroupedData html plot.nfnGroupedData html plot.nmGroupedData html plot.ranef.lmList html plot.ranef.lme html Rd warning: /usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic Rd warning: /usr/src/tmp/RtmpftsdG2/R.INSTALL160e2e3b24d651/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic pooledSD html predict.gls html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'Matrix' ... ** package 'Matrix' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c TMatrix_as.c -o TMatrix_as.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c CHMfactor.c -o CHMfactor.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Tsparse.c -o Tsparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cs_utils.c -o cs_utils.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chm_common.c -o chm_common.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dense.c -o dense.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgTMatrix.c -o dgTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Mutils.c -o Mutils.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dpoMatrix.c -o dpoMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc 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make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dspMatrix.c -o dspMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dsyMatrix.c -o dsyMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtTMatrix.c -o dtTMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtCMatrix.c -o dtCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtpMatrix.c -o dtpMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dgeMatrix.c -o dgeMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dtrMatrix.c -o dtrMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c Csparse.c -o Csparse.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ldense.c -o ldense.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' ( cd Lib ; make clean ) ( cd Source ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c factorizations.c -o factorizations.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c lgCMatrix.c -o lgCMatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' ( cd Source ; make clean ) make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c abIndex.c -o abIndex.o make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' ( cd Lib ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile ) make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cs.c -o cs.o cs.c: In function 'cs_qr': cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable] csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai, ^ make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c sparseQR.c -o sparseQR.o In file included from /usr/src/RPM/BUILD/R-3.6.1/include/R.h:91, from Mutils.h:12, from sparseQR.h:4, from sparseQR.c:1: sparseQR.c: In function 'sparseQR_coef': /usr/src/RPM/BUILD/R-3.6.1/include/R_ext/RS.h:74:25: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] #define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) ^~~~~~~~~~ sparseQR.c:172:53: note: 'x' was declared here double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x; ^ make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_add.c -o cholmod_add.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_aat.c -o cholmod_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_band.c -o cholmod_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_common.c -o cholmod_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_copy.c -o cholmod_copy.o ../Core/cholmod_copy.c: In function 'cholmod_copy': ../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^~ ../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_complex.c -o cholmod_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_error.c -o cholmod_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_memory.c -o cholmod_memory.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_sparse.c -o cholmod_sparse.o ../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse': ../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] Int p, pend, j, ncol, packed, nzmax, nz, xtype ; ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_version.c -o cholmod_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_factor.c -o cholmod_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_dense.c -o cholmod_dense.o In file included from ../Core/cholmod_dense.c:48: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ In file included from ../Core/cholmod_dense.c:50: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ In file included from ../Core/cholmod_dense.c:52: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/cholmod_dense.c: In function 'cholmod_eye': ../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, n, nz ; ^~ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_triplet.c -o cholmod_triplet.o In file included from ../Core/cholmod_triplet.c:108: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ In file included from ../Core/cholmod_triplet.c:110: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ In file included from ../Core/cholmod_triplet.c:112: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse': ../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] Int i, j, p, k, stype, nrow, ncol, nz, ok ; ^~ ../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o In file included from ../Core/cholmod_change_factor.c:116: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ In file included from ../Core/cholmod_change_factor.c:118: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] Int nsuper, xsize, ssize ; ^~~~~ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^~ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^~ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; ^ ../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^~~ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_read.c -o cholmod_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_write.c -o cholmod_write.o ../Check/cholmod_write.c: In function 'cholmod_write_sparse': ../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2': ../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, ^~~~ ../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^~~~~~~ ../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o ../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p': ../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; ^ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Core/cholmod_transpose.c -o cholmod_transpose.o In file included from ../Core/cholmod_transpose.c:124: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:126: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:128: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:131: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:133: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ In file included from ../Core/cholmod_transpose.c:136: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Check/cholmod_check.c -o cholmod_check.o ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; ^~~~~~~~~~ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; ^~ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; ^~~ ../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable] count, precise, init_print, ilast, lnz, head, tail, jprev, plast, ^~~~~~~ ../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] Int totsize ; ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ In file included from ../Supernodal/cholmod_super_solve.c:30: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:164: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:166: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:168: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:172: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:174: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:176: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:78: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ In file included from ../Supernodal/cholmod_super_numeric.c:80: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o ../Core/cholmod_copy.c: In function 'cholmod_l_copy': ../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^~ ../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable] Int nrow, ncol, up, lo, values, diag, astype ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o In file included from ../Core/cholmod_dense.c:48: ../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ In file included from ../Core/cholmod_dense.c:50: ../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ In file included from ../Core/cholmod_dense.c:52: ../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense': ../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Xx, *Az, *Xz ; ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse': ../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Cx, *Xz, *Cz ; ^~ ../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2': ../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz, *Yx, *Yz ; ^~ ../Core/cholmod_dense.c: In function 'cholmod_l_eye': ../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, n, nz ; ^~ ../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Xx, *Xz ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:46: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ In file included from ../MatrixOps/cholmod_sdmult.c:50: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o In file included from ../Cholesky/cholmod_solve.c:66: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^~ In file included from ../Cholesky/cholmod_solve.c:69: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^~ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o ../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse': ../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] Int p, pend, j, ncol, packed, nzmax, nz, xtype ; ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o In file included from ../Core/cholmod_change_factor.c:116: ../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ In file included from ../Core/cholmod_change_factor.c:118: ../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric': ../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic': ../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable] Int nsuper, xsize, ssize ; ^~~~~ ../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric': ../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^~ ../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable] Int *Lp, *Li, *Lnz ; ^~ ../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable] double *Lx, *Lz ; ^~ ../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric': ../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ; ^ ../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^~~ ../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable] Int *Ls, *Lpi, *Lpx, *Super, *Li ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o In file included from ../Core/cholmod_triplet.c:108: ../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ In file included from ../Core/cholmod_triplet.c:110: ../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ In file included from ../Core/cholmod_triplet.c:112: ../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse': ../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable] double *Rx, *Rz, *Tx, *Tz ; ^~ ../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse': ../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable] Int i, j, p, k, stype, nrow, ncol, nz, ok ; ^~ ../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable] Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o ../Check/cholmod_write.c: In function 'cholmod_l_write_sparse': ../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable] Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype, ^~~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o ../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p': ../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable] Int nrow, ncol, stype, convert, n, nsuper, grow2, status ; ^ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o ../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2': ../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable] Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol, ^~~~ ../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^~~~~~~ ../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable] Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent, ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o In file included from ../Core/cholmod_transpose.c:124: ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:126: ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:128: ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:131: ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ ../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ ../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Fx, *Fz ; ^~ In file included from ../Core/cholmod_transpose.c:133: ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ In file included from ../Core/cholmod_transpose.c:136: ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym': ../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~~~~ ../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ; ^~~~ ../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~~ ../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ; ^~ ../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym': ../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable] Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o ../Check/cholmod_check.c: In function 'check_common': ../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable] Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ; ^~~~~~~~~~ ../Check/cholmod_check.c: In function 'check_dense': ../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable] Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ; ^~ ../Check/cholmod_check.c: In function 'check_factor': ../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable] ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ; ^~~ ../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable] count, precise, init_print, ilast, lnz, head, tail, jprev, plast, ^~~~~~~ ../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable] Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor, ^~~~~~~~ ../Check/cholmod_check.c: In function 'check_factor.constprop': ../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized] jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol, ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o In file included from ../Cholesky/cholmod_rowfac.c:164: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:166: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:168: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ In file included from ../Cholesky/cholmod_rowfac.c:172: ../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:174: ../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ ../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ ../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ; ^~ In file included from ../Cholesky/cholmod_rowfac.c:176: ../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask': ../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable] use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ; ^~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o In file included from ../Supernodal/cholmod_super_solve.c:28: ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ In file included from ../Supernodal/cholmod_super_solve.c:30: ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve': ../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ ../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve': ../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable] nsrow2, n, ps2, j, i, d, nrhs ; ^ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o ../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2': ../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable] Int totsize ; ^~~~~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o In file included from ../Cholesky/cholmod_solve.c:66: ../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^~ In file included from ../Cholesky/cholmod_solve.c:69: ../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve': ../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Lx, *Yx, *Yz ; ^~ ../Cholesky/cholmod_solve.c: In function 'iperm': ../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable] Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o In file included from ../MatrixOps/cholmod_sdmult.c:46: ../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ In file included from ../MatrixOps/cholmod_sdmult.c:48: ../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ ../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ ../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ; ^~ In file included from ../MatrixOps/cholmod_sdmult.c:50: ../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult': ../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] Int packed, nrow, ncol, j, k, p, pend, kcol, i ; ^~~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o In file included from ../Supernodal/cholmod_super_numeric.c:78: ../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ In file included from ../Supernodal/cholmod_super_numeric.c:80: ../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric': ../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ ../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable] double *Lx, *Ax, *Fx, *Az, *Fz, *C ; ^~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c ../Modify/cholmod_updown.c -o cholmod_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_updown_mask': ../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o ../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask': ../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable] *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ; ^~~ make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/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/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/CHOLMOD/Lib' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colamd_global.c -o colamd_global.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c colamd.c -o colamd.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c colamd.c -o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/COLAMD/Source' ( cd Source ; make -f "/usr/src/RPM/BUILD/R-3.6.1/etc/Makeconf" -f Makefile lib ) make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_1.c -o amd_l_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_1.c -o amd_i_1.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_control.c -o amd_i_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_control.c -o amd_l_control.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_order.c -o amd_i_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_order.c -o amd_l_order.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_info.c -o amd_i_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_info.c -o amd_l_info.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_global.c -o amd_i_global.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_global.c -o amd_l_global.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDLONG -c amd_2.c -o amd_l_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -I../Include -DDINT -c amd_2.c -o amd_i_2.o make[5]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[5]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/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/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/AMD/Source' make[4]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/SuiteSparse_config' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -DNTIMER -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c SuiteSparse_config.c -o SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/SuiteSparse_config' make[4]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/SuiteSparse_config' ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o make[4]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src/SuiteSparse_config' make[3]: Entering directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lopenblas -lgfortran -lm -lquadmath -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'chol2inv' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix' Creating a generic function for 'diag' from package 'base' in package 'Matrix' Creating a generic function for 'drop' from package 'base' in package 'Matrix' Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix' Creating a generic function for 'unname' from package 'base' in package 'Matrix' Creating a generic function for 'norm' from package 'base' in package 'Matrix' Creating a generic function for 'rcond' from 'base' in package 'Matrix' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr" in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo" in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc" in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr" in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo" in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc" Creating a generic function for 'colSums' from package 'base' in package 'Matrix' Creating a generic function for 'colMeans' from package 'base' in package 'Matrix' Creating a generic function for 'rowSums' from package 'base' in package 'Matrix' Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix' in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix" Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix' Creating a generic function for 'diag<-' from package 'base' in package 'Matrix' Creating a generic function for 'crossprod' from package 'base' in package 'Matrix' Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix' Creating a generic function for 'which' from package 'base' in package 'Matrix' in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM" in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph" in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph" in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL" in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph" in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'qr.R' from package 'base' in package 'Matrix' Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix' Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix' Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix' Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix' Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix' Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix' ** help *** installing help indices converting help for package 'Matrix' finding HTML links ... done BunchKaufman-methods html CAex html CHMfactor-class html Cholesky-class html Cholesky html CsparseMatrix-class html Diagonal html Hilbert html KNex html KhatriRao html LU-class html Matrix-class html Matrix html MatrixClass html MatrixFactorization-class html RsparseMatrix-class html Schur-class html Schur html SparseM-conv html Subassign-methods html TsparseMatrix-class html USCounties html Xtrct-methods html abIndex-class html Rd warning: /usr/src/tmp/RtmpDGG3m0/R.INSTALL160e24602870b3/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/RtmpDGG3m0/R.INSTALL160e24602870b3/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/RtmpDGG3m0/R.INSTALL160e24602870b3/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/RtmpDGG3m0/R.INSTALL160e24602870b3/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic nMatrix-class html ndenseMatrix-class html nearPD html ngeMatrix-class html nnzero html norm html nsparseMatrix-classes html nsyMatrix-class html ntrMatrix-class html number-class html pMatrix-class html printSpMatrix html qr-methods html rankMatrix html rcond html rep2abI html replValue-class html rleDiff-class html rsparsematrix html solve-methods html spMatrix html sparse.model.matrix html sparseLU-class html sparseMatrix-class html sparseMatrix html sparseQR-class html sparseVector-class html sparseVector html symmetricMatrix-class html symmpart html triangularMatrix-class html uniqTsparse html unpack html unused-classes html updown html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package survival make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package mgcv make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agexact.c -o agexact.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart2.c -o agmart2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart.c -o agmart.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit4.c -o agfit4.o agfit4.c: In function 'agfit4': agfit4.c:575:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized] if (tstop[p] < dtime) break; /* no more to add */ ^ make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agmart3.c -o agmart3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agscore.c -o agscore.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv4.c -o agsurv4.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv5.c -o agsurv5.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agfit5.c -o agfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chinv2.c -o chinv2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chinv3.c -o chinv3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky2.c -o cholesky2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c agsurv3.c -o agsurv3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky5.c -o cholesky5.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve2.c -o chsolve2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cholesky3.c -o cholesky3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve5.c -o chsolve5.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c chsolve3.c -o chsolve3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c concordance1.c -o concordance1.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxdetail.c -o coxdetail.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxcount1.c -o coxcount1.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c concordance3.c -o concordance3.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxmart.c -o coxmart.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxsafe.c -o coxsafe.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxmart2.c -o coxmart2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxscho.c -o coxscho.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxfit6.c -o coxfit6.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxexact.c -o coxexact.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxscore.c -o coxscore.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c dmatrix.c -o dmatrix.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c doloop.c -o doloop.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c finegray.c -o finegray.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c gchol.c -o gchol.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pyears1.c -o pyears1.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c norisk.c -o norisk.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pyears2.c -o pyears2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pystep.c -o pystep.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxfit5.c -o coxfit5.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survdiff2.c -o survdiff2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survConcordance.c -o survConcordance.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfit4.c -o survfit4.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c pyears3b.c -o pyears3b.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survpenal.c -o survpenal.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfitci.c -o survfitci.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survregc1.c -o survregc1.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survreg6.c -o survreg6.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c tmerge.c -o tmerge.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survsplit.c -o survsplit.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survregc2.c -o survregc2.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survfitkm.c -o survfitkm.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c survreg7.c -o survreg7.o make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' make[3]: Entering directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory '/usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/survival/src' installing to /usr/src/RPM/BUILD/R-3.6.1/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'survival' finding HTML links ... done Surv html Survmethods html aareg html aeqSurv html agreg.fit html aml html anova.coxph html attrassign html basehaz html bladder html cch html cgd html cgd0 html cipoisson html Rd warning: /usr/src/tmp/RtmppphNoA/R.INSTALL16d9c64a368ced/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/RtmppphNoA/R.INSTALL16d9c64a368ced/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 concordancefit 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 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 reliability 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-deprecated 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 *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) Making 'packages.html' ... done make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' begin installing recommended package boot make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'boot' ... ** package 'boot' successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'boot' finding HTML links ... done EEF.profile html Imp.Estimates html 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-3.6.1/src/library/Recommended' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/src/library/Recommended' * installing *source* package 'mgcv' ... ** package 'mgcv' successfully unpacked and MD5 sums checked ** using non-staged installation ** libs make[3]: Entering directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c init.c -o init.o make[3]: Leaving directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches -Wall -g -O2 -fno-strict-aliasing -c coxph.c -o coxph.o make[3]: Leaving directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' x86_64-alt-linux-gcc -I"/usr/src/RPM/BUILD/R-3.6.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -pipe -frecord-gcc-switches 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[-Wmisleading-indentation] if (j_max>j_hi) j_max = j_hi; if (j_maxj_hi) j_max = j_hi; if (j_max1) R[1] = -2.0;return; /* signals error */ ^~ mat.c:1872:29: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (*n>1) R[1] = -2.0;return; /* signals error */ ^~~~~~ mat.c: In function 'Rlanczos': mat.c:3467:15: warning: 'cir' may be used uninitialized in this function [-Wmaybe-uninitialized] #pragma omp parallel private(i,ri) num_threads(*nt) ^~~ make[3]: Leaving directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' make[3]: Entering directory '/usr/src/tmp/RtmpesB9lB/R.INSTALL16d9bd28f62289/mgcv/src' x86_64-alt-linux-gcc -shared -L/usr/src/RPM/BUILD/R-3.6.1/lib -L/usr/local/lib64 -o mgcv.so coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -llapack -lopenblas -lgfortran -lm -lquadmath -fopenmp -L/usr/src/RPM/BUILD/R-3.6.1/lib -lR make[3]: Leaving directory 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Writing index file R-admin.vr (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] Cross reference values unknown; you must run TeX again. [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Underfull \hbox (badness 7685) in paragraph at lines 1367--1371 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1584--1588 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [17] [18] Chapter 4 [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1962--1974 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [21] Chapter 5 [22] Chapter 6 [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 3421--3421 []@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 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5044--5044 []@texttt CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX. sdk/usr/include"[] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5146--5146 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [60] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5183--5183 []@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 5628--5628 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [66] [67] Appendix D [68] [69] [70] (Function and variable index) [71] No file R-admin.vrs. (Concept index) [72] No file R-admin.cps. (Environment variable index) [73] No file R-admin.ens. [74] ) (see the transcript file for additional information) Output written on R-admin.pdf (77 pages, 471617 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-admin.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-admin.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-admin.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Underfull \hbox (badness 7685) in paragraph at lines 1367--1371 []@textrm or per-haps bet-ter, set the en-vi-ron-ment vari-able @texttt TAR_OP TIONS[] @textrm to the value [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1584--1588 []@textrm Parallel check-ing of pack-age sources (part of @texttt make check-de vel[] @textrm and @texttt make [17] [18] Chapter 4 [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1962--1974 @texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@ textrm , @texttt org.r-project.x86_ [21] Chapter 5 [22] Chapter 6 [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 3421--3421 []@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 5036--5036 []@texttt /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_m acOS_10.14.pkg \[] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5044--5044 []@texttt CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX. sdk/usr/include"[] [59] Overfull \hbox (56.55324pt too wide) in paragraph at lines 5146--5146 []@texttt PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr /lib/pkgconfig \[] [60] Overfull \hbox (85.29668pt too wide) in paragraph at lines 5183--5183 []@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 5628--5628 []@texttt PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgc onfig:/usr/lib/64/pkgconfig[] [66] [67] Appendix D [68] [69] [70] (Function and variable index) [71] (Concept index) [72] (Environment variable index) [73] [74] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9.pfb> Output written on R-admin.pdf (79 pages, 516716 bytes). Transcript written on R-admin.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) 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 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, 270429 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.6.1/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, 310021 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-data.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.6.1/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, 310026 bytes). Transcript written on R-data.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/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] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] No file R-ints.vrs. (Concept index) [62] No file R-ints.cps. [63] ) (see the transcript file for additional information)< /usr/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb> Output written on R-ints.pdf (66 pages, 397970 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/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] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] ) (see the transcript file for additional information) Output written on R-ints.pdf (68 pages, 448501 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc [-1]) [-2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-ints.toc) Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Overfull \hbox (27.8098pt too wide) in paragraph at lines 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$`.__T__Ops:base`) # 71 methods for the 'Ops' (group)generic[] Overfull \hbox (137.03487pt too wide) in paragraph at lines 1458--1458 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3 [27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Chapter 7 [43] Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal ly, Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, as Underfull \hbox (badness 10000) in paragraph at lines 3631--3640 @textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re- solves to [44] Chapter 8 [45] [46] Underfull \hbox (badness 10000) in paragraph at lines 3852--3857 @textrm the reg-is-tra-tion in-for-ma-tion (num-ber of ar-gu-ments, cor-rect c hoice of [47] [48] [49] [50] [51] [52] Underfull \hbox (badness 7326) in paragraph at lines 4254--4260 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @ texttt &&[] @textrm and [53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12 [59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] ) (see the transcript file for additional information) Output written on R-ints.pdf (68 pages, 448501 bytes). Transcript written on R-ints.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' TEXINPUTS=".:$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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/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, 326400 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/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, 374862 bytes). Transcript written on R-lang.log. tar: R-lang.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 293--294 @textbf storage.mode| [3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27] [28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7 [39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] Underfull \hbox (badness 10000) in paragraph at lines 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, 383526 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-lang.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/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, 374872 bytes). Transcript written on R-lang.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/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. tar: R-intro.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-3.6.1/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, 637478 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-intro.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-intro.toc) (Preface) (/usr/src/RPM/BUILD/R-3.6.1/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, 628364 bytes). Transcript written on R-intro.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/usr/share/texmf-dist/tex/texinfo/txi-en.tex) [1{/usr/share/texmf-dist/fonts/m ap/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (50 pages, 359219 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 375772 bytes). Transcript written on R-FAQ.log. tar: R-FAQ.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) Chapter 1 Cross reference values unknown; you must run TeX again. [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 377218 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 375772 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.toc) Chapter 1 (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20] [21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] Writing index file R-FAQ.fn [39] [40] [41] Underfull \hbox (badness 10000) in paragraph at lines 3271--3279 @texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas ed on the [42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] ) (see the transcript file for additional information) Output written on R-FAQ.pdf (52 pages, 375764 bytes). Transcript written on R-FAQ.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/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] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@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 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(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] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @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 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7102--7108 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8398--8407 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8675--8676 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8807--8807 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8835--8837 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8967--8967 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9301--9301 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 9317--9317 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10159--10159 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10739--10739 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12620--12620 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163] [164] [165] [166] [167] [168] Underfull \hbox (badness 10000) in paragraph at lines 14450--14456 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [169] [170] Chapter 8 [171] [172] [173] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14862--14862 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [174] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14921--14921 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [175] [176] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 15424--15431 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 15547--15551 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [183] No file R-exts.vrs. (Concept index) [184] No file R-exts.cps. [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 (188 pages, 898640 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.6.1/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] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@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 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(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] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @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 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7102--7108 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8398--8407 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8675--8676 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8807--8807 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8835--8837 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8967--8967 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9301--9301 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 9317--9317 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10159--10159 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10739--10739 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12620--12620 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163] [164] [165] [166] [167] [168] Underfull \hbox (badness 10000) in paragraph at lines 14450--14456 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [169] [170] Chapter 8 [171] [172] [173] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14862--14862 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [174] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14921--14921 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [175] [176] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 15424--15431 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 15547--15551 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [183] [184] [185] [186] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [187] [188] [189] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (195 pages, 961739 bytes). Transcript written on R-exts.log. tar: R-exts.aux: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/usr/src/RPM/BUILD/R-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.6.1/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] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@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 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(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] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @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 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7102--7108 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8398--8407 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8675--8676 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8807--8807 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8835--8837 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8967--8967 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9301--9301 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 9317--9317 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10159--10159 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10739--10739 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12620--12620 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163] [164] [165] [166] [167] [168] Underfull \hbox (badness 10000) in paragraph at lines 14450--14456 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [169] [170] Chapter 8 [171] [172] [173] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14862--14862 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [174] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14921--14921 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [175] [176] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 15424--15431 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 15547--15551 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [183] [184] [185] [186] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [187] [188] [189] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (195 pages, 972372 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.6.1/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] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@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 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(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] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @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 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7102--7108 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8398--8407 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8675--8676 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8807--8807 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8835--8837 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8967--8967 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9301--9301 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 9317--9317 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10159--10159 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10739--10739 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12620--12620 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163] [164] [165] [166] [167] [168] Underfull \hbox (badness 10000) in paragraph at lines 14450--14456 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [169] [170] Chapter 8 [171] [172] [173] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14862--14862 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [174] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14921--14921 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [175] [176] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 15424--15431 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 15547--15551 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [183] [184] [185] [186] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [187] [188] [189] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (195 pages, 961744 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-3.6.1/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-3.6.1/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-3.6.1/doc/manual/R-defs.texi (/usr/share/texmf-dist/tex/texinfo/txi-en.tex)) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/version.texi) [1{/usr/share/texmf-dist/f onts/map/pdftex/updmap/pdftex.map}] [2] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc [-1] [-2] [-3]) [-4] (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (/usr/src/RPM/BUILD/R-3.6.1/doc/manual/R-exts.toc) (Acknowledgements) (/usr/src/RPM/BUILD/R-3.6.1/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] [26] Overfull \hbox (46.15797pt too wide) in paragraph at lines 2335--2335 []@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 2337--2337 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [27] [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 2586--2588 [][][]@smallrm The changes are linked from [][]@smalltt https: / / isocpp . org / std / standing-documents / [30] Overfull \hbox (39.30717pt too wide) in paragraph at lines 2719--2719 [] @texttt CXX="$(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] [53] Overfull \hbox (32.24495pt too wide) in paragraph at lines 4729--4729 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (26.49626pt too wide) in paragraph at lines 4731--4731 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (43.74232pt too wide) in paragraph at lines 4732--4732 [] @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 4747--4747 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (32.24495pt too wide) in paragraph at lines 5401--5401 []@texttt 'register' storage class specifier is deprecated and incompatible wi th C++17[] [62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6923--6930 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [79] [80] Underfull \hbox (badness 10000) in paragraph at lines 7102--7108 []@textrm The @texttt \out{@textttsl literal@texttt }[] @textrm macro would usu -ally be used within the @textsl text[] @textrm part of [81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92] Chapter 4 [93] [94] [95] [96] [97] Underfull \hbox (badness 10000) in paragraph at lines 8398--8407 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. [98] [99] [100] Overfull \hbox (22.55893pt too wide) in paragraph at lines 8675--8676 [][][]@smallrm see [][]@smalltt http: / / llvm . org / devmtg / 2014-04 / PDFs / LightningTalks / EuroLLVM%202014%20--%20container%20overflow . [101] [102] Overfull \hbox (56.55324pt too wide) in paragraph at lines 8807--8807 []@texttt setenv ASAN_OPTIONS 'alloc_dealloc_mismatch=0:detect_leaks=0:detect_ odr_violation=0'[] Underfull \hbox (badness 10000) in paragraph at lines 8835--8837 []@textrm This san-i-tizer can be com-bined with the Ad-dress San-i-tizer by [103] Overfull \hbox (50.80455pt too wide) in paragraph at lines 8967--8967 []@texttt Fortran runtime error: Index '1' of dimension 1 of array 'x' above u pper bound of 0[] [104] [105] [106] [107] Overfull \hbox (102.54274pt too wide) in paragraph at lines 9301--9301 []@texttt boot.f:61: warning: type of 'ddot' does not match original declarati on [-Wlto-type-mismatch][] Overfull \hbox (125.53749pt too wide) in paragraph at lines 9317--9317 []@texttt rkpk2.f:77:5: warning: type of 'dstup' does not match original decla ration [-Wlto-type-mismatch][] [108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] Overfull \hbox (30.03963pt too wide) in paragraph at lines 10159--10159 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [119] [120] [121] [122] [123] [124] [125] Overfull \hbox (16.31242pt too wide) in paragraph at lines 10739--10739 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [126] [127] [128] [129] [130] [131] [132] [133] [134] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] Overfull \hbox (22.06111pt too wide) in paragraph at lines 12620--12620 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] Warning: unbalanced parentheses in @def... [163] [164] [165] [166] [167] [168] Underfull \hbox (badness 10000) in paragraph at lines 14450--14456 []@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic sEngine.h[]@textrm , @texttt R_ Chapter 7 [169] [170] Chapter 8 [171] [172] [173] Overfull \hbox (22.06111pt too wide) in paragraph at lines 14862--14862 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a s tatic libR[] [174] Overfull \hbox (33.55849pt too wide) in paragraph at lines 14921--14921 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [175] [176] [177] [178] [179] [180] Underfull \hbox (badness 10000) in paragraph at lines 15424--15431 @texttt MACHINE\Software\R-core\R\InstallPath[] @textrm from an ad-min-is-tra- tive in-stall and [181] [182] Underfull \hbox (badness 10000) in paragraph at lines 15547--15551 []@textrm If the de-sired ar-chi-tec-ture is known, look in @texttt Software\R -core\R32[] @textrm or (Function and variable index) [183] [184] [185] [186] Overfull \vbox (1.73251pt too high) has occurred while \output is active Overfull \vbox (1.73251pt too high) has occurred while \output is active (Concept index) [187] [188] [189] ) (see the transcript file for additional information)pdfTeX warning (\pdffontatt r): fonts @textsl and @defsl have conflicting attributes; I will ignore the att ributes assigned to @textsl Output written on R-exts.pdf (195 pages, 961761 bytes). 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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 377. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 377. ) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texmf-dist/tex/latex/base/makeidx.sty) Writing index file fullrefman.idx No file fullrefman.aux. (/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texmf-dist/fon ts/map/pdftex/updmap/pdftex.map}] [1] [2] [1] [2] (./base-pkg.tex Chapter 1. (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4] Underfull \hbox (badness 6741) in paragraph at lines 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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 135--141 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 135--141 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 5050) in paragraph at lines 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 . It Underfull \hbox (badness 1028) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 141--149 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] [9] [10] 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 (4.38043pt too wide) in paragraph at lines 873--873 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [27] Underfull \hbox (badness 1303) in paragraph at lines 1698--1701 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1816--1818 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [38] Underfull \hbox (badness 1107) in paragraph at lines 2460--2462 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [39] [40] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [51] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] [64] Underfull \hbox (badness 4927) in paragraph at lines 4267--4271 []\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 4267--4271 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [65] [66] [67] Underfull \hbox (badness 4595) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [68] [69] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 4590--4590 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = NA)[] Underfull \hbox (badness 1199) in paragraph at lines 4596--4602 []\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 4607--4610 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [70] [71] [72] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4780--4780 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 5033--5035 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 5430--5438 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 1796) in paragraph at lines 5993--6001 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [90] [91] [92] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6187--6187 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6189--6189 []\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 6190--6190 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [93] [94] Underfull \hbox (badness 1242) in paragraph at lines 6325--6329 \T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment. Underfull \hbox (badness 1635) in paragraph at lines 6367--6370 []\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 6371--6374 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [95] Underfull \hbox (badness 1308) in paragraph at lines 6402--6410 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [96] [97] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6556--6556 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [98] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6598--6600 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6746--6749 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6746--6749 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [101] [102] Underfull \hbox (badness 1406) in paragraph at lines 6928--6934 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6948--6950 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [103] Underfull \hbox (badness 1067) in paragraph at lines 6990--6997 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7182--7182 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [107] Underfull \hbox (badness 1231) in paragraph at lines 7307--7313 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [108] [109] [110] [111] Underfull \hbox (badness 10000) in paragraph at lines 7518--7520 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [112] [113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7663--7663 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [114] [115] [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7901--7901 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [117] [118] Underfull \hbox (badness 8132) in paragraph at lines 8002--8006 []\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 8002--8006 \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 8021--8031 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8021--8031 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [119] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8053--8057 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [120] [121] [122] [123] [124] [125] Underfull \hbox (badness 1629) in paragraph at lines 8539--8551 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8539--8551 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [126] [127] [128] Underfull \hbox (badness 10000) in paragraph at lines 8801--8802 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [129] [130] [131] Underfull \hbox (badness 10000) in paragraph at lines 8987--8991 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [132] [133] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9078--9078 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9080--9080 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9105--9105 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [134] [135] Underfull \hbox (badness 5403) in paragraph at lines 9224--9226 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9243--9245 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n /10 formula[][][]\T1/ptm/m/n/10 s, with [136] [137] [138] Underfull \hbox (badness 1603) in paragraph at lines 9454--9457 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1917) in paragraph at lines 10060--10065 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has Overfull \hbox (36.7804pt too wide) in paragraph at lines 10115--10115 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10116--10116 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [148] [149] Underfull \hbox (badness 1168) in paragraph at lines 10218--10223 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [150] Underfull \hbox (badness 10000) in paragraph at lines 10257--10263 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10264--10267 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [151] [152] Underfull \hbox (badness 2828) in paragraph at lines 10423--10427 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10423--10427 \T1/pcr/m/n/10 org / wiki / IEEE _ 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr /m/n/10 https : / / en . wikipedia . org / wiki / Double _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10456--10456 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [153] [154] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10529--10529 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [155] [156] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10673--10673 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [157] [158] [159] Underfull \hbox (badness 6396) in paragraph at lines 10862--10870 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 5288) in paragraph at lines 11786--11788 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [172] Underfull \hbox (badness 3039) in paragraph at lines 11796--11801 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 11856--11858 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [173] [174] Underfull \hbox (badness 4569) in paragraph at lines 11978--11982 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11978--11982 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 12093--12095 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12934--12934 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 2221) in paragraph at lines 13380--13389 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13380--13389 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 13641--13643 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] [199] Underfull \hbox (badness 2573) in paragraph at lines 13756--13758 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr /m/n/10 fsep = [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13906--13908 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 14015--14019 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14026--14029 [][][]$\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 14047--14047 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [204] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14070--14070 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [205] Underfull \hbox (badness 10000) in paragraph at lines 14162--14165 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14172--14172 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [206] Underfull \hbox (badness 10000) in paragraph at lines 14238--14241 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14255--14255 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14284--14284 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14308--14315 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14308--14315 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14316--14320 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14479--14479 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14480--14480 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [211] [212] [213] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14714--14714 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [214] Underfull \hbox (badness 1168) in paragraph at lines 14798--14802 []\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 14798--14802 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [215] Underfull \hbox (badness 6944) in paragraph at lines 14896--14899 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14921--14921 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 15059--15061 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15079--15079 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15085--15085 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [219] Underfull \hbox (badness 2790) in paragraph at lines 15092--15095 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 1024) in paragraph at lines 15123--15130 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [220] Underfull \hbox (badness 10000) in paragraph at lines 15198--15200 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15198--15200 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15220--15225 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15226--15228 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [221] Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15237--15245 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15345--15345 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [223] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15367--15367 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16184--16184 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [236] Underfull \hbox (badness 2418) in paragraph at lines 16293--16297 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16300--16303 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [237] Underfull \hbox (badness 2326) in paragraph at lines 16335--16342 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [238] [239] [240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16581--16581 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [241] Underfull \hbox (badness 1867) in paragraph at lines 16606--16613 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [242] [243] [244] [245] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16875--16875 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16904--16904 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [247] [248] [249] [250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17320--17320 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [251] [252] [253] [254] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17574--17574 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [255] [256] [257] [258] Underfull \hbox (badness 2435) in paragraph at lines 17837--17839 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [259] Underfull \hbox (badness 2285) in paragraph at lines 17903--17905 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17911--17911 []\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 17921--17921 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17941--17941 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [260] [261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18075--18075 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18081--18081 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] [262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18084--18084 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [263] [264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18217--18217 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18225--18225 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [265] [266] [267] Underfull \hbox (badness 10000) in paragraph at lines 18430--18432 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [268] Underfull \hbox (badness 4217) in paragraph at lines 18514--18523 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18529--18545 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 4699) in paragraph at lines 18948--18951 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [275] [276] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19071--19071 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 19206--19208 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19255--19255 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19256--19256 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [280] [281] [282] [283] [284] [285] [286] [287] [288] Underfull \hbox (badness 1975) in paragraph at lines 19834--19837 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1077) in paragraph at lines 20229--20234 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [295] Underfull \hbox (badness 10000) in paragraph at lines 20243--20250 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [296] Underfull \hbox (badness 10000) in paragraph at lines 20317--20321 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [297] [298] Underfull \hbox (badness 10000) in paragraph at lines 20466--20470 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20466--20470 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 20471--20478 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack- [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 20602--20609 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [301] Underfull \hbox (badness 10000) in paragraph at lines 20723--20727 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [302] Underfull \hbox (badness 5161) in paragraph at lines 20793--20798 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [303] [304] [305] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20960--20960 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [306] Underfull \hbox (badness 3343) in paragraph at lines 21020--21024 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [307] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21106--21106 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21117--21117 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [308] [309] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 21231--21231 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 21276--21281 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [310] [311] Underfull \hbox (badness 2564) in paragraph at lines 21367--21370 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21397--21397 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [312] [313] Underfull \hbox (badness 1400) in paragraph at lines 21565--21569 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class [314] [315] [316] Underfull \hbox (badness 2469) in paragraph at lines 21735--21741 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [317] [318] [319] [320] [321] [322] [323] [324] [325] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22363--22363 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22366--22366 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [326] [327] Underfull \hbox (badness 1655) in paragraph at lines 22490--22494 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [328] [329] [330] [331] Underfull \hbox (badness 2277) in paragraph at lines 22739--22742 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 23304--23312 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 23304--23312 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [340] [341] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23381--23381 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1448) in paragraph at lines 23886--23894 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [349] [350] Underfull \hbox (badness 3849) in paragraph at lines 24000--24005 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [351] Underfull \hbox (badness 7308) in paragraph at lines 24077--24083 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24077--24083 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24077--24083 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [352] [353] Underfull \hbox (badness 10000) in paragraph at lines 24240--24242 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [354] [355] [356] Underfull \hbox (badness 6188) in paragraph at lines 24459--24462 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2197) in paragraph at lines 24943--24947 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24943--24947 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use [364] Underfull \hbox (badness 2846) in paragraph at lines 24957--24961 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24957--24961 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 24999--24999 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [365] Underfull \hbox (badness 10000) in paragraph at lines 25051--25057 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25051--25057 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25064--25066 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25115--25115 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [367] [368] [369] Underfull \hbox (badness 8189) in paragraph at lines 25308--25314 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] [370] [371] [372] Underfull \hbox (badness 1694) in paragraph at lines 25530--25533 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [373] [374] [375] Underfull \hbox (badness 1603) in paragraph at lines 25777--25779 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [376] [377] Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [378] [379] Underfull \hbox (badness 3271) in paragraph at lines 26111--26114 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [380] [381] [382] Underfull \hbox (badness 3138) in paragraph at lines 26411--26417 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [383] Underfull \hbox (badness 1194) in paragraph at lines 26424--26427 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 26450--26452 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 26470--26476 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26485--26490 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 26503--26506 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [384] Underfull \hbox (badness 10000) in paragraph at lines 26519--26522 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 []\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma- Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 26541--26548 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [385] [386] [387] [388] Underfull \vbox (badness 10000) has occurred while \output is active [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [390] [391] Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27045--27048 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 27314--27320 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 27314--27320 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and [395] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27336--27336 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 1817) in paragraph at lines 27782--27786 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [403] Underfull \hbox (badness 1796) in paragraph at lines 27850--27853 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [404] [405] [406] Underfull \hbox (badness 10000) in paragraph at lines 28050--28053 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [417] [418] [419] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29004--29004 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29010--29010 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29011--29011 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29014--29014 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [421] Underfull \hbox (badness 7415) in paragraph at lines 29089--29093 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [422] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [423] [424] Underfull \hbox (badness 3713) in paragraph at lines 29279--29290 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [425] Underfull \hbox (badness 1248) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [426] [427] Underfull \hbox (badness 1533) in paragraph at lines 29541--29544 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [428] [429] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [430] Underfull \hbox (badness 1038) in paragraph at lines 29704--29715 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [431] [432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29848--29848 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29851--29851 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29852--29852 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29853--29853 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29860--29860 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [433] [434] [435] [436] [437] Underfull \hbox (badness 4048) in paragraph at lines 30207--30212 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 30207--30212 \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 30207--30212 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [438] [439] [440] [441] [442] [443] [444] [445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 7558) in paragraph at lines 31250--31254 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 31260--31262 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 31265--31268 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and [453] Underfull \hbox (badness 10000) in paragraph at lines 31269--31271 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 31272--31274 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 31677--31681 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [459] [460] [461] [462] [463] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32024--32024 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [464] [465] [466] [467] [468] [469] [470] Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [471] [472] [473] [474] [475] [476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [477] Underfull \hbox (badness 1158) in paragraph at lines 32947--32952 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [478] Underfull \hbox (badness 10000) in paragraph at lines 32974--32980 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 32974--32980 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [479] [480] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33132--33132 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [481] [482] [483] Underfull \hbox (badness 8151) in paragraph at lines 33392--33395 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 . [484] [485] [486] [487] Underfull \hbox (badness 1210) in paragraph at lines 33627--33629 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp ly(nvec,seq_len)) \T1/ptm/m/n/10 and it [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [502] [503] [504] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34816--34816 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34818--34818 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [505] Underfull \hbox (badness 4954) in paragraph at lines 34861--34867 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 34861--34867 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [506] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34972--34972 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [507] [508] [509] [510] [511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35300--35300 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] [512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35315--35315 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [513] [514] [515] [516] [517] [518] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35756--35756 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35757--35757 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [519] [520] [521] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [522] Underfull \hbox (badness 6110) in paragraph at lines 36105--36115 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 36105--36115 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [523] Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 36161--36168 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [524] [525] [526] [527] Overfull \hbox (60.78088pt too wide) in paragraph at lines 36438--36438 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37000--37000 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37248--37248 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37292--37292 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [541] [542] [543] [544] [545] [546] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37726--37726 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37729--37729 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [547] Underfull \hbox (badness 10000) in paragraph at lines 37780--37787 []\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 37780--37787 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37833--37833 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [549] [550] [551] [552] Overfull \hbox (31.3804pt too wide) in paragraph at lines 38134--38134 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [553] Underfull \vbox (badness 10000) has occurred while \output is active [554] [555] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38299--38299 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38337--38337 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 4792) in paragraph at lines 38386--38391 []\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 38386--38391 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [557] Underfull \hbox (badness 2452) in paragraph at lines 38476--38479 \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 38476--38479 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [558] [559] [560] Underfull \hbox (badness 10000) in paragraph at lines 38664--38668 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38679--38682 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [561] [562] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38811--38811 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [563] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38881--38881 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [564] [565] [566] Underfull \hbox (badness 1082) in paragraph at lines 39025--39028 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [567] [568] Underfull \hbox (badness 1038) in paragraph at lines 39216--39219 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [569] [570] [571] [572] [573] [574] Underfull \hbox (badness 1442) in paragraph at lines 39579--39583 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout = TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout = [575] [576] [577] Underfull \hbox (badness 4096) in paragraph at lines 39825--39828 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [578] [579] Underfull \hbox (badness 7888) in paragraph at lines 39939--39943 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10 length(bin) > [580] [581] Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 40095--40095 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] [582] Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 40110--40112 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [583] Underfull \hbox (badness 10000) in paragraph at lines 40190--40193 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [584] [585] Underfull \hbox (badness 3872) in paragraph at lines 40308--40311 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [586] Underfull \hbox (badness 5475) in paragraph at lines 40374--40378 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 40792--40799 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40848--40857 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40848--40857 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40858--40866 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40858--40866 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 2503) in paragraph at lines 40858--40866 \T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [593] Underfull \hbox (badness 1337) in paragraph at lines 40924--40932 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40933--40936 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [594] Underfull \hbox (badness 3460) in paragraph at lines 40987--40990 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 40991--40993 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 41000--41000 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [595] [596] [597] Underfull \hbox (badness 10000) in paragraph at lines 41217--41219 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [598] [599] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41339--41339 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41341--41341 []\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 [600] [601] [602] [603] [604] Underfull \hbox (badness 6542) in paragraph at lines 41703--41705 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [605] [606] Overfull \hbox (30.78088pt too wide) in paragraph at lines 41822--41822 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [607] Underfull \hbox (badness 1708) in paragraph at lines 41890--41898 []\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 41890--41898 \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 4859) in paragraph at lines 41920--41925 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [608] Underfull \hbox (badness 3895) in paragraph at lines 41982--41994 []\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 41982--41994 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [609] [610] [611] [612] [613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 42305--42305 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [614] [615] [616] [617] [618] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42772--42772 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [620] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42781--42781 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [621] Underfull \hbox (badness 1803) in paragraph at lines 42906--42909 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [622] Underfull \hbox (badness 3471) in paragraph at lines 42910--42917 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [623] [624] [625] Underfull \hbox (badness 3668) in paragraph at lines 43125--43127 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [626] Overfull \hbox (36.78088pt too wide) in paragraph at lines 43229--43229 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43304--43304 []\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 43312--43312 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [628] [629] Underfull \hbox (badness 6220) in paragraph at lines 43442--43447 []\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 43442--43447 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, [630] Underfull \hbox (badness 10000) in paragraph at lines 43463--43468 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 4229) in paragraph at lines 43463--43468 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [631] Underfull \hbox (badness 2818) in paragraph at lines 43553--43559 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [632] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43588--43588 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [633] Underfull \hbox (badness 1622) in paragraph at lines 43682--43684 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [634] [635] [636] [637] [638] Underfull \hbox (badness 2846) in paragraph at lines 44045--44049 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44085--44085 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 44106--44110 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [640]) (./compiler-pkg.tex Chapter 2. [641] Underfull \hbox (badness 2884) in paragraph at lines 105--119 []\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 105--119 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [642] [643] [644]) (./datasets-pkg.tex Chapter 3. [645] [646] [647] [648] [649] 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,[] [650] 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 [651] [652] [653] [654] [655] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [656] [657] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [658] [659] 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. [660] [661] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [662] [663] [664] [665] [666] 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)")[] [667] [668] 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 [669] [670] [671] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [672] 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)[] [673] [674] 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]]))))[] [675] [676] [677] [678] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [679] [680] [681] Overfull \vbox (4.29591pt too high) has occurred while \output is active [682] [683] [684] [685] [686] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [687] Overfull \vbox (13.87083pt too high) has occurred while \output is active [688] Underfull \vbox (badness 2376) has occurred while \output is active [689] [690] Overfull \vbox (12.25539pt too high) has occurred while \output is active [691] [692] Overfull \vbox (17.12102pt too high) has occurred while \output is active [693] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [694] [695] [696] [697] [698] [699] [700] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [701] [702] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [703] Overfull \vbox (10.49593pt too high) has occurred while \output is active [704] Overfull \vbox (15.49593pt too high) has occurred while \output is active [705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3989--3992 []\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 3998--4000 []\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 3998--4000 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719]) (./grDevices-pkg.tex [720] Chapter 4. [721] [722] [723] [724] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in [725] [726] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 379--387 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [727] [728] Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [738] [739] Underfull \hbox (badness 10000) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [740] Underfull \hbox (badness 1173) in paragraph at lines 1322--1325 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [741] [742] [743] [744] [745] [746] [747] [748] Underfull \hbox (badness 1565) in paragraph at lines 1810--1815 []\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 1810--1815 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [749] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 1934--1944 []\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 1934--1944 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [750] [751] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [752] [753] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [754] [755] Underfull \hbox (badness 2326) in paragraph at lines 2341--2351 \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 2341--2351 \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 2341--2351 \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 2341--2351 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [756] [757] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444 []\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 [758] Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE) Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE)[] [759] [760] [761] [762] [763] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [764] [765] [766] [767] [768] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [769] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245 []\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 3246--3246 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [770] [771] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3384--3389 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [772] [773] [774] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) Underfull \hbox (badness 8170) in paragraph at lines 3571--3574 []\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 , [775] Underfull \hbox (badness 10000) in paragraph at lines 3655--3659 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [776] [777] Underfull \hbox (badness 5260) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [778] [779] [780] [781] [782] Underfull \hbox (badness 5939) in paragraph at lines 4113--4118 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [783] [784] [785] [786] [787] [788] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / Underfull \hbox (badness 3612) in paragraph at lines 4514--4519 \T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat . [789] [790] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [791] [792] Underfull \hbox (badness 1348) in paragraph at lines 4828--4831 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [793] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 4892--4898 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [794] Underfull \hbox (badness 1112) in paragraph at lines 4923--4927 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), \T1/pcr/m/n/10 "CP1251.enc" [795] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [796] [797] [798] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\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 5256--5260 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [799] [800] Underfull \hbox (badness 1552) in paragraph at lines 5380--5389 \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 5380--5389 \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 5380--5389 \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 5390--5392 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5422--5428 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [801] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [802] [803] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [804] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [805] [806] Underfull \hbox (badness 10000) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [807] [808] [809] [810] [811] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112 []\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 6125--6128 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [812] [813] [814] [815] [816] [817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 6728--6733 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [822] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [823] Underfull \hbox (badness 5954) in paragraph at lines 6872--6875 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : [824] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [825] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [826] Underfull \hbox (badness 10000) in paragraph at lines 7084--7091 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7084--7091 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [827] Underfull \hbox (badness 5607) in paragraph at lines 7168--7172 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [828] [829] Underfull \hbox (badness 5637) in paragraph at lines 7345--7351 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , [830] Underfull \hbox (badness 1721) in paragraph at lines 7378--7381 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [831] [832] Underfull \hbox (badness 1231) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [833] [834] [835]) (./graphics-pkg.tex [836] Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use \T1/pcr/m/n/10 library(help = [837] [838] [839] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [840] 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- [841] [842] [843] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [844] [845] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [846] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [847] [848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 960--964 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able. Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [852] [853] [854] [855] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1265--1265 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [856] [857] [858] Underfull \hbox (badness 1024) in paragraph at lines 1427--1435 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1461--1463 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [859] [860] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1531--1531 []\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 1532--1532 []\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 1538--1538 []\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 1539--1539 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [861] [862] [863] [864] Underfull \hbox (badness 10000) in paragraph at lines 1839--1845 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [865] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [866] [867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1970--1970 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [868] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2099--2099 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] [869] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2104--2104 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [870] [871] [872] [873] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2390--2397 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [874] Underfull \hbox (badness 7273) in paragraph at lines 2472--2476 [][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 2485--2485 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [875] [876] [877] [878] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2719--2719 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [879] [880] [881] Underfull \hbox (badness 1226) in paragraph at lines 2880--2884 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy Overfull \hbox (15.18042pt too wide) in paragraph at lines 2933--2933 []\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 2937--2937 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [882] Underfull \hbox (badness 10000) in paragraph at lines 2989--2992 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [883] [884] [885] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3194--3194 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3199--3199 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [886] [887] Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [888] [889] [890] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3524--3524 []\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 3543--3543 [] \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 3547--3547 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [891] [892] [893] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3724--3724 [] \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 3725--3725 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3764--3764 [] \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 [895] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3816--3816 []\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 3824--3824 []\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 3826--3826 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3834--3834 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [896] Underfull \hbox (badness 10000) in paragraph at lines 3897--3901 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [897] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4008--4008 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [898] [899] [900] [901] Underfull \hbox (badness 3930) in paragraph at lines 4215--4217 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [902] [903] [904] [905] Underfull \hbox (badness 1286) in paragraph at lines 4526--4529 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing [906] Underfull \hbox (badness 3229) in paragraph at lines 4534--4539 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4631--4631 []\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 4636--4636 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [908] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4680--4680 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [909] Underfull \hbox (badness 1264) in paragraph at lines 4754--4767 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4891--4897 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [912] Underfull \hbox (badness 10000) in paragraph at lines 5022--5025 [913 ] Underfull \hbox (badness 10000) in paragraph at lines 5083--5085 Underfull \vbox (badness 10000) has occurred while \output is active [914] [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5273--5275 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [917] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5329--5329 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5330--5330 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [918] [919] [920] [921] [922] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5695--5695 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [923] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5696--5696 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 1360) in paragraph at lines 5747--5751 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type = [924] [925] [926] [927] [928] [929] [930] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6181--6181 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6187--6187 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [931] [932] [933] [934] [935] [936] Underfull \hbox (badness 10000) in paragraph at lines 6614--6616 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [937] [938] Underfull \hbox (badness 1028) in paragraph at lines 6708--6710 []\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 6751--6752 [][] [939 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6845--6845 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [940] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6876--6876 [] \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 [941] [942] Underfull \hbox (badness 10000) in paragraph at lines 6998--7000 []\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 7025--7025 [] \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 7031--7031 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [943] Underfull \hbox (badness 2600) in paragraph at lines 7091--7093 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7323--7323 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [948] [949] [950] [951] [952] [953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7714--7714 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [954] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7726--7726 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [955] [956] [957] [958] [959] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8075--8075 []\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 8078--8078 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8082--8082 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [960] [961] [962] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8253--8253 []\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 8254--8254 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [963] [964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8358--8358 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8369--8374 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [965] Underfull \hbox (badness 1112) in paragraph at lines 8417--8421 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [966] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8477--8477 []\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 8492--8492 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8623--8623 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [969] [970] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8808--8808 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [971] Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8838--8840 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8870--8876 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8918 \HeaderA{units}{Graphical Units}{units} [973] Underfull \hbox (badness 1205) in paragraph at lines 8983--8985 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [974] [975] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9102--9102 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [976]) (./grid-pkg.tex Chapter 6. [977] [978] [979] [980] [981] [982] [983] [984] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 476--482 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [995] [996] [997] [998] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1005] [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981 []\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 1982--1982 []\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 1983--1983 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1008] Underfull \hbox (badness 2961) in paragraph at lines 2018--2023 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [1009] Underfull \hbox (badness 1430) in paragraph at lines 2077--2082 []\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 2106--2109 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [1010] [1011] [1012] Underfull \hbox (badness 2894) in paragraph at lines 2313--2320 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1013] [1014] [1015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2481--2486 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1016] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1017] [1018] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1019] [1020] [1021] [1022] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1023] [1024] [1025] [1026] [1027] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1029] Underfull \hbox (badness 2799) in paragraph at lines 3411--3417 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1032] [1033] [1034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1035] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1048] Underfull \hbox (badness 1430) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1049] [1050] [1051] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] Underfull \hbox (badness 6859) in paragraph at lines 6056--6062 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6056--6062 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1072] [1073] [1074] [1075] [1076] Underfull \hbox (badness 1867) in paragraph at lines 6366--6368 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1077] Underfull \hbox (badness 10000) in paragraph at lines 6403--6409 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1078] [1079] Underfull \hbox (badness 1371) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1083]) (./methods-pkg.tex [1084] Chapter 7. [1085] [1086] 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 [1087] [1088] [1089] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1090] [1091] 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[] [1092] 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 [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] 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[] [1109] [1110] 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 [1111] [1112] [1113] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1114] [1115] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[] [][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call 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}:[] [1116] [1117] [1118] 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 [1119] 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))[] [1120] [1121] [1122] 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:[] [1123] [1124] [1125] [1126] [1127] [1128] [1129] 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 [1130] [1131] 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 [1132] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1133] [1134] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1135] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1136] [1137] [1138] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1139] [1140] [1141] 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,[] [1142] 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) [1143] [1144] [1145] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1146] [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1149] [1150] [1151] [1152] 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[] [1153] 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 [1154] [1155] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1156] [1157] 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 [1158] [1159] [1160] 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 [1161] [1162] [1163] [1164] [1165] [1166] 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 [1167] [1168] 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 [1169] 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 [1170] [1171] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1172] Underfull \vbox (badness 10000) has occurred while \output is active [1173] [1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1176] 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().[] [1177] [1178] 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")[] [1179]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 [1180] 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 , [1181] [1182] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see 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 [1183] [1184] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] 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 [1196] 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(), [1197] 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 =,[] [1198] [1199] [1200] [1201] 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[] [1202] [1203] [1204] 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")[] [1205] [1206] [1207] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1208] [1209] [1210] [1211] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1212] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class 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 [1223] [1224] [1225]) (./parallel-pkg.tex [1226] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1227] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1228] [1229] 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 [1230] [1231] [1232] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1233] [1234] [1235] [1236] Underfull \hbox (badness 1917) in paragraph at lines 744--753 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 744--753 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1237] [1238] Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1239] [1240] [1241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1242] Underfull \hbox (badness 5388) in paragraph at lines 1145--1150 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1243] Underfull \hbox (badness 10000) in paragraph at lines 1169--1177 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1246] Underfull \hbox (badness 1577) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1411--1413 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1247] [1248]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1257] Underfull \hbox (badness 1424) in paragraph at lines 594--596 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1258] [1259] Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1260] [1261] [1262]) (./stats-pkg.tex Chapter 10. [1263] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1264] [1265] [1266] [1267] [1268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1269] Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1024) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1285] [1286] [1287] [1288] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1302] [1303] [1304] [1305] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 3175--3177 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3223--3223 []\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 3224--3224 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1310] [1311] [1312] [1313] [1314] [1315] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3615--3615 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1316] [1317] [1318] [1319] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3893--3893 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1320] [1321] [1322] [1323] [1324] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4182--4182 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4183--4183 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1328] [1329] [1330] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4589--4589 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1331] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1332] [1333] [1334] [1335] [1336] [1337] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5066--5066 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5068--5068 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1338] [1339] [1340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5289--5289 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5307--5307 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1341] [1342] [1343] Underfull \hbox (badness 1436) in paragraph at lines 5517--5522 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1344] [1345] [1346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1347] [1348] [1349] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1350] [1351] [1352] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6067--6067 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1353] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6175--6175 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1354] Underfull \hbox (badness 10000) in paragraph at lines 6242--6247 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1355] [1356] [1357] [1358] Underfull \hbox (badness 5954) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1359] Underfull \hbox (badness 2503) in paragraph at lines 6520--6523 []\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 6524--6526 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6527--6532 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, Underfull \hbox (badness 7238) in paragraph at lines 6563--6566 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6598--6598 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6613--6613 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6628--6628 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [1361] [1362] [1363] [1364] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1365] [1366] [1367] [1368] [1369] [1370] Underfull \hbox (badness 10000) in paragraph at lines 7270--7274 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1371] Underfull \hbox (badness 6493) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1372] [1373] Underfull \hbox (badness 10000) in paragraph at lines 7506--7509 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1374] [1375] [1376] [1377] [1378] [1379] [1380] Underfull \hbox (badness 10000) in paragraph at lines 7918--7923 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 1210) in paragraph at lines 8273--8275 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1386] [1387] [1388] [1389] [1390] [1391] [1392] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8736--8736 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] Underfull \vbox (badness 10000) has occurred while \output is active [1393] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8781--8781 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8784--8784 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1394] [1395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8922--8922 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1396] [1397] [1398] [1399] [1400] [1401] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9350--9350 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1402] [1403] [1404] Underfull \hbox (badness 7291) in paragraph at lines 9529--9531 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1405] [1406] [1407] [1408] [1409] [1410] Underfull \hbox (badness 6944) in paragraph at lines 9990--9996 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1411] [1412] [1413] Underfull \hbox (badness 3758) in paragraph at lines 10203--10206 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1414] [1415] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10465--10470 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1418] Underfull \hbox (badness 4132) in paragraph at lines 10504--10508 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10558--10564 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1419] Underfull \hbox (badness 10000) in paragraph at lines 10609--10612 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1420] [1421] [1422] Underfull \hbox (badness 2142) in paragraph at lines 10825--10828 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1423] [1424] Underfull \hbox (badness 1708) in paragraph at lines 10906--10910 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10948--10954 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, [1425] Underfull \hbox (badness 1418) in paragraph at lines 10986--10991 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1426] Underfull \hbox (badness 2635) in paragraph at lines 11119--11122 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1427] [1428] [1429] Underfull \hbox (badness 1694) in paragraph at lines 11302--11305 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1431] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11449--11453 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1432] [1433] [1434] Underfull \hbox (badness 7379) in paragraph at lines 11629--11632 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1435] [1436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11783 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1438] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11901--11906 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11918--11920 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1439] [1440] [1441] [1442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1443] [1444] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12534--12536 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1449] Underfull \hbox (badness 2753) in paragraph at lines 12603--12605 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1450] [1451] [1452] [1453] Underfull \hbox (badness 6910) in paragraph at lines 12841--12843 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of \T1/pcr/m/n/10 ob Underfull \hbox (badness 2894) in paragraph at lines 12847--12851 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12847--12851 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1464] Underfull \hbox (badness 4518) in paragraph at lines 13597--13602 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1465] [1466] [1467] Underfull \hbox (badness 10000) in paragraph at lines 13796--13800 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 1163) in paragraph at lines 14129--14137 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1473] Underfull \hbox (badness 4518) in paragraph at lines 14249--14254 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1474] [1475] [1476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14436--14436 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1477] [1478] [1479] [1480] [1481] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14780--14780 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1482] [1483] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1484] [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2726) in paragraph at lines 15279--15282 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1501] [1502] Underfull \hbox (badness 1490) in paragraph at lines 16136--16141 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1503] Underfull \hbox (badness 1648) in paragraph at lines 16202--16204 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1504] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1514] [1515] [1516] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Underfull \vbox (badness 10000) has occurred while \output is active [1528] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1529] [1530] [1531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18043--18043 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] Underfull \hbox (badness 1248) in paragraph at lines 18581--18584 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18594--18598 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce [1541] Underfull \hbox (badness 1478) in paragraph at lines 18602--18606 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18660--18662 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1542] [1543] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1544] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18830--18830 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18850--18850 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1545] Underfull \hbox (badness 2564) in paragraph at lines 18888--18899 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18888--18899 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1547] [1548] [1549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1550] Underfull \hbox (badness 1337) in paragraph at lines 19252--19255 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1557] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 19661--19661 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1558] Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su ch it-er-a-tions for Underfull \hbox (badness 5260) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa r-tic-u-larly de-sir-able for [1559] Underfull \hbox (badness 3049) in paragraph at lines 19748--19752 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1560] [1561] [1562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] [1563] Underfull \hbox (badness 1194) in paragraph at lines 20006--20009 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1564] Underfull \hbox (badness 1107) in paragraph at lines 20064--20066 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1565] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1566] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1567] [1568] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1569] Underfull \hbox (badness 7740) in paragraph at lines 20408--20410 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1570] [1571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20553--20553 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1585] Underfull \hbox (badness 6859) in paragraph at lines 21474--21481 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21485--21491 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1598] [1599] [1600] [1601] [1602] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 1337) in paragraph at lines 22834--22840 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1616] [1617] Underfull \hbox (badness 1028) in paragraph at lines 23540--23543 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1618] [1619] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1620] Underfull \hbox (badness 7944) in paragraph at lines 23705--23707 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1621] Underfull \hbox (badness 7944) in paragraph at lines 23767--23769 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1622] [1623] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1624] [1625] [1626] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1627] [1628] Underfull \hbox (badness 10000) in paragraph at lines 24235--24238 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1629] Underfull \hbox (badness 2134) in paragraph at lines 24287--24291 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24300--24300 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \vbox (badness 10000) has occurred while \output is active [1636] [1637] Underfull \hbox (badness 6268) in paragraph at lines 24777--24782 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1638] [1639] [1640] Underfull \hbox (badness 1867) in paragraph at lines 24982--24984 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1641] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1642] [1643] [1644] Underfull \hbox (badness 2495) in paragraph at lines 25221--25230 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1645] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25310--25312 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1646] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25422--25422 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25425--25425 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1647] [1648] [1649] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25651--25657 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1650] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25718--25718 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1651] Underfull \hbox (badness 1019) in paragraph at lines 25780--25785 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1652] [1653] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1654] [1655] [1656] [1657] [1658] [1659] [1660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1661] [1662] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f or when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26487--26487 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1663] Underfull \hbox (badness 2922) in paragraph at lines 26556--26561 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1664] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26593--26593 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26605--26605 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26606--26606 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26610--26610 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1665] Underfull \hbox (badness 3240) in paragraph at lines 26664--26667 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1666] Overfull \hbox (36.7804pt too wide) in paragraph at lines 26685--26685 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26688--26688 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26771--26771 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26775--26775 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26785--26785 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1668] Underfull \hbox (badness 2922) in paragraph at lines 26826--26832 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26848--26848 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1669] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26864--26864 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1670] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26978--26978 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1671] Underfull \hbox (badness 2922) in paragraph at lines 27040--27045 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1672] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27078--27078 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1673] Underfull \hbox (badness 2922) in paragraph at lines 27127--27132 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27158--27158 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1674] Underfull \hbox (badness 2922) in paragraph at lines 27192--27197 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27217--27217 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27221--27221 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] [1675] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27241--27241 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27251--27251 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27286--27291 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1676] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27308--27308 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27326--27326 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1677] Underfull \hbox (badness 6493) in paragraph at lines 27378--27383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27405--27405 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1678] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27410--27410 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27413--27413 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692] Underfull \hbox (badness 3396) in paragraph at lines 28337--28339 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1693] [1694] [1695] Underfull \hbox (badness 2237) in paragraph at lines 28514--28516 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1696] [1697] Underfull \hbox (badness 2591) in paragraph at lines 28678--28680 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1698] Underfull \hbox (badness 2237) in paragraph at lines 28724--28727 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1699] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28797--28797 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1700] [1701] Underfull \hbox (badness 3407) in paragraph at lines 28905--28909 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1702] [1703] Underfull \hbox (badness 1337) in paragraph at lines 29038--29042 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1704] [1705] [1706] [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29286--29286 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29314--29314 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1708] Underfull \hbox (badness 1616) in paragraph at lines 29340--29343 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1709] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29419--29419 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1710] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29496--29496 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1711] [1712] Underfull \hbox (badness 2205) in paragraph at lines 29585--29590 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30180--30180 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30181--30181 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1722] [1723] [1724] [1725] [1726] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30481--30481 [] \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 30482--30482 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1727] [1728] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30608--30608 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30617--30617 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Underfull \hbox (badness 1337) in paragraph at lines 30834--30838 []\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 [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1337) in paragraph at lines 31361--31365 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31788--31788 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1747] Underfull \hbox (badness 6775) in paragraph at lines 31845--31850 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31908--31908 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1749]) (./stats4-pkg.tex [1750] Chapter 11. [1751] [1752] [1753] 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))[] [1754] [1755] [1756]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} [1757] [1758] [1759]) (./tcltk-pkg.tex [1760] Chapter 12. [1761] [1762] [1763] [1764] 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[] [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] 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 [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] 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 [1780]) (./tools-pkg.tex Chapter 13. [1781] 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.[] [1782] 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 [1783] 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)[] [1784] 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 , [1785] 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 [1786] [1787] [1788] [1789] [1790] [1791] [1792] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1793] [1794] Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1795] [1796] [1797] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1139--1149 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1798] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\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 1169--1171 []\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 1206--1209 []\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 1206--1209 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1799] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\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 [1800] [1801] Underfull \hbox (badness 10000) in paragraph at lines 1363--1366 []\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 [1802] [1803] [1804] [1805] [1806] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1807] [1808] [1809]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1810] [1811] [1812] [1813] Underfull \hbox (badness 1142) in paragraph at lines 2168--2174 []\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 2202--2202 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1814] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2230--2237 []\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 2230--2237 \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 2230--2237 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1815] Underfull \hbox (badness 1342) in paragraph at lines 2282--2288 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1817] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1818] [1819] [1820] [1821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2705--2705 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1822] Underfull \hbox (badness 2486) in paragraph at lines 2750--2758 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1072) in paragraph at lines 3128--3130 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1828] [1829] [1830] [1831] [1832] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1833] [1834] [1835] [1836] Underfull \hbox (badness 4108) in paragraph at lines 3712--3719 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1837] [1838] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3812--3812 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3815--3815 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\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 3849--3855 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1839] [1840] Underfull \hbox (badness 7832) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1841] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4047--4047 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1842] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4258--4258 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1846] [1847] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4420--4420 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4431--4434 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1848] Underfull \hbox (badness 6859) in paragraph at lines 4447--4452 []\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 4455--4461 []\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 4455--4461 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1849] [1850] [1851] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4654--4654 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4655--4655 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4667--4670 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4671--4681 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4706--4712 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4706--4712 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1852] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4760--4765 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\ T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing ex-ist-ing [1853] [1854] [1855]) (./utils-pkg.tex [1856] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1857] [1858] [1859] [1860] 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[] [1861] Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1862] Underfull \hbox (badness 10000) in paragraph at lines 382--384 []\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han- dles, by de-fault pro-duced by [1863] Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1864] [1865] Underfull \hbox (badness 1946) in paragraph at lines 624--628 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1866] Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674 []\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 680--680 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 717--723 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1868] Underfull \hbox (badness 4505) in paragraph at lines 850--856 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1869] [1870] [1871] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1872] Underfull \hbox (badness 1748) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/ ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1661) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \ T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1873] Underfull \hbox (badness 10000) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1874] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1883] [1884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1885] [1886] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1887] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1888] [1889] [1890] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1891] [1892] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1893] Underfull \hbox (badness 1082) in paragraph at lines 2561--2565 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2597--2599 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1894] [1895] Underfull \hbox (badness 10000) in paragraph at lines 2685--2687 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1896] [1897] [1898] Underfull \hbox (badness 10000) in paragraph at lines 2902--2904 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1899] [1900] [1901] [1902] Underfull \hbox (badness 1762) in paragraph at lines 3196--3199 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package = [1903] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1904] Underfull \hbox (badness 2452) in paragraph at lines 3359--3362 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1905] [1906] [1907] [1908] [1909] [1910] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3849--3853 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1913] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1914] [1915] Underfull \hbox (badness 4660) in paragraph at lines 4119--4122 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1916] [1917] [1918] Underfull \hbox (badness 1565) in paragraph at lines 4328--4332 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1920] Underfull \hbox (badness 1931) in paragraph at lines 4446--4453 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1921] [1922] [1923] [1924] [1925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1943] Underfull \hbox (badness 10000) in paragraph at lines 6036--6038 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1944] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1945] [1946] [1947] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1948] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6338--6341 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1949] [1950] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1951] [1952] Underfull \hbox (badness 5091) in paragraph at lines 6628--6630 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 5331) in paragraph at lines 6644--6650 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") [1953] Underfull \hbox (badness 1270) in paragraph at lines 6673--6683 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., [1954] Underfull \hbox (badness 10000) in paragraph at lines 6778--6782 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , Underfull \hbox (badness 2376) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1955] Underfull \hbox (badness 1314) in paragraph at lines 6879--6886 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1956] Underfull \hbox (badness 10000) in paragraph at lines 6936--6941 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1957] Underfull \hbox (badness 5133) in paragraph at lines 6995--6999 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7009--7012 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1958] [1959] Underfull \hbox (badness 4132) in paragraph at lines 7176--7178 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1960] [1961] [1962] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1963] [1964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1965] Underfull \hbox (badness 10000) in paragraph at lines 7526--7528 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1966] [1967] Underfull \hbox (badness 10000) in paragraph at lines 7711--7713 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 7716--7718 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1968] [1969] [1970] [1971] Underfull \hbox (badness 1859) in paragraph at lines 7939--7942 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1972] Underfull \hbox (badness 1655) in paragraph at lines 8032--8035 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8043--8043 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1973] [1974] Underfull \hbox (badness 1917) in paragraph at lines 8134--8136 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [1975] [1976] [1977] [1978] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8407--8407 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8408--8408 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] Underfull \hbox (badness 10000) in paragraph at lines 8436--8438 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from [1979] Underfull \hbox (badness 10000) in paragraph at lines 8450--8452 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8458--8463 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, Overfull \hbox (9.78043pt too wide) in paragraph at lines 8504--8504 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8505--8505 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1980] [1981] Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8634--8639 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [1982] [1983] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8757--8757 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8758--8758 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8929--8929 [] \T1/pcr/m/n/9 "S original, "),[] [1986] [1987] Underfull \hbox (badness 1789) in paragraph at lines 9060--9062 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 5203) in paragraph at lines 9633--9636 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1996] [1997] [1998] Underfull \hbox (badness 1394) in paragraph at lines 9859--9866 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1999] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9883--9883 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2000] [2001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10044--10044 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2002] [2003] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10225--10225 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2004] [2005] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10311--10311 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10314--10314 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10319--10319 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2006] Underfull \hbox (badness 2027) in paragraph at lines 10391--10394 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2007] [2008] [2009] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10664--10664 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 10665--10665 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] [2010] Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2011] [2012] [2013] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10905--10905 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2014] [2015] [2016] [2017] Underfull \hbox (badness 10000) in paragraph at lines 11165--11169 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [2018] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11183--11183 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11188--11188 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2019] [2020] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11372--11372 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2021] [2022] Underfull \hbox (badness 1917) in paragraph at lines 11496--11499 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11496--11499 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [2023] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2024] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []\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 Underfull \hbox (badness 6725) in paragraph at lines 11632--11641 \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 11632--11641 \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 11632--11641 \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 11632--11641 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2025] [2026] Underfull \hbox (badness 3646) in paragraph at lines 11758--11760 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2027] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11796--11796 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2028] [2029] [2030] Underfull \hbox (badness 10000) in paragraph at lines 11977--11981 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12008--12014 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2031] [2032] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12184--12184 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12202--12214 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2033] Underfull \hbox (badness 2600) in paragraph at lines 12239--12241 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2034] Underfull \hbox (badness 1043) in paragraph at lines 12282--12287 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2035] [2036] [2037] [2038] Underfull \hbox (badness 1888) in paragraph at lines 12575--12578 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 12590--12593 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2039] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12631--12631 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] Underfull \hbox (badness 2158) in paragraph at lines 12686--12689 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [2040] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12734--12734 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2041] [2042] Underfull \hbox (badness 2302) in paragraph at lines 12891--12893 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2043] [2044] Underfull \hbox (badness 3333) in paragraph at lines 12998--13000 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2045] [2046] [2047] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13163--13163 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13187--13192 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][ ]\T1/pcr/m/n/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13196--13199 []\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 13196--13199 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2048] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2049] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13282--13282 []\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 13289--13289 []\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 13291--13291 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2050] [2051] Underfull \hbox (badness 10000) in paragraph at lines 13459--13461 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2052] [2053] [2054] Underfull \hbox (badness 6300) in paragraph at lines 13616--13623 []\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 13616--13623 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 13616--13623 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2055] [2056] Underfull \hbox (badness 2020) in paragraph at lines 13785--13801 \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 13785--13801 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2057] [2058] Underfull \hbox (badness 5022) in paragraph at lines 13925--13929 []\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 13932--13935 [][][]$\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 13932--13935 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2059] [2060] [2061] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14096--14096 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2062] [2063] [2064] [2065] [2066] [2067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14536--14536 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14542--14542 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14563--14565 []\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 14576--14580 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 14590--14594 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 14596--14601 []\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 14596--14601 \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 14596--14601 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2068] Underfull \hbox (badness 10000) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 14653--14658 []\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 14661--14664 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2069] Overfull \hbox (9.78043pt too wide) in paragraph at lines 14715--14715 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2070] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 14917--14920 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 14917--14920 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2073] Overfull \hbox (42.18039pt too wide) in paragraph at lines 14933--14933 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15000--15000 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15022--15022 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2075] [2076] Underfull \hbox (badness 1297) in paragraph at lines 15153--15155 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2077] Underfull \hbox (badness 4036) in paragraph at lines 15200--15202 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2078] [2079] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15337--15337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2080] Underfull \hbox (badness 1715) in paragraph at lines 15389--15392 []\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 15434--15436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/pcr/m/n/10 file = [2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex Chapter 15. [2087] 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) [2088] [2089] [2090] [2091] [2092] 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, [2093] [2094] [2095] [2096]) (./MASS-pkg.tex Chapter 16. [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] 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))[] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] 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"),[] [2131] [2132] [2133] [2134] 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 [2135] [2136] [2137] 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 10000) 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 , [2138] [2139] 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 [2140] [2141] [2142] 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, ...)[] [2143] 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")[] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] 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 [2156] [2157] [2158] [2159] [2160] [2161] [2162] 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", ...)[] [2163] [2164] [2165] 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, [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] 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) [2180] 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") [2181] [2182]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} [2183] 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 [2184] [2185] [2186] [2187] Underfull \vbox (badness 10000) has occurred while \output is active [2188] 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)))[] [2189] 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"))[] [2190] [2191] [2192] [2193] [2194] [2195] 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"))[] [2196] 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 ) = [2197] 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)[] [2198] [2199] 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 [2200] [2201] 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")[] [2202] 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"), ...)[] [2203] [2204] [2205] [2206] [2207] [2208] 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 [2209] [2210] 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 [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] 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, ...)[] [2231] Underfull \hbox (badness 2035) in paragraph at lines 9595--9597 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1 /pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 , Underfull \hbox (badness 1158) in paragraph at lines 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), [2232] 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)[] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]) (./Matrix-pkg.tex [2246] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2247] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2248] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2249] 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 [2250] [2251] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) 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 [2252] 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)],[] [2253] [2254] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] 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)[] [2255] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2256] [2257] [2258] 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"), ...)[] [2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) 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} [2261pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] Underfull \hbox (badness 2285) in paragraph at lines 1220--1225 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2262] 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[] [2263] 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 [2264] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2265] 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)))[] [2266] Underfull \hbox (badness 10000) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or 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 [2267]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} [2268] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2269] [2270] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2271] [2272] [2273] [2274] [2275] Underfull \hbox (badness 1484) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2276] Underfull \hbox (badness 7379) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2277] [2278] [2279] Underfull \hbox (badness 4846) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2280] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2281] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2282] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2283] Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2286] Underfull \hbox (badness 2469) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2287] [2288] Underfull \hbox (badness 10000) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3528--3532 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2289] Underfull \hbox (badness 2285) in paragraph at lines 3578--3581 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2290] [2291] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2292] Underfull \hbox (badness 10000) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2293] [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2296] Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2297] [2298] Underfull \hbox (badness 3158) in paragraph at lines 4288--4292 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2299] [2300] [2301] [2302] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2307] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2308] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2309] [2310] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2311] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2312] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5279--5282 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5292--5295 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2313] Underfull \hbox (badness 4765) in paragraph at lines 5310--5313 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2314] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2315] [2316] [2317] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2318] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2319] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2321] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2322] Underfull \hbox (badness 6063) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2323] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2324] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2325] Underfull \hbox (badness 3179) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2326] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2327] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2328] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2330] [2331] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2332] [2333]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.det}) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 10000) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2334]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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} Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2335] [2336pdfTeX warning (ext4): destination with the same identifier (name{R fn.crossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7426--7431 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7431--7435 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7431--7435 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2337] [2338] Underfull \hbox (badness 1009) in paragraph at lines 7577--7579 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2339] Underfull \hbox (badness 6063) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2340] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2341] [2342] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2343] Underfull \hbox (badness 2635) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7912--7917 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2344] Underfull \hbox (badness 3482) in paragraph at lines 7994--8000 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2345] Underfull \hbox (badness 1867) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim- [2346]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8356--8366 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2348] Underfull \hbox (badness 3179) in paragraph at lines 8427--8430 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2349] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2350] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2352] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8721--8724 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8727--8734 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2353] [2354] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8855--8865 []\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 8855--8865 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2355] [2356]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2357] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040 []\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 9044--9044 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2358] Underfull \hbox (badness 10000) in paragraph at lines 9122--9128 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9139--9142 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2359] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2360] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232 []\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 9233--9233 []\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.9252 ... the Reciprocal Condition Number}{rcond} [2361] [2362] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2363] [2364] Underfull \hbox (badness 10000) in paragraph at lines 9550--9552 []\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 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2365] [2366] Underfull \hbox (badness 1558) in paragraph at lines 9701--9704 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2367] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926 [] \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 9931--9931 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2369] Underfull \hbox (badness 1616) in paragraph at lines 9966--9978 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 9983--9986 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10005--10015 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10005--10015 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, [2370] Underfull \hbox (badness 6032) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10039--10041 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10062--10063 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10068--10070 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10072--10073 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10080--10083 [][][]\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 10098--10098 []\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 10102--10102 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2371] Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\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 10151--10153 []\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 10159--10162 []\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 10159--10162 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\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 10170--10174 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for [2372] Underfull \hbox (badness 6592) in paragraph at lines 10181--10183 []\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 Underfull \hbox (badness 1158) in paragraph at lines 10199--10205 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2373] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2374] [2375] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2376] Underfull \hbox (badness 4621) in paragraph at lines 10485--10489 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2377] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2379] Underfull \hbox (badness 10000) in paragraph at lines 10733--10741 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class [2380] Underfull \hbox (badness 10000) in paragraph at lines 10784--10788 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2381] [2382] Underfull \hbox (badness 10000) in paragraph at lines 10954--10956 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2383] Underfull \hbox (badness 2970) in paragraph at lines 11143--11149 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11143--11149 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2384] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2385] Underfull \hbox (badness 10000) in paragraph at lines 11234--11239 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11249--11251 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2386] [2387] Underfull \hbox (badness 2698) in paragraph at lines 11374--11380 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2388] Underfull \hbox (badness 10000) in paragraph at lines 11467--11469 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11485--11490 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11493--11498 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2389] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2390] [2391] Underfull \hbox (badness 6641) in paragraph at lines 11651--11654 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11691--11695 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11691--11695 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2392] Underfull \hbox (badness 7649) in paragraph at lines 11798--11800 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2393] [2394] [2395] Underfull \hbox (badness 7362) in paragraph at lines 11999--12001 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2396] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2397] [2398] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2399] [2400] [2401]) (./boot-pkg.tex [2402] Chapter 18. [2403] [2404] [2405] [2406] [2407] [2408] [2409] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2410] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2411] [2412] [2413] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2414] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2415] [2416] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2417] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2418] [2419] [2420] [2421] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2422] [2423] [2424] [2425] [2426] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2427] [2428] [2429] Underfull \vbox (badness 10000) has occurred while \output is active [2430] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2431] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2432] [2433] [2434] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2435] Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2436] [2437] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2438] [2439] [2440] [2441] [2442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2443] [2444] [2445] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2446] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2447] [2448] [2449] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2450] [2451] [2452] [2453] [2454] [2455] [2456] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2457] [2458] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2459] [2460] [2461] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2474] [2475] [2476] [2477] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2478] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2487] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2488] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2489] [2490] [2491] [2492] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2493] [2494] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2495] [2496] [2497] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2498] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex [2508] Chapter 19. [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex Chapter 20. [2525] Underfull \hbox (badness 1655) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 133--142 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 133--142 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 133--142 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2526] [2527] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2528] [2529] Underfull \vbox (badness 10000) has occurred while \output is active [2530] [2531] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2532] [2533] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2534] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2535] [2536] Underfull \hbox (badness 2941) in paragraph at lines 779--782 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2537] Underfull \hbox (badness 10000) in paragraph at lines 864--866 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2538] Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2539] Underfull \hbox (badness 4872) in paragraph at lines 975--977 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 989--993 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2541] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2542] Underfull \hbox (badness 4144) in paragraph at lines 1190--1194 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2543] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1272--1272 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2544] [2545] Underfull \hbox (badness 10000) in paragraph at lines 1411--1416 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1459--1462 [2546] Underfull \hbox (badness 10000) in paragraph at lines 1476--1480 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1500--1500 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1510--1510 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2547] Underfull \hbox (badness 5741) in paragraph at lines 1550--1553 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2549] Underfull \hbox (badness 1540) in paragraph at lines 1733--1741 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 = [2550] [2551] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1843--1843 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2552] [2553] [2554] [2555] Underfull \hbox (badness 10000) in paragraph at lines 2162--2165 [2556] Underfull \hbox (badness 3179) in paragraph at lines 2176--2182 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2557] [2558] Underfull \hbox (badness 10000) in paragraph at lines 2334--2337 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2559] Underfull \hbox (badness 1292) in paragraph at lines 2402--2405 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2411--2413 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2434--2437 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2560] [2561] [2562] [2563] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2564] [2565] [2566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2567] [2568] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2569] [2570] [2571] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2572] Underfull \hbox (badness 10000) in paragraph at lines 3286--3289 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2573] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2574] [2575] [2576] Underfull \hbox (badness 10000) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for [2577] Underfull \hbox (badness 10000) in paragraph at lines 3585--3590 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2578] Underfull \hbox (badness 3884) in paragraph at lines 3647--3652 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m /n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx Underfull \hbox (badness 6268) in paragraph at lines 3659--3662 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2579] [2580] [2581] Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3875--3878 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2582] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3939--3941 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2583] [2584] [2585] [2586] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4134--4134 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2587] [2588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4286--4286 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4288--4288 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4295--4295 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2589] [2590] [2591] [2592] [2593] [2594] Underfull \hbox (badness 10000) in paragraph at lines 4668--4674 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4684--4686 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side [2595] Overfull \hbox (52.98038pt too wide) in paragraph at lines 4697--4697 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4699--4699 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4713--4713 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2596]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] 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,[] [2597] 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 [2598] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2599] [2600] [2601]) (./foreign-pkg.tex [2602] Chapter 22. [2603] 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 . [2604] [2605] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2606] 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, [2607] [2608] [2609] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2610] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] 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/10 , 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 [2611] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] 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,[] [2613] 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="")[] [2614] [2615] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2616] [2617] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2618] 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 . [2619] [2620] 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"))[] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2623] Underfull \hbox (badness 2088) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2624]) (./lattice-pkg.tex Chapter 23. [2625] [2626] [2627] 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"),[] [2628] 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"),[] [2629] [2630] [2631] [2632] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2633] [2634] [2635] [2636] 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. [2637] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2638] [2639] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a 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 [2640] [2641] [2642] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2643] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2644] Underfull \vbox (badness 10000) has occurred while \output is active [2645] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2646] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2647] [2648] [2649] [2650] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2651] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2652] [2653] [2654] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2655] [2656] [2657] [2658] [2659] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2660] [2661] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as 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 [2662] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- 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 [2663] [2664] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] 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"),[] [2665] Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \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"),[] [2670] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2671] [2672] [2673] [2674] [2675] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2676] Underfull \hbox (badness 2277) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by 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 [2677] [2678] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) 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 [2679] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2680] [2681] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , 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 [2682] [2683] [2684] [2685] [2686] [2687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2688] [2689] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2690] [2691] 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 [2692] [2693] [2694] [2695] [2696] [2697] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or 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],[] [2698] 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 [2699] 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 [2700] 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,[] [2701] 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 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 [2702] [2703] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and 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 [2704] [2705] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2706] [2707] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2708] [2709] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round 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 [2710] 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,[] [2711] [2712] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2713] 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 [2714] [2715] [2716] [2717] [2718] [2719] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- 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 [2720] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2721] 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 [2722] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2723] [2724] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2725] 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))[] [2726] [2727] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to [2728] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] 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),[] [2729] 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)[] [2730] [2731] [2732] 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")[] [2733] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2742] [2743] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] 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, ...)[] [2744] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2745] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2746] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2747] [2748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2749] [2750] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2751] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2752] [2753] [2754] [2755] [2756] [2757] [2758] Underfull \hbox (badness 7238) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2762] [2763] [2764] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower 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),[] [2765] [2766]) (./mgcv-pkg.tex Chapter 24. [2767] [2768] 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,[] [2769] 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. [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][]\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 365--372 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2774] Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2775] [2776] [2777] Underfull \hbox (badness 2922) in paragraph at lines 607--608 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2778] [2779] [2780] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2781] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2782] Underfull \vbox (badness 10000) has occurred while \output is active [2783] [2784] [2785] [2786] [2787] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164 []\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 1165--1165 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2788] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178 []\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 1180--1180 []\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 1182--1182 [] \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 1213--1213 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] [2790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285 [] \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 1319--1319 []\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 [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2800] [2801] [2802] [2803] [2804] [2805] Underfull \hbox (badness 1052) in paragraph at lines 2197--2205 \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 2214--2214 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2226--2229 []\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 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2806] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2807] [2808] Underfull \hbox (badness 1043) in paragraph at lines 2428--2434 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2809] [2810] Underfull \hbox (badness 10000) in paragraph at lines 2564--2570 [][][]\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 2564--2570 [][]\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 2564--2570 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2811] Underfull \vbox (badness 10000) has occurred while \output is active [2812] Underfull \vbox (badness 10000) has occurred while \output is active [2813] Underfull \vbox (badness 10000) has occurred while \output is active [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220 [] \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 3223--3223 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2822] [2823] [2824] [2825] [2826] [2827] Underfull \hbox (badness 5189) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2828] [2829] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2830] [2831] [2832] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2833] [2834] [2835] [2836] [2837] [2838] [2839] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2840] [2841] [2842] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2843] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2844] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2845] Underfull \hbox (badness 10000) in paragraph at lines 4660--4669 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2846] [2847] Underfull \hbox (badness 5970) in paragraph at lines 4777--4783 [][][]\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 4777--4783 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2848] Underfull \vbox (badness 10000) has occurred while \output is active [2849] [2850] [2851] Underfull \hbox (badness 1577) in paragraph at lines 5057--5060 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2852] [2853] [2854] [2855] [2856] [2857] [2858] Underfull \hbox (badness 6708) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(..., fit=FALSE) \T1/ptm/m/n/10 or [2859] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2860] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527 [] \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 5556--5556 [] \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 [2861] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2862] [2863] [2864] [2865] [2866] [2867] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933 []\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 5935--5935 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2868] [2869] [2870] [2871] [2872] [2873] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1 ,deriv=2) Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2874] [2875] [2876] [2877] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] [2880] [2881] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702 []\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 6729--6729 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2891] [2892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422 []\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 7441--7441 [] \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 [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] Underfull \vbox (badness 10000) has occurred while \output is active [2913] [2914] Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2915] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\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 8717--8720 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2916] [2917] [2918] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937 []\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 8938--8938 [] \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 8941--8941 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2919] [2920] [2921] Underfull \hbox (badness 1629) in paragraph at lines 9099--9104 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2922] [2923] [2924] [2925] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2926] [2927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2928] [2929] [2930] [2931] Underfull \vbox (badness 10000) has occurred while \output is active [2932] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2933] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \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 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2934] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\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 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2935] Underfull \hbox (badness 10000) in paragraph at lines 9939--9942 []\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 9939--9942 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2936] [2937] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2938] [2939] [2940] [2941] Underfull \hbox (badness 1946) in paragraph at lines 10247--10254 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2942] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2943] [2944] [2945] [2946] [2947] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2948] [2949] [2950] [2951] [2952] [2953] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985 []\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 10998--11002 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2954] Underfull \hbox (badness 10000) in paragraph at lines 11038--11042 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2955] [2956] [2957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2958] Underfull \hbox (badness 1803) in paragraph at lines 11267--11271 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11279--11291 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2959] [2960] [2961] Underfull \vbox (badness 10000) has occurred while \output is active [2962] Underfull \hbox (badness 6876) in paragraph at lines 11491--11497 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2963] [2964] Underfull \hbox (badness 10000) in paragraph at lines 11649--11650 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2965] [2966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2967] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2968] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 \T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m /n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or [2969] [2970] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2972] [2973] [2974] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2975] [2976] [2977] [2978] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2979] Underfull \hbox (badness 10000) in paragraph at lines 12468--12470 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2980] [2981] Underfull \vbox (badness 10000) has occurred while \output is active [2982] Underfull \hbox (badness 10000) in paragraph at lines 12627--12630 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12627--12630 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12627--12630 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 12754--12760 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2985] [2986] [2987] Underfull \vbox (badness 10000) has occurred while \output is active [2988] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2989] Underfull \hbox (badness 10000) in paragraph at lines 13071--13079 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [2990] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2991] [2992] [2993] [2994] Underfull \hbox (badness 3396) in paragraph at lines 13358--13361 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2995] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2996] [2997] [2998] [2999] Underfull \hbox (badness 10000) in paragraph at lines 13627--13630 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13627--13630 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3000] Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3006] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3007] [3008] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3009] [3010] Underfull \hbox (badness 4846) in paragraph at lines 14294--14297 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3031] [3032] [3033] [3034] [3035] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3036] [3037] [3038]) (./nlme-pkg.tex Chapter 25. [3039] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3040] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3041] [3042] [3043] [3044] [3045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3046] [3047] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3056] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3057] [3058] [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3064] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3070] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3071] Underfull \hbox (badness 1132) in paragraph at lines 2145--2147 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3072] [3073] Underfull \hbox (badness 4168) in paragraph at lines 2256--2262 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 2844--2848 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3135] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3136] Underfull \hbox (badness 2057) in paragraph at lines 6243--6254 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3137] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3138] [3139] [3140] [3141] Underfull \hbox (badness 7133) in paragraph at lines 6557--6561 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3142] Underfull \hbox (badness 10000) in paragraph at lines 6656--6662 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3143] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3145] [3146] [3147] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3148] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7039--7041 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3149] [3150] [3151] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3152] [3153] [3154] Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7406--7414 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3155] [3156] [3157] Underfull \hbox (badness 3354) in paragraph at lines 7644--7646 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8208--8230 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3166] [3167] [3168] [3169] [3170] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3171] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3184] Underfull \hbox (badness 6300) in paragraph at lines 9417--9420 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3189] Underfull \hbox (badness 10000) in paragraph at lines 9706--9709 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9750--9753 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9750--9753 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] Underfull \hbox (badness 7291) in paragraph at lines 10214--10216 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3198] [3199] [3200] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3201] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3202] [3203] [3204] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3205] [3206] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10797--10802 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3207] Underfull \hbox (badness 8075) in paragraph at lines 10819--10823 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3208] [3209] [3210] [3211] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3212] [3213] [3214] [3215] [3216] [3217] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3218] [3219] [3220] [3221] [3222] [3223] Underfull \hbox (badness 6268) in paragraph at lines 11906--11916 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 12167--12173 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3228] [3229] [3230] [3231] [3232] Underfull \hbox (badness 6876) in paragraph at lines 12489--12491 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3233] [3234] Underfull \hbox (badness 2452) in paragraph at lines 12645--12652 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3235] Underfull \hbox (badness 10000) in paragraph at lines 12710--12716 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3245] [3246] [3247] [3248] [3249] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3250] Underfull \hbox (badness 10000) in paragraph at lines 13691--13694 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3251] Underfull \hbox (badness 1838) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13734--13741 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3252] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13798--13801 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13826--13829 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13826--13829 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3253] Underfull \hbox (badness 10000) in paragraph at lines 13906--13909 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3254] Underfull \hbox (badness 1472) in paragraph at lines 13931--13938 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3255] Underfull \hbox (badness 10000) in paragraph at lines 14000--14002 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3256] [3257] [3258] [3259] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3260] [3261] [3262] [3263] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] Underfull \hbox (badness 1009) in paragraph at lines 15834--15843 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3283] [3284] [3285] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3286] [3287] [3288] [3289] [3290] Underfull \hbox (badness 10000) in paragraph at lines 16316--16322 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3291] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3292] [3293] [3294] [3295] [3296] [3297] [3298] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1867) in paragraph at lines 17171--17180 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3304] Underfull \hbox (badness 1521) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat ion of variance Underfull \hbox (badness 10000) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat ions per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 1694) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and [3305] [3306] [3307] [3308] Underfull \hbox (badness 10000) in paragraph at lines 17482--17489 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3309] [3310] [3311] [3312] [3313] [3314] [3315] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3316] Underfull \hbox (badness 3579) in paragraph at lines 18055--18060 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3317] Underfull \hbox (badness 3579) in paragraph at lines 18119--18124 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3318] Underfull \hbox (badness 3579) in paragraph at lines 18182--18187 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3319] Underfull \hbox (badness 1577) in paragraph at lines 18243--18245 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18245--18250 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3320] Underfull \hbox (badness 3579) in paragraph at lines 18308--18313 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3321] Underfull \hbox (badness 3579) in paragraph at lines 18380--18385 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3322] [3323] Underfull \hbox (badness 1009) in paragraph at lines 18526--18535 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3324] [3325] Underfull \hbox (badness 1009) in paragraph at lines 18658--18667 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \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} [3335] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3336] [3337] [3338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3340] [3341] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3342]) (./rpart-pkg.tex Chapter 27. [3343] [3344] [3345] [3346] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3347] [3348] [3349] [3350] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3351] [3352] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3353] [3354] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3355] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3356] [3357] [3358] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3359] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3360] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3361] [3362] [3363] [3364] [3365] [3366] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3367] [3368] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3369] [3370] [3371]) (./spatial-pkg.tex [3372] Chapter 28. [3373] [3374] [3375] [3376] [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391]) (./survival-pkg.tex [3392] Chapter 29. [3393] [3394] 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.[] [3395] [3396]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} [3397] [3398] 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)[] [3399] 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)[] [3400] [3401] Underfull \vbox (badness 10000) has occurred while \output is active [3402] 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"),[] [3403] [3404] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3405] [3406] [3407] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3408] [3409] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3410]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3411] 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"),[] [3412] [3413] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] [3414] [3415] [3416] [3417] [3418] Underfull \hbox (badness 1337) in paragraph at lines 1799--1803 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3419] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3420] [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3427] [3428] [3429] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3430] [3431] [3432] [3433] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3434] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3435] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3437] [3438] Underfull \vbox (badness 10000) has occurred while \output is active [3439] Underfull \vbox (badness 10000) has occurred while \output is active [3440] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3441] [3442] [3443] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3446] Underfull \vbox (badness 10000) has occurred while \output is active [3447] [3448] [3449] [3450] [3451] [3452] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3453] [3454] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3455] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3458] [3459] Underfull \hbox (badness 1852) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3460] [3461] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3462] [3463] [3464] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3465] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3466] [3467] [3468] [3469] [3470] Underfull \vbox (badness 2126) has occurred while \output is active [3471] [3472] [3473] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5560--5563 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3474] [3475] [3476] [3477] [3478] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3479] [3480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3481] [3482] [3483] [3484] [3485] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3486] [3487] [3488] [3489] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3490] [3491] [3492] Underfull \hbox (badness 1253) in paragraph at lines 6915--6918 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3493] [3494] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 7041--7050 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3495] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3496] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3497] Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3498] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3499] [3500] [3501] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3502] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3503] [3504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3505] [3506] [3507] Underfull \hbox (badness 3058) in paragraph at lines 7969--7974 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3509] [3510] [3511] [3512] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3513] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3514] [3515] Underfull \hbox (badness 2035) in paragraph at lines 8597--8604 \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 8597--8604 \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 8597--8604 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3516] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3517] [3518] [3519] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3520] [3521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 [] \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 8965--8965 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3522] [3523] [3524] [3525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267 []\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 9268--9268 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3526] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274 [] \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 9276--9276 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3527] [3528] [3529] [3530] [3531] [3532] [3533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3534] [3535] [3536]) No file fullrefman.ind. 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Transcript written on fullrefman.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file fullrefman.idx............................done (24193 entries accepted, 76 rejected). Sorting entries.........................................................................................................................................................................................................................................................................done (392383 comparisons). Generating output file fullrefman.ind..........................done (25144 lines written, 116 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Mageia) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./fullrefman.tex LaTeX2e <2018-04-01> patch level 2 Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (/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 377. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 377. ) (/usr/share/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texmf-dist/tex/latex/base/makeidx.sty) Writing index file fullrefman.idx (./fullrefman.aux) (/usr/share/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./fullrefman.out) (./fullrefman.out) (/usr/share/texmf-dist/tex/latex/psnfss/t1phv.fd) (./version.tex) (/usr/share/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/usr/share/texmf-dist/fon ts/map/pdftex/updmap/pdftex.map}] (./fullrefman.toc (/usr/share/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49]) [50] [1] [2] (./base-pkg.tex Chapter 1. [3] [4] Underfull \hbox (badness 6741) 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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 135--141 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 135--141 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 5050) in paragraph at lines 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 . It Underfull \hbox (badness 1028) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 141--149 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] [9] [10] 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 (4.38043pt too wide) in paragraph at lines 873--873 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [27] Underfull \hbox (badness 1303) in paragraph at lines 1698--1701 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1816--1818 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [38] Underfull \hbox (badness 1107) in paragraph at lines 2460--2462 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [39] [40] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [51] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] [64] Underfull \hbox (badness 4927) in paragraph at lines 4267--4271 []\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 4267--4271 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [65] [66] [67] Underfull \hbox (badness 4595) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [68] [69] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 4590--4590 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = NA)[] Underfull \hbox (badness 1199) in paragraph at lines 4596--4602 []\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 4607--4610 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [70] [71] [72] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4780--4780 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 5033--5035 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 5430--5438 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 1796) in paragraph at lines 5993--6001 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. For an i n-tro-duc-tion see [][]$\T1/pcr/m/n/10 https : / / [90] [91] [92] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6187--6187 []\T1/pcr/m/n/9 ## The exact result of this *depends* on the platform, compile r, math-library:[] Overfull \hbox (90.78033pt too wide) in paragraph at lines 6189--6189 []\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 6190--6190 []\T1/pcr/m/n/9 showC(NpNA)# but not always is {shows \TS1/pcr/m/n/9 '\T1/pcr /m/n/9 (R = NaN, I = NA)\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 on some platforms}[] [93] [94] Underfull \hbox (badness 1242) in paragraph at lines 6325--6329 \T1/ptm/m/n/10 ror con-di-tions of a par-tic-u-lar class with ad-di-tional fiel ds spec-i-fied as the \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 ar-gu-ment. Underfull \hbox (badness 1635) in paragraph at lines 6367--6370 []\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 6371--6374 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [95] Underfull \hbox (badness 1308) in paragraph at lines 6402--6410 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [96] [97] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6556--6556 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [98] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6598--6600 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6746--6749 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6746--6749 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [101] [102] Underfull \hbox (badness 1406) in paragraph at lines 6928--6934 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6948--6950 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [103] Underfull \hbox (badness 1067) in paragraph at lines 6990--6997 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7182--7182 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [107] Underfull \hbox (badness 1231) in paragraph at lines 7307--7313 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [108] [109] [110] [111] Underfull \hbox (badness 10000) in paragraph at lines 7518--7520 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [112] [113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7663--7663 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [114] [115] [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7901--7901 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [117] [118] Underfull \hbox (badness 8132) in paragraph at lines 8002--8006 []\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 8002--8006 \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 8021--8031 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8021--8031 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [119] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8053--8057 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [120] [121] [122] [123] [124] [125] Underfull \hbox (badness 1629) in paragraph at lines 8539--8551 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8539--8551 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [126] [127] [128] Underfull \hbox (badness 10000) in paragraph at lines 8801--8802 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [129] [130] [131] Underfull \hbox (badness 10000) in paragraph at lines 8987--8991 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [132] [133] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9078--9078 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9080--9080 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9105--9105 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [134] [135] Underfull \hbox (badness 5403) in paragraph at lines 9224--9226 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9243--9245 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n /10 formula[][][]\T1/ptm/m/n/10 s, with [136] [137] [138] Underfull \hbox (badness 1603) in paragraph at lines 9454--9457 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1917) in paragraph at lines 10060--10065 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has Overfull \hbox (36.7804pt too wide) in paragraph at lines 10115--10115 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10116--10116 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [148] [149] Underfull \hbox (badness 1168) in paragraph at lines 10218--10223 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [150] Underfull \hbox (badness 10000) in paragraph at lines 10257--10263 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10264--10267 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [151] [152] Underfull \hbox (badness 2828) in paragraph at lines 10423--10427 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10423--10427 \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 _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10456--10456 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [153] [154] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10529--10529 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [155] [156] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10673--10673 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [157] [158] [159] Underfull \hbox (badness 6396) in paragraph at lines 10862--10870 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 5288) in paragraph at lines 11786--11788 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [172] Underfull \hbox (badness 3039) in paragraph at lines 11796--11801 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 11856--11858 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [173] [174] Underfull \hbox (badness 4569) in paragraph at lines 11978--11982 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11978--11982 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 12093--12095 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12934--12934 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 2221) in paragraph at lines 13380--13389 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13380--13389 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 13641--13643 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] [199] Underfull \hbox (badness 2573) in paragraph at lines 13756--13758 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr /m/n/10 fsep = [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13906--13908 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 14015--14019 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14026--14029 [][][]$\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 14047--14047 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [204] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14070--14070 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [205] Underfull \hbox (badness 10000) in paragraph at lines 14162--14165 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14172--14172 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [206] Underfull \hbox (badness 10000) in paragraph at lines 14238--14241 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14255--14255 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14284--14284 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14308--14315 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14308--14315 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14316--14320 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14479--14479 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14480--14480 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [211] [212] [213] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14714--14714 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [214] Underfull \hbox (badness 1168) in paragraph at lines 14798--14802 []\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 14798--14802 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [215] Underfull \hbox (badness 6944) in paragraph at lines 14896--14899 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14921--14921 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 15059--15061 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15079--15079 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15085--15085 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [219] Underfull \hbox (badness 2790) in paragraph at lines 15092--15095 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 1024) in paragraph at lines 15123--15130 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [220] Underfull \hbox (badness 10000) in paragraph at lines 15198--15200 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15198--15200 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15220--15225 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15226--15228 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [221] Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15237--15245 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15345--15345 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [223] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15367--15367 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16184--16184 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [236] Underfull \hbox (badness 2418) in paragraph at lines 16293--16297 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16300--16303 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [237] Underfull \hbox (badness 2326) in paragraph at lines 16335--16342 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [238] [239] [240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16581--16581 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [241] Underfull \hbox (badness 1867) in paragraph at lines 16606--16613 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [242] [243] [244] [245] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16875--16875 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16904--16904 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [247] [248] [249] [250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17320--17320 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [251] [252] [253] [254] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17574--17574 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [255] [256] [257] [258] Underfull \hbox (badness 2435) in paragraph at lines 17837--17839 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [259] Underfull \hbox (badness 2285) in paragraph at lines 17903--17905 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17911--17911 []\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 17921--17921 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17941--17941 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [260] [261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18075--18075 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18081--18081 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] [262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18084--18084 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [263] [264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18217--18217 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18225--18225 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [265] [266] [267] Underfull \hbox (badness 10000) in paragraph at lines 18430--18432 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [268] Underfull \hbox (badness 4217) in paragraph at lines 18514--18523 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18529--18545 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 4699) in paragraph at lines 18948--18951 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [275] [276] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19071--19071 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 19206--19208 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19255--19255 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19256--19256 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [280] [281] [282] [283] [284] [285] [286] [287] [288] Underfull \hbox (badness 1975) in paragraph at lines 19834--19837 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1077) in paragraph at lines 20229--20234 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [295] Underfull \hbox (badness 10000) in paragraph at lines 20243--20250 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [296] Underfull \hbox (badness 10000) in paragraph at lines 20317--20321 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [297] [298] Underfull \hbox (badness 10000) in paragraph at lines 20466--20470 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20466--20470 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 20471--20478 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack- [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 20602--20609 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [301] Underfull \hbox (badness 10000) in paragraph at lines 20723--20727 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [302] Underfull \hbox (badness 5161) in paragraph at lines 20793--20798 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [303] [304] [305] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20960--20960 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [306] Underfull \hbox (badness 3343) in paragraph at lines 21020--21024 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [307] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21106--21106 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21117--21117 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [308] [309] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 21231--21231 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 21276--21281 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [310] [311] Underfull \hbox (badness 2564) in paragraph at lines 21367--21370 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21397--21397 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [312] [313] Underfull \hbox (badness 1400) in paragraph at lines 21565--21569 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class [314] [315] [316] Underfull \hbox (badness 2469) in paragraph at lines 21735--21741 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [317] [318] [319] [320] [321] [322] [323] [324] [325] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22363--22363 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22366--22366 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [326] [327] Underfull \hbox (badness 1655) in paragraph at lines 22490--22494 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [328] [329] [330] [331] Underfull \hbox (badness 2277) in paragraph at lines 22739--22742 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 23304--23312 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 23304--23312 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [340] [341] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23381--23381 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1448) in paragraph at lines 23886--23894 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [349] [350] Underfull \hbox (badness 3849) in paragraph at lines 24000--24005 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [351] Underfull \hbox (badness 7308) in paragraph at lines 24077--24083 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24077--24083 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24077--24083 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [352] [353] Underfull \hbox (badness 10000) in paragraph at lines 24240--24242 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [354] [355] [356] Underfull \hbox (badness 6188) in paragraph at lines 24459--24462 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2197) in paragraph at lines 24943--24947 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24943--24947 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use [364] Underfull \hbox (badness 2846) in paragraph at lines 24957--24961 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24957--24961 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 24999--24999 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [365] Underfull \hbox (badness 10000) in paragraph at lines 25051--25057 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25051--25057 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25064--25066 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25115--25115 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [367] [368] [369] Underfull \hbox (badness 8189) in paragraph at lines 25308--25314 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] [370] [371] [372] Underfull \hbox (badness 1694) in paragraph at lines 25530--25533 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [373] [374] [375] Underfull \hbox (badness 1603) in paragraph at lines 25777--25779 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [376] [377] Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [378] [379] Underfull \hbox (badness 3271) in paragraph at lines 26111--26114 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [380] [381] [382] Underfull \hbox (badness 3138) in paragraph at lines 26411--26417 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [383] Underfull \hbox (badness 1194) in paragraph at lines 26424--26427 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 26450--26452 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 26470--26476 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26485--26490 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 26503--26506 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [384] Underfull \hbox (badness 10000) in paragraph at lines 26519--26522 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 []\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma- Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 26541--26548 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [385] [386] [387] [388] Underfull \vbox (badness 10000) has occurred while \output is active [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [390] [391] Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27045--27048 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 27314--27320 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 27314--27320 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and [395] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27336--27336 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 1817) in paragraph at lines 27782--27786 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [403] Underfull \hbox (badness 1796) in paragraph at lines 27850--27853 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [404] [405] [406] Underfull \hbox (badness 10000) in paragraph at lines 28050--28053 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [417] [418] [419] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29004--29004 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29010--29010 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29011--29011 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29014--29014 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [421] Underfull \hbox (badness 7415) in paragraph at lines 29089--29093 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [422] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [423] [424] Underfull \hbox (badness 3713) in paragraph at lines 29279--29290 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [425] Underfull \hbox (badness 1248) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [426] [427] Underfull \hbox (badness 1533) in paragraph at lines 29541--29544 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [428] [429] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [430] Underfull \hbox (badness 1038) in paragraph at lines 29704--29715 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [431] [432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29848--29848 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29851--29851 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29852--29852 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29853--29853 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29860--29860 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [433] [434] [435] [436] [437] Underfull \hbox (badness 4048) in paragraph at lines 30207--30212 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 30207--30212 \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 30207--30212 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [438] [439] [440] [441] [442] [443] [444] [445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 7558) in paragraph at lines 31250--31254 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 31260--31262 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 31265--31268 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and [453] Underfull \hbox (badness 10000) in paragraph at lines 31269--31271 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 31272--31274 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 31677--31681 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [459] [460] [461] [462] [463] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32024--32024 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [464] [465] [466] [467] [468] [469] [470] Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [471] [472] [473] [474] [475] [476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [477] Underfull \hbox (badness 1158) in paragraph at lines 32947--32952 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [478] Underfull \hbox (badness 10000) in paragraph at lines 32974--32980 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 32974--32980 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [479] [480] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33132--33132 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [481] [482] [483] Underfull \hbox (badness 8151) in paragraph at lines 33392--33395 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 . [484] [485] [486] [487] Underfull \hbox (badness 1210) in paragraph at lines 33627--33629 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp ly(nvec,seq_len)) \T1/ptm/m/n/10 and it [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [502] [503] [504] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34816--34816 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34818--34818 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [505] Underfull \hbox (badness 4954) in paragraph at lines 34861--34867 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 34861--34867 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [506] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34972--34972 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [507] [508] [509] [510] [511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35300--35300 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] [512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35315--35315 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [513] [514] [515] [516] [517] [518] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35756--35756 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35757--35757 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [519] [520] [521] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [522] Underfull \hbox (badness 6110) in paragraph at lines 36105--36115 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 36105--36115 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [523] Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 36161--36168 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [524] [525] [526] [527] Overfull \hbox (60.78088pt too wide) in paragraph at lines 36438--36438 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37000--37000 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37248--37248 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37292--37292 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [541] [542] [543] [544] [545] [546] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37726--37726 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37729--37729 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [547] Underfull \hbox (badness 10000) in paragraph at lines 37780--37787 []\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 37780--37787 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37833--37833 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [549] [550] [551] [552] Overfull \hbox (31.3804pt too wide) in paragraph at lines 38134--38134 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [553] Underfull \vbox (badness 10000) has occurred while \output is active [554] [555] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38299--38299 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38337--38337 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 4792) in paragraph at lines 38386--38391 []\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 38386--38391 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [557] Underfull \hbox (badness 2452) in paragraph at lines 38476--38479 \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 38476--38479 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [558] [559] [560] Underfull \hbox (badness 10000) in paragraph at lines 38664--38668 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38679--38682 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [561] [562] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38811--38811 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [563] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38881--38881 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [564] [565] [566] Underfull \hbox (badness 1082) in paragraph at lines 39025--39028 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [567] [568] Underfull \hbox (badness 1038) in paragraph at lines 39216--39219 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [569] [570] [571] [572] [573] [574] Underfull \hbox (badness 1442) in paragraph at lines 39579--39583 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout = TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout = [575] [576] [577] Underfull \hbox (badness 4096) in paragraph at lines 39825--39828 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [578] [579] Underfull \hbox (badness 7888) in paragraph at lines 39939--39943 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10 length(bin) > [580] [581] Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 40095--40095 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] [582] Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 40110--40112 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [583] Underfull \hbox (badness 10000) in paragraph at lines 40190--40193 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [584] [585] Underfull \hbox (badness 3872) in paragraph at lines 40308--40311 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [586] Underfull \hbox (badness 5475) in paragraph at lines 40374--40378 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 40792--40799 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40848--40857 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40848--40857 \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 40858--40866 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40858--40866 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 2503) in paragraph at lines 40858--40866 \T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [593] Underfull \hbox (badness 1337) in paragraph at lines 40924--40932 \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 40933--40936 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [594] Underfull \hbox (badness 3460) in paragraph at lines 40987--40990 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 40991--40993 [][][]$\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 41000--41000 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [595] [596] [597] Underfull \hbox (badness 10000) in paragraph at lines 41217--41219 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [598] [599] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41339--41339 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41341--41341 []\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 [600] [601] [602] [603] [604] Underfull \hbox (badness 6542) in paragraph at lines 41703--41705 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [605] [606] Overfull \hbox (30.78088pt too wide) in paragraph at lines 41822--41822 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [607] Underfull \hbox (badness 1708) in paragraph at lines 41890--41898 []\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 41890--41898 \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 4859) in paragraph at lines 41920--41925 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [608] Underfull \hbox (badness 3895) in paragraph at lines 41982--41994 []\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 41982--41994 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [609] [610] [611] [612] [613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 42305--42305 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [614] [615] [616] [617] [618] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42772--42772 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [620] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42781--42781 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [621] Underfull \hbox (badness 1803) in paragraph at lines 42906--42909 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [622] Underfull \hbox (badness 3471) in paragraph at lines 42910--42917 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [623] [624] [625] Underfull \hbox (badness 3668) in paragraph at lines 43125--43127 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [626] Overfull \hbox (36.78088pt too wide) in paragraph at lines 43229--43229 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43304--43304 []\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 43312--43312 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [628] [629] Underfull \hbox (badness 6220) in paragraph at lines 43442--43447 []\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 43442--43447 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, [630] Underfull \hbox (badness 10000) in paragraph at lines 43463--43468 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 4229) in paragraph at lines 43463--43468 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [631] Underfull \hbox (badness 2818) in paragraph at lines 43553--43559 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [632] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43588--43588 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [633] Underfull \hbox (badness 1622) in paragraph at lines 43682--43684 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [634] [635] [636] [637] [638] Underfull \hbox (badness 2846) in paragraph at lines 44045--44049 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44085--44085 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 44106--44110 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [640]) (./compiler-pkg.tex Chapter 2. [641] Underfull \hbox (badness 2884) in paragraph at lines 105--119 []\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 105--119 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [642] [643] [644]) (./datasets-pkg.tex Chapter 3. [645] [646] [647] [648] [649] 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,[] [650] 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 [651] [652] [653] [654] [655] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [656] [657] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [658] [659] 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. [660] [661] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [662] [663] [664] [665] [666] 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)")[] [667] [668] 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 [669] [670] [671] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [672] 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)[] [673] [674] 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]]))))[] [675] [676] [677] [678] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [679] [680] [681] Overfull \vbox (4.29591pt too high) has occurred while \output is active [682] [683] [684] [685] [686] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [687] Overfull \vbox (13.87083pt too high) has occurred while \output is active [688] Underfull \vbox (badness 2376) has occurred while \output is active [689] [690] Overfull \vbox (12.25539pt too high) has occurred while \output is active [691] [692] Overfull \vbox (17.12102pt too high) has occurred while \output is active [693] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [694] [695] [696] [697] [698] [699] [700] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [701] [702] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [703] Overfull \vbox (10.49593pt too high) has occurred while \output is active [704] Overfull \vbox (15.49593pt too high) has occurred while \output is active [705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3989--3992 []\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 3998--4000 []\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 3998--4000 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719]) (./grDevices-pkg.tex [720] Chapter 4. [721] [722] [723] [724] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in [725] [726] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 379--387 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [727] [728] Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [738] [739] Underfull \hbox (badness 10000) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [740] Underfull \hbox (badness 1173) in paragraph at lines 1322--1325 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [741] [742] [743] [744] [745] [746] [747] [748] Underfull \hbox (badness 1565) in paragraph at lines 1810--1815 []\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 1810--1815 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [749] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 1934--1944 []\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 1934--1944 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [750] [751] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [752] [753] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [754] [755] Underfull \hbox (badness 2326) in paragraph at lines 2341--2351 \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 2341--2351 \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 2341--2351 \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 2341--2351 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [756] [757] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444 []\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 [758] Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE) Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE)[] [759] [760] [761] [762] [763] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [764] [765] [766] [767] [768] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [769] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245 []\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 3246--3246 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [770] [771] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3384--3389 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [772] [773] [774] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) Underfull \hbox (badness 8170) in paragraph at lines 3571--3574 []\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 , [775] Underfull \hbox (badness 10000) in paragraph at lines 3655--3659 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [776] [777] Underfull \hbox (badness 5260) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [778] [779] [780] [781] [782] Underfull \hbox (badness 5939) in paragraph at lines 4113--4118 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [783] [784] [785] [786] [787] [788] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / Underfull \hbox (badness 3612) in paragraph at lines 4514--4519 \T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat . [789] [790] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [791] [792] Underfull \hbox (badness 1348) in paragraph at lines 4828--4831 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [793] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 4892--4898 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [794] Underfull \hbox (badness 1112) in paragraph at lines 4923--4927 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), \T1/pcr/m/n/10 "CP1251.enc" [795] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [796] [797] [798] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\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 5256--5260 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [799] [800] Underfull \hbox (badness 1552) in paragraph at lines 5380--5389 \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 5380--5389 \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 5380--5389 \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 5390--5392 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5422--5428 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [801] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [802] [803] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [804] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [805] [806] Underfull \hbox (badness 10000) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [807] [808] [809] [810] [811] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112 []\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 6125--6128 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [812] [813] [814] [815] [816] [817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 6728--6733 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [822] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [823] Underfull \hbox (badness 5954) in paragraph at lines 6872--6875 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : [824] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [825] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [826] Underfull \hbox (badness 10000) in paragraph at lines 7084--7091 []\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 7084--7091 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [827] Underfull \hbox (badness 5607) in paragraph at lines 7168--7172 []\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 Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [828] [829] Underfull \hbox (badness 5637) in paragraph at lines 7345--7351 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , [830] Underfull \hbox (badness 1721) in paragraph at lines 7378--7381 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [831] [832] Underfull \hbox (badness 1231) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [833] [834] [835]) (./graphics-pkg.tex [836] Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use \T1/pcr/m/n/10 library(help = [837] [838] [839] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [840] 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- [841] [842] [843] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [844] [845] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [846] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [847] [848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 960--964 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able. Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [852] [853] [854] [855] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1265--1265 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [856] [857] [858] Underfull \hbox (badness 1024) in paragraph at lines 1427--1435 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1461--1463 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [859] [860] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1531--1531 []\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 1532--1532 []\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 1538--1538 []\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 1539--1539 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [861] [862] [863] [864] Underfull \hbox (badness 10000) in paragraph at lines 1839--1845 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [865] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [866] [867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1970--1970 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [868] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2099--2099 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] [869] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2104--2104 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [870] [871] [872] [873] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2390--2397 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [874] Underfull \hbox (badness 7273) in paragraph at lines 2472--2476 [][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 2485--2485 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [875] [876] [877] [878] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2719--2719 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [879] [880] [881] Underfull \hbox (badness 1226) in paragraph at lines 2880--2884 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy Overfull \hbox (15.18042pt too wide) in paragraph at lines 2933--2933 []\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 2937--2937 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [882] Underfull \hbox (badness 10000) in paragraph at lines 2989--2992 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [883] [884] [885] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3194--3194 []\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 3199--3199 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [886] [887] Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 []\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 3338--3343 [][]\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 3338--3343 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [888] [889] [890] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3524--3524 []\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 3543--3543 [] \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 3547--3547 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [891] [892] [893] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3724--3724 [] \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 3725--3725 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3764--3764 [] \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 [895] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3816--3816 []\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 3824--3824 []\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 3826--3826 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3834--3834 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [896] Underfull \hbox (badness 10000) in paragraph at lines 3897--3901 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [897] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4008--4008 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [898] [899] [900] [901] Underfull \hbox (badness 3930) in paragraph at lines 4215--4217 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [902] [903] [904] [905] Underfull \hbox (badness 1286) in paragraph at lines 4526--4529 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing [906] Underfull \hbox (badness 3229) in paragraph at lines 4534--4539 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4631--4631 []\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 4636--4636 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [908] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4680--4680 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [909] Underfull \hbox (badness 1264) in paragraph at lines 4754--4767 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4891--4897 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [912] Underfull \hbox (badness 10000) in paragraph at lines 5022--5025 [913 ] Underfull \hbox (badness 10000) in paragraph at lines 5083--5085 Underfull \vbox (badness 10000) has occurred while \output is active [914] [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5273--5275 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [917] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5329--5329 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5330--5330 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [918] [919] [920] [921] [922] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5695--5695 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [923] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5696--5696 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 1360) in paragraph at lines 5747--5751 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type = [924] [925] [926] [927] [928] [929] [930] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6181--6181 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6187--6187 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [931] [932] [933] [934] [935] [936] Underfull \hbox (badness 10000) in paragraph at lines 6614--6616 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [937] [938] Underfull \hbox (badness 1028) in paragraph at lines 6708--6710 []\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 6751--6752 [][] [939 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6845--6845 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [940] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6876--6876 [] \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 [941] [942] Underfull \hbox (badness 10000) in paragraph at lines 6998--7000 []\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 7025--7025 [] \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 7031--7031 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [943] Underfull \hbox (badness 2600) in paragraph at lines 7091--7093 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7323--7323 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [948] [949] [950] [951] [952] [953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7714--7714 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [954] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7726--7726 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [955] [956] [957] [958] [959] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8075--8075 []\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 8078--8078 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8082--8082 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [960] [961] [962] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8253--8253 []\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 8254--8254 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [963] [964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8358--8358 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8369--8374 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [965] Underfull \hbox (badness 1112) in paragraph at lines 8417--8421 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [966] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8477--8477 []\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 8492--8492 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8623--8623 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [969] [970] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8808--8808 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [971] Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8838--8840 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8870--8876 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8918 \HeaderA{units}{Graphical Units}{units} [973] Underfull \hbox (badness 1205) in paragraph at lines 8983--8985 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [974] [975] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9102--9102 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [976]) (./grid-pkg.tex Chapter 6. [977] [978] [979] [980] [981] [982] [983] [984] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 476--482 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [995] [996] [997] [998] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1005] [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981 []\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 1982--1982 []\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 1983--1983 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1008] Underfull \hbox (badness 2961) in paragraph at lines 2018--2023 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [1009] Underfull \hbox (badness 1430) in paragraph at lines 2077--2082 []\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 2106--2109 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [1010] [1011] [1012] Underfull \hbox (badness 2894) in paragraph at lines 2313--2320 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1013] [1014] [1015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2481--2486 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1016] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1017] [1018] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1019] [1020] [1021] [1022] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1023] [1024] [1025] [1026] [1027] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1029] Underfull \hbox (badness 2799) in paragraph at lines 3411--3417 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1032] [1033] [1034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1035] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1048] Underfull \hbox (badness 1430) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1049] [1050] [1051] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] Underfull \hbox (badness 6859) in paragraph at lines 6056--6062 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6056--6062 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1072] [1073] [1074] [1075] [1076] Underfull \hbox (badness 1867) in paragraph at lines 6366--6368 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1077] Underfull \hbox (badness 10000) in paragraph at lines 6403--6409 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1078] [1079] Underfull \hbox (badness 1371) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1083]) (./methods-pkg.tex [1084] Chapter 7. [1085] [1086] 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 [1087] [1088] [1089] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1090] [1091] 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[] [1092] 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 [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] 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[] [1109] [1110] 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 [1111] [1112] [1113] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1114] [1115] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[] [][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call 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}:[] [1116] [1117] [1118] 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 [1119] 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))[] [1120] [1121] [1122] 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:[] [1123] [1124] [1125] [1126] [1127] [1128] [1129] 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 [1130] [1131] 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 [1132] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1133] [1134] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1135] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1136] [1137] [1138] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1139] [1140] [1141] 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,[] [1142] 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) [1143] [1144] [1145] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1146] [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1149] [1150] [1151] [1152] 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[] [1153] 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 [1154] [1155] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1156] [1157] 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 [1158] [1159] [1160] 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 [1161] [1162] [1163] [1164] [1165] [1166] 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 [1167] [1168] 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 [1169] 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 [1170] [1171] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1172] Underfull \vbox (badness 10000) has occurred while \output is active [1173] [1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1176] 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().[] [1177] [1178] 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")[] [1179]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 [1180] 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 , [1181] [1182] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see 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 [1183] [1184] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] 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 [1196] 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(), [1197] 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 =,[] [1198] [1199] [1200] [1201] 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[] [1202] [1203] [1204] 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")[] [1205] [1206] [1207] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1208] [1209] [1210] [1211] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1212] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class 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 [1223] [1224] [1225]) (./parallel-pkg.tex [1226] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1227] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1228] [1229] 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 [1230] [1231] [1232] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1233] [1234] [1235] [1236] Underfull \hbox (badness 1917) in paragraph at lines 744--753 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 744--753 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1237] [1238] Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1239] [1240] [1241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1242] Underfull \hbox (badness 5388) in paragraph at lines 1145--1150 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1243] Underfull \hbox (badness 10000) in paragraph at lines 1169--1177 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1246] Underfull \hbox (badness 1577) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1411--1413 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1247] [1248]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1257] Underfull \hbox (badness 1424) in paragraph at lines 594--596 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1258] [1259] Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1260] [1261] [1262]) (./stats-pkg.tex Chapter 10. [1263] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1264] [1265] [1266] [1267] [1268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1269] Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1024) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1285] [1286] [1287] [1288] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1302] [1303] [1304] [1305] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 3175--3177 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3223--3223 []\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 3224--3224 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1310] [1311] [1312] [1313] [1314] [1315] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3615--3615 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1316] [1317] [1318] [1319] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3893--3893 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1320] [1321] [1322] [1323] [1324] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4182--4182 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4183--4183 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1328] [1329] [1330] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4589--4589 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1331] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1332] [1333] [1334] [1335] [1336] [1337] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5066--5066 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5068--5068 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1338] [1339] [1340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5289--5289 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5307--5307 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1341] [1342] [1343] Underfull \hbox (badness 1436) in paragraph at lines 5517--5522 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1344] [1345] [1346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1347] [1348] [1349] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1350] [1351] [1352] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6067--6067 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1353] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6175--6175 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1354] Underfull \hbox (badness 10000) in paragraph at lines 6242--6247 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1355] [1356] [1357] [1358] Underfull \hbox (badness 5954) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1359] Underfull \hbox (badness 2503) in paragraph at lines 6520--6523 []\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 6524--6526 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6527--6532 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, Underfull \hbox (badness 7238) in paragraph at lines 6563--6566 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6598--6598 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6613--6613 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6628--6628 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [1361] [1362] [1363] [1364] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1365] [1366] [1367] [1368] [1369] [1370] Underfull \hbox (badness 10000) in paragraph at lines 7270--7274 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1371] Underfull \hbox (badness 6493) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1372] [1373] Underfull \hbox (badness 10000) in paragraph at lines 7506--7509 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1374] [1375] [1376] [1377] [1378] [1379] [1380] Underfull \hbox (badness 10000) in paragraph at lines 7918--7923 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 1210) in paragraph at lines 8273--8275 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1386] [1387] [1388] [1389] [1390] [1391] [1392] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8736--8736 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] Underfull \vbox (badness 10000) has occurred while \output is active [1393] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8781--8781 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8784--8784 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1394] [1395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8922--8922 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1396] [1397] [1398] [1399] [1400] [1401] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9350--9350 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1402] [1403] [1404] Underfull \hbox (badness 7291) in paragraph at lines 9529--9531 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1405] [1406] [1407] [1408] [1409] [1410] Underfull \hbox (badness 6944) in paragraph at lines 9990--9996 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1411] [1412] [1413] Underfull \hbox (badness 3758) in paragraph at lines 10203--10206 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1414] [1415] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10465--10470 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1418] Underfull \hbox (badness 4132) in paragraph at lines 10504--10508 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10558--10564 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1419] Underfull \hbox (badness 10000) in paragraph at lines 10609--10612 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1420] [1421] [1422] Underfull \hbox (badness 2142) in paragraph at lines 10825--10828 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1423] [1424] Underfull \hbox (badness 1708) in paragraph at lines 10906--10910 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10948--10954 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, [1425] Underfull \hbox (badness 1418) in paragraph at lines 10986--10991 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1426] Underfull \hbox (badness 2635) in paragraph at lines 11119--11122 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1427] [1428] [1429] Underfull \hbox (badness 1694) in paragraph at lines 11302--11305 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1431] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11449--11453 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1432] [1433] [1434] Underfull \hbox (badness 7379) in paragraph at lines 11629--11632 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1435] [1436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11783 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1438] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11901--11906 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11918--11920 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1439] [1440] [1441] [1442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1443] [1444] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12534--12536 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1449] Underfull \hbox (badness 2753) in paragraph at lines 12603--12605 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1450] [1451] [1452] [1453] Underfull \hbox (badness 6910) in paragraph at lines 12841--12843 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of \T1/pcr/m/n/10 ob Underfull \hbox (badness 2894) in paragraph at lines 12847--12851 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12847--12851 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1464] Underfull \hbox (badness 4518) in paragraph at lines 13597--13602 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1465] [1466] [1467] Underfull \hbox (badness 10000) in paragraph at lines 13796--13800 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 1163) in paragraph at lines 14129--14137 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1473] Underfull \hbox (badness 4518) in paragraph at lines 14249--14254 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1474] [1475] [1476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14436--14436 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1477] [1478] [1479] [1480] [1481] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14780--14780 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1482] [1483] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1484] [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2726) in paragraph at lines 15279--15282 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1501] [1502] Underfull \hbox (badness 1490) in paragraph at lines 16136--16141 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1503] Underfull \hbox (badness 1648) in paragraph at lines 16202--16204 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1504] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1514] [1515] [1516] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Underfull \vbox (badness 10000) has occurred while \output is active [1528] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1529] [1530] [1531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18043--18043 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] Underfull \hbox (badness 1248) in paragraph at lines 18581--18584 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18594--18598 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce [1541] Underfull \hbox (badness 1478) in paragraph at lines 18602--18606 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18660--18662 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1542] [1543] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1544] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18830--18830 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18850--18850 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1545] Underfull \hbox (badness 2564) in paragraph at lines 18888--18899 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18888--18899 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1547] [1548] [1549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1550] Underfull \hbox (badness 1337) in paragraph at lines 19252--19255 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1557] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 19661--19661 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1558] Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su ch it-er-a-tions for Underfull \hbox (badness 5260) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa r-tic-u-larly de-sir-able for [1559] Underfull \hbox (badness 3049) in paragraph at lines 19748--19752 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1560] [1561] [1562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] [1563] Underfull \hbox (badness 1194) in paragraph at lines 20006--20009 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1564] Underfull \hbox (badness 1107) in paragraph at lines 20064--20066 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1565] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1566] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1567] [1568] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1569] Underfull \hbox (badness 7740) in paragraph at lines 20408--20410 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1570] [1571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20553--20553 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1585] Underfull \hbox (badness 6859) in paragraph at lines 21474--21481 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21485--21491 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1598] [1599] [1600] [1601] [1602] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 1337) in paragraph at lines 22834--22840 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1616] [1617] Underfull \hbox (badness 1028) in paragraph at lines 23540--23543 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1618] [1619] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1620] Underfull \hbox (badness 7944) in paragraph at lines 23705--23707 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1621] Underfull \hbox (badness 7944) in paragraph at lines 23767--23769 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1622] [1623] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1624] [1625] [1626] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1627] [1628] Underfull \hbox (badness 10000) in paragraph at lines 24235--24238 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1629] Underfull \hbox (badness 2134) in paragraph at lines 24287--24291 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24300--24300 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \vbox (badness 10000) has occurred while \output is active [1636] [1637] Underfull \hbox (badness 6268) in paragraph at lines 24777--24782 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1638] [1639] [1640] Underfull \hbox (badness 1867) in paragraph at lines 24982--24984 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1641] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1642] [1643] [1644] Underfull \hbox (badness 2495) in paragraph at lines 25221--25230 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1645] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25310--25312 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1646] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25422--25422 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25425--25425 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1647] [1648] [1649] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25651--25657 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1650] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25718--25718 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1651] Underfull \hbox (badness 1019) in paragraph at lines 25780--25785 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1652] [1653] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1654] [1655] [1656] [1657] [1658] [1659] [1660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1661] [1662] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f or when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26487--26487 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1663] Underfull \hbox (badness 2922) in paragraph at lines 26556--26561 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1664] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26593--26593 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26605--26605 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26606--26606 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26610--26610 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1665] Underfull \hbox (badness 3240) in paragraph at lines 26664--26667 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1666] Overfull \hbox (36.7804pt too wide) in paragraph at lines 26685--26685 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26688--26688 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26771--26771 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26775--26775 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26785--26785 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1668] Underfull \hbox (badness 2922) in paragraph at lines 26826--26832 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26848--26848 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1669] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26864--26864 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1670] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26978--26978 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1671] Underfull \hbox (badness 2922) in paragraph at lines 27040--27045 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1672] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27078--27078 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1673] Underfull \hbox (badness 2922) in paragraph at lines 27127--27132 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27158--27158 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1674] Underfull \hbox (badness 2922) in paragraph at lines 27192--27197 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27217--27217 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27221--27221 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] [1675] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27241--27241 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27251--27251 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27286--27291 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1676] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27308--27308 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27326--27326 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1677] Underfull \hbox (badness 6493) in paragraph at lines 27378--27383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27405--27405 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1678] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27410--27410 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27413--27413 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692] Underfull \hbox (badness 3396) in paragraph at lines 28337--28339 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1693] [1694] [1695] Underfull \hbox (badness 2237) in paragraph at lines 28514--28516 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1696] [1697] Underfull \hbox (badness 2591) in paragraph at lines 28678--28680 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1698] Underfull \hbox (badness 2237) in paragraph at lines 28724--28727 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1699] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28797--28797 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1700] [1701] Underfull \hbox (badness 3407) in paragraph at lines 28905--28909 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1702] [1703] Underfull \hbox (badness 1337) in paragraph at lines 29038--29042 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1704] [1705] [1706] [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29286--29286 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29314--29314 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1708] Underfull \hbox (badness 1616) in paragraph at lines 29340--29343 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1709] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29419--29419 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1710] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29496--29496 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1711] [1712] Underfull \hbox (badness 2205) in paragraph at lines 29585--29590 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30180--30180 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30181--30181 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1722] [1723] [1724] [1725] [1726] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30481--30481 [] \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 30482--30482 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1727] [1728] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30608--30608 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30617--30617 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Underfull \hbox (badness 1337) in paragraph at lines 30834--30838 []\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 [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1337) in paragraph at lines 31361--31365 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31788--31788 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1747] Underfull \hbox (badness 6775) in paragraph at lines 31845--31850 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31908--31908 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1749]) (./stats4-pkg.tex [1750] Chapter 11. [1751] [1752] [1753] 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))[] [1754] [1755] [1756]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} [1757] [1758] [1759]) (./tcltk-pkg.tex [1760] Chapter 12. [1761] [1762] [1763] [1764] 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[] [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] 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 [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] 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 [1780]) (./tools-pkg.tex Chapter 13. [1781] 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.[] [1782] 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 [1783] 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)[] [1784] 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 , [1785] 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 [1786] [1787] [1788] [1789] [1790] [1791] [1792] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1793] [1794] Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1795] [1796] [1797] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1139--1149 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1798] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\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 1169--1171 []\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 1206--1209 []\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 1206--1209 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1799] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\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 [1800] [1801] Underfull \hbox (badness 10000) in paragraph at lines 1363--1366 []\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 [1802] [1803] [1804] [1805] [1806] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1807] [1808] [1809]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1810] [1811] [1812] [1813] Underfull \hbox (badness 1142) in paragraph at lines 2168--2174 []\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 2202--2202 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1814] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2230--2237 []\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 2230--2237 \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 2230--2237 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1815] Underfull \hbox (badness 1342) in paragraph at lines 2282--2288 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1817] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1818] [1819] [1820] [1821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2705--2705 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1822] Underfull \hbox (badness 2486) in paragraph at lines 2750--2758 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1072) in paragraph at lines 3128--3130 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1828] [1829] [1830] [1831] [1832] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1833] [1834] [1835] [1836] Underfull \hbox (badness 4108) in paragraph at lines 3712--3719 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1837] [1838] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3812--3812 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3815--3815 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\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 3849--3855 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1839] [1840] Underfull \hbox (badness 7832) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1841] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4047--4047 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1842] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4258--4258 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1846] [1847] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4420--4420 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4431--4434 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1848] Underfull \hbox (badness 6859) in paragraph at lines 4447--4452 []\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 4455--4461 []\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 4455--4461 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1849] [1850] [1851] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4654--4654 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4655--4655 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4667--4670 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4671--4681 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4706--4712 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4706--4712 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1852] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4760--4765 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\ T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing ex-ist-ing [1853] [1854] [1855]) (./utils-pkg.tex [1856] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1857] [1858] [1859] [1860] 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[] [1861] Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1862] Underfull \hbox (badness 10000) in paragraph at lines 382--384 []\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han- dles, by de-fault pro-duced by [1863] Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1864] [1865] Underfull \hbox (badness 1946) in paragraph at lines 624--628 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1866] Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674 []\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 680--680 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 717--723 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1868] Underfull \hbox (badness 4505) in paragraph at lines 850--856 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1869] [1870] [1871] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1872] Underfull \hbox (badness 1748) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/ ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1661) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \ T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1873] Underfull \hbox (badness 10000) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1874] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1883] [1884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1885] [1886] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1887] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1888] [1889] [1890] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1891] [1892] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1893] Underfull \hbox (badness 1082) in paragraph at lines 2561--2565 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2597--2599 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1894] [1895] Underfull \hbox (badness 10000) in paragraph at lines 2685--2687 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1896] [1897] [1898] Underfull \hbox (badness 10000) in paragraph at lines 2902--2904 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1899] [1900] [1901] [1902] Underfull \hbox (badness 1762) in paragraph at lines 3196--3199 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package = [1903] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1904] Underfull \hbox (badness 2452) in paragraph at lines 3359--3362 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1905] [1906] [1907] [1908] [1909] [1910] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3849--3853 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1913] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1914] [1915] Underfull \hbox (badness 4660) in paragraph at lines 4119--4122 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1916] [1917] [1918] Underfull \hbox (badness 1565) in paragraph at lines 4328--4332 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1920] Underfull \hbox (badness 1931) in paragraph at lines 4446--4453 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1921] [1922] [1923] [1924] [1925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1943] Underfull \hbox (badness 10000) in paragraph at lines 6036--6038 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1944] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1945] [1946] [1947] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1948] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6338--6341 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1949] [1950] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1951] [1952] Underfull \hbox (badness 5091) in paragraph at lines 6628--6630 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 5331) in paragraph at lines 6644--6650 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") [1953] Underfull \hbox (badness 1270) in paragraph at lines 6673--6683 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., [1954] Underfull \hbox (badness 10000) in paragraph at lines 6778--6782 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , Underfull \hbox (badness 2376) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1955] Underfull \hbox (badness 1314) in paragraph at lines 6879--6886 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1956] Underfull \hbox (badness 10000) in paragraph at lines 6936--6941 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1957] Underfull \hbox (badness 5133) in paragraph at lines 6995--6999 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7009--7012 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1958] [1959] Underfull \hbox (badness 4132) in paragraph at lines 7176--7178 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1960] [1961] [1962] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1963] [1964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1965] Underfull \hbox (badness 10000) in paragraph at lines 7526--7528 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1966] [1967] Underfull \hbox (badness 10000) in paragraph at lines 7711--7713 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 7716--7718 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1968] [1969] [1970] [1971] Underfull \hbox (badness 1859) in paragraph at lines 7939--7942 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1972] Underfull \hbox (badness 1655) in paragraph at lines 8032--8035 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8043--8043 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1973] [1974] Underfull \hbox (badness 1917) in paragraph at lines 8134--8136 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [1975] [1976] [1977] [1978] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8407--8407 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8408--8408 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] Underfull \hbox (badness 10000) in paragraph at lines 8436--8438 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from [1979] Underfull \hbox (badness 10000) in paragraph at lines 8450--8452 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8458--8463 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, Overfull \hbox (9.78043pt too wide) in paragraph at lines 8504--8504 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8505--8505 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1980] [1981] Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8634--8639 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [1982] [1983] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8757--8757 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8758--8758 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8929--8929 [] \T1/pcr/m/n/9 "S original, "),[] [1986] [1987] Underfull \hbox (badness 1789) in paragraph at lines 9060--9062 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 5203) in paragraph at lines 9633--9636 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1996] [1997] [1998] Underfull \hbox (badness 1394) in paragraph at lines 9859--9866 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1999] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9883--9883 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2000] [2001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10044--10044 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2002] [2003] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10225--10225 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2004] [2005] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10311--10311 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10314--10314 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10319--10319 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2006] Underfull \hbox (badness 2027) in paragraph at lines 10391--10394 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2007] [2008] [2009] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10664--10664 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 10665--10665 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] [2010] Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2011] [2012] [2013] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10905--10905 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2014] [2015] [2016] [2017] Underfull \hbox (badness 10000) in paragraph at lines 11165--11169 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [2018] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11183--11183 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11188--11188 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2019] [2020] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11372--11372 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2021] [2022] Underfull \hbox (badness 1917) in paragraph at lines 11496--11499 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11496--11499 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [2023] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2024] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []\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 Underfull \hbox (badness 6725) in paragraph at lines 11632--11641 \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 11632--11641 \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 11632--11641 \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 11632--11641 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2025] [2026] Underfull \hbox (badness 3646) in paragraph at lines 11758--11760 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2027] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11796--11796 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2028] [2029] [2030] Underfull \hbox (badness 10000) in paragraph at lines 11977--11981 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12008--12014 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2031] [2032] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12184--12184 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12202--12214 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2033] Underfull \hbox (badness 2600) in paragraph at lines 12239--12241 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2034] Underfull \hbox (badness 1043) in paragraph at lines 12282--12287 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2035] [2036] [2037] [2038] Underfull \hbox (badness 1888) in paragraph at lines 12575--12578 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 12590--12593 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2039] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12631--12631 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] Underfull \hbox (badness 2158) in paragraph at lines 12686--12689 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [2040] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12734--12734 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2041] [2042] Underfull \hbox (badness 2302) in paragraph at lines 12891--12893 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2043] [2044] Underfull \hbox (badness 3333) in paragraph at lines 12998--13000 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2045] [2046] [2047] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13163--13163 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13187--13192 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][ ]\T1/pcr/m/n/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13196--13199 []\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 13196--13199 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2048] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2049] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13282--13282 []\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 13289--13289 []\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 13291--13291 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2050] [2051] Underfull \hbox (badness 10000) in paragraph at lines 13459--13461 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2052] [2053] [2054] Underfull \hbox (badness 6300) in paragraph at lines 13616--13623 []\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 13616--13623 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 13616--13623 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2055] [2056] Underfull \hbox (badness 2020) in paragraph at lines 13785--13801 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 13785--13801 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2057] [2058] Underfull \hbox (badness 5022) in paragraph at lines 13925--13929 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 13932--13935 [][][]$\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 13932--13935 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2059] [2060] [2061] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14096--14096 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2062] [2063] [2064] [2065] [2066] [2067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14536--14536 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14542--14542 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14563--14565 []\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 14576--14580 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 14590--14594 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 14596--14601 []\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 14596--14601 \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 14596--14601 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2068] Underfull \hbox (badness 10000) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 14653--14658 []\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 14661--14664 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2069] Overfull \hbox (9.78043pt too wide) in paragraph at lines 14715--14715 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2070] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 14917--14920 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 14917--14920 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2073] Overfull \hbox (42.18039pt too wide) in paragraph at lines 14933--14933 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15000--15000 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15022--15022 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2075] [2076] Underfull \hbox (badness 1297) in paragraph at lines 15153--15155 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2077] Underfull \hbox (badness 4036) in paragraph at lines 15200--15202 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2078] [2079] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15337--15337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2080] Underfull \hbox (badness 1715) in paragraph at lines 15389--15392 []\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 15434--15436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/pcr/m/n/10 file = [2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex Chapter 15. [2087] 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) [2088] [2089] [2090] [2091] [2092] 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, [2093] [2094] [2095] [2096]) (./MASS-pkg.tex Chapter 16. [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] 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))[] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] 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"),[] [2131] [2132] [2133] [2134] 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 [2135] [2136] [2137] 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 10000) 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 , [2138] [2139] 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 [2140] [2141] [2142] 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, ...)[] [2143] 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")[] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] 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 [2156] [2157] [2158] [2159] [2160] [2161] [2162] 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", ...)[] [2163] [2164] [2165] 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, [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] 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) [2180] 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") [2181] [2182]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} [2183] 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 [2184] [2185] [2186] [2187] Underfull \vbox (badness 10000) has occurred while \output is active [2188] 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)))[] [2189] 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"))[] [2190] [2191] [2192] [2193] [2194] [2195] 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"))[] [2196] 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 ) = [2197] 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)[] [2198] [2199] 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 [2200] [2201] 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")[] [2202] 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"), ...)[] [2203] [2204] [2205] [2206] [2207] [2208] 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 [2209] [2210] 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 [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] 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, ...)[] [2231] Underfull \hbox (badness 2035) in paragraph at lines 9595--9597 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1 /pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 , Underfull \hbox (badness 1158) in paragraph at lines 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), [2232] 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)[] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]) (./Matrix-pkg.tex [2246] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2247] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2248] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2249] 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 [2250] [2251] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) 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 [2252] 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)],[] [2253] [2254] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] 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)[] [2255] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2256] [2257] [2258] 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"), ...)[] [2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) 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} [2261pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] Underfull \hbox (badness 2285) in paragraph at lines 1220--1225 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2262] 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[] [2263] 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 [2264] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2265] 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)))[] [2266] Underfull \hbox (badness 10000) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or 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 [2267]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} [2268] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2269] [2270] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2271] [2272] [2273] [2274] [2275] Underfull \hbox (badness 1484) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2276] Underfull \hbox (badness 7379) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2277] [2278] [2279] Underfull \hbox (badness 4846) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2280] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2281] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2282] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2283] Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2286] Underfull \hbox (badness 2469) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2287] [2288] Underfull \hbox (badness 10000) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3528--3532 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2289] Underfull \hbox (badness 2285) in paragraph at lines 3578--3581 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2290] [2291] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2292] Underfull \hbox (badness 10000) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2293] [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2296] Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2297] [2298] Underfull \hbox (badness 3158) in paragraph at lines 4288--4292 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2299] [2300] [2301] [2302] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2307] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2308] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2309] [2310] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2311] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2312] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5279--5282 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5292--5295 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2313] Underfull \hbox (badness 4765) in paragraph at lines 5310--5313 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2314] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2315] [2316] [2317] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2318] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2319] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2321] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2322] Underfull \hbox (badness 6063) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2323] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2324] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2325] Underfull \hbox (badness 3179) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2326] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2327] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2328] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2330] [2331] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2332] [2333]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.det}) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 10000) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2334]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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} Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2335] [2336pdfTeX warning (ext4): destination with the same identifier (name{R fn.crossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7426--7431 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7431--7435 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7431--7435 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2337] [2338] Underfull \hbox (badness 1009) in paragraph at lines 7577--7579 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2339] Underfull \hbox (badness 6063) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2340] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2341] [2342] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2343] Underfull \hbox (badness 2635) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7912--7917 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2344] Underfull \hbox (badness 3482) in paragraph at lines 7994--8000 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2345] Underfull \hbox (badness 1867) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim- [2346]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8356--8366 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2348] Underfull \hbox (badness 3179) in paragraph at lines 8427--8430 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2349] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2350] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2352] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8721--8724 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8727--8734 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2353] [2354] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8855--8865 []\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 8855--8865 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2355] [2356]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2357] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040 []\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 9044--9044 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2358] Underfull \hbox (badness 10000) in paragraph at lines 9122--9128 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9139--9142 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2359] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2360] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232 []\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 9233--9233 []\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.9252 ... the Reciprocal Condition Number}{rcond} [2361] [2362] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2363] [2364] Underfull \hbox (badness 10000) in paragraph at lines 9550--9552 []\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 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2365] [2366] Underfull \hbox (badness 1558) in paragraph at lines 9701--9704 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2367] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926 [] \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 9931--9931 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2369] Underfull \hbox (badness 1616) in paragraph at lines 9966--9978 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 9983--9986 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10005--10015 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10005--10015 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, [2370] Underfull \hbox (badness 6032) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10039--10041 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10062--10063 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10068--10070 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10072--10073 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10080--10083 [][][]\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 10098--10098 []\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 10102--10102 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2371] Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\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 10151--10153 []\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 10159--10162 []\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 10159--10162 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\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 10170--10174 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for [2372] Underfull \hbox (badness 6592) in paragraph at lines 10181--10183 []\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 Underfull \hbox (badness 1158) in paragraph at lines 10199--10205 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2373] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2374] [2375] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2376] Underfull \hbox (badness 4621) in paragraph at lines 10485--10489 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2377] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2379] Underfull \hbox (badness 10000) in paragraph at lines 10733--10741 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class [2380] Underfull \hbox (badness 10000) in paragraph at lines 10784--10788 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2381] [2382] Underfull \hbox (badness 10000) in paragraph at lines 10954--10956 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2383] Underfull \hbox (badness 2970) in paragraph at lines 11143--11149 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11143--11149 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2384] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2385] Underfull \hbox (badness 10000) in paragraph at lines 11234--11239 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11249--11251 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2386] [2387] Underfull \hbox (badness 2698) in paragraph at lines 11374--11380 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2388] Underfull \hbox (badness 10000) in paragraph at lines 11467--11469 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11485--11490 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11493--11498 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2389] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2390] [2391] Underfull \hbox (badness 6641) in paragraph at lines 11651--11654 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11691--11695 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11691--11695 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2392] Underfull \hbox (badness 7649) in paragraph at lines 11798--11800 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2393] [2394] [2395] Underfull \hbox (badness 7362) in paragraph at lines 11999--12001 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2396] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2397] [2398] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2399] [2400] [2401]) (./boot-pkg.tex [2402] Chapter 18. [2403] [2404] [2405] [2406] [2407] [2408] [2409] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2410] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2411] [2412] [2413] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2414] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2415] [2416] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2417] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2418] [2419] [2420] [2421] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2422] [2423] [2424] [2425] [2426] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2427] [2428] [2429] Underfull \vbox (badness 10000) has occurred while \output is active [2430] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2431] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2432] [2433] [2434] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2435] Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2436] [2437] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2438] [2439] [2440] [2441] [2442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2443] [2444] [2445] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2446] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2447] [2448] [2449] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2450] [2451] [2452] [2453] [2454] [2455] [2456] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2457] [2458] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2459] [2460] [2461] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2474] [2475] [2476] [2477] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2478] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2487] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2488] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2489] [2490] [2491] [2492] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2493] [2494] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2495] [2496] [2497] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2498] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex [2508] Chapter 19. [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex Chapter 20. [2525] Underfull \hbox (badness 1655) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 133--142 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 133--142 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 133--142 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2526] [2527] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2528] [2529] Underfull \vbox (badness 10000) has occurred while \output is active [2530] [2531] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2532] [2533] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2534] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2535] [2536] Underfull \hbox (badness 2941) in paragraph at lines 779--782 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2537] Underfull \hbox (badness 10000) in paragraph at lines 864--866 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2538] Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2539] Underfull \hbox (badness 4872) in paragraph at lines 975--977 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 989--993 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2541] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2542] Underfull \hbox (badness 4144) in paragraph at lines 1190--1194 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2543] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1272--1272 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2544] [2545] Underfull \hbox (badness 10000) in paragraph at lines 1411--1416 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1459--1462 [2546] Underfull \hbox (badness 10000) in paragraph at lines 1476--1480 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1500--1500 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1510--1510 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2547] Underfull \hbox (badness 5741) in paragraph at lines 1550--1553 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2549] Underfull \hbox (badness 1540) in paragraph at lines 1733--1741 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 = [2550] [2551] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1843--1843 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2552] [2553] [2554] [2555] Underfull \hbox (badness 10000) in paragraph at lines 2162--2165 [2556] Underfull \hbox (badness 3179) in paragraph at lines 2176--2182 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2557] [2558] Underfull \hbox (badness 10000) in paragraph at lines 2334--2337 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2559] Underfull \hbox (badness 1292) in paragraph at lines 2402--2405 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2411--2413 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2434--2437 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2560] [2561] [2562] [2563] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2564] [2565] [2566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2567] [2568] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2569] [2570] [2571] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2572] Underfull \hbox (badness 10000) in paragraph at lines 3286--3289 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2573] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2574] [2575] [2576] Underfull \hbox (badness 10000) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for [2577] Underfull \hbox (badness 10000) in paragraph at lines 3585--3590 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2578] Underfull \hbox (badness 3884) in paragraph at lines 3647--3652 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m /n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx Underfull \hbox (badness 6268) in paragraph at lines 3659--3662 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2579] [2580] [2581] Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3875--3878 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2582] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3939--3941 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2583] [2584] [2585] [2586] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4134--4134 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2587] [2588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4286--4286 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4288--4288 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4295--4295 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2589] [2590] [2591] [2592] [2593] [2594] Underfull \hbox (badness 10000) in paragraph at lines 4668--4674 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4684--4686 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side [2595] Overfull \hbox (52.98038pt too wide) in paragraph at lines 4697--4697 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4699--4699 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4713--4713 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2596]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2597] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2598] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2599] [2600] [2601]) (./foreign-pkg.tex [2602] Chapter 22. [2603] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2604] [2605] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2606] 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, [2607] [2608] [2609] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2610] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] 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/10 , 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 [2611] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] 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,[] [2613] 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="")[] [2614] [2615] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2616] [2617] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2618] 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 [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2619] [2620] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\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"))[] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2623] Underfull \hbox (badness 2088) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2624]) (./lattice-pkg.tex Chapter 23. [2625] [2626] [2627] 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"),[] [2628] 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"),[] [2629] [2630] [2631] [2632] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2633] [2634] [2635] [2636] 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. [2637] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2638] [2639] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a 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 [2640] [2641] [2642] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2643] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2644] Underfull \vbox (badness 10000) has occurred while \output is active [2645] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2646] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2647] [2648] [2649] [2650] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2651] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2652] [2653] [2654] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2655] [2656] [2657] [2658] [2659] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2660] [2661] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as 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 [2662] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- 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 [2663] [2664] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] 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"),[] [2665] Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \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"),[] [2670] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2671] [2672] [2673] [2674] [2675] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2676] Underfull \hbox (badness 2277) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by 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 [2677] [2678] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) 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 [2679] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2680] [2681] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , 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 [2682] [2683] [2684] [2685] [2686] [2687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2688] [2689] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2690] [2691] 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 [2692] [2693] [2694] [2695] [2696] [2697] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or 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],[] [2698] 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 [2699] 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 [2700] 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,[] [2701] 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 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 [2702] [2703] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and 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 [2704] [2705] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2706] [2707] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2708] [2709] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round 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 [2710] 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,[] [2711] [2712] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2713] 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 [2714] [2715] [2716] [2717] [2718] [2719] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- 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 [2720] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2721] 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 [2722] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2723] [2724] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2725] 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))[] [2726] [2727] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to [2728] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] 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),[] [2729] 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)[] [2730] [2731] [2732] 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")[] [2733] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2742] [2743] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] 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, ...)[] [2744] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2745] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2746] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2747] [2748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2749] [2750] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2751] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2752] [2753] [2754] [2755] [2756] [2757] [2758] Underfull \hbox (badness 7238) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2762] [2763] [2764] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower 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),[] [2765] [2766]) (./mgcv-pkg.tex Chapter 24. [2767] [2768] 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,[] [2769] 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. [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][]\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 365--372 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2774] Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2775] [2776] [2777] Underfull \hbox (badness 2922) in paragraph at lines 607--608 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2778] [2779] [2780] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2781] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2782] Underfull \vbox (badness 10000) has occurred while \output is active [2783] [2784] [2785] [2786] [2787] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164 []\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 1165--1165 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2788] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178 []\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 1180--1180 []\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 1182--1182 [] \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 1213--1213 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] [2790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285 [] \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 1319--1319 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] Underfull \vbox (badness 10000) has occurred while \output is active [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2800] [2801] [2802] [2803] [2804] [2805] Underfull \hbox (badness 1052) in paragraph at lines 2197--2205 \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 2214--2214 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2226--2229 []\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 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2806] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2807] [2808] Underfull \hbox (badness 1043) in paragraph at lines 2428--2434 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2809] [2810] Underfull \hbox (badness 10000) in paragraph at lines 2564--2570 [][][]\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 2564--2570 [][]\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 2564--2570 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2811] Underfull \vbox (badness 10000) has occurred while \output is active [2812] Underfull \vbox (badness 10000) has occurred while \output is active [2813] Underfull \vbox (badness 10000) has occurred while \output is active [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220 [] \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 3223--3223 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2822] [2823] [2824] [2825] [2826] [2827] Underfull \hbox (badness 5189) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2828] [2829] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2830] [2831] [2832] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2833] [2834] [2835] [2836] [2837] [2838] [2839] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2840] [2841] [2842] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2843] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2844] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2845] Underfull \hbox (badness 10000) in paragraph at lines 4660--4669 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2846] [2847] Underfull \hbox (badness 5970) in paragraph at lines 4777--4783 [][][]\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 4777--4783 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2848] Underfull \vbox (badness 10000) has occurred while \output is active [2849] [2850] [2851] Underfull \hbox (badness 1577) in paragraph at lines 5057--5060 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2852] [2853] [2854] [2855] [2856] [2857] [2858] Underfull \hbox (badness 6708) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(..., fit=FALSE) \T1/ptm/m/n/10 or [2859] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2860] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5556--5556 [] \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 [2861] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2862] [2863] [2864] [2865] [2866] [2867] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933 []\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 5935--5935 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2868] [2869] [2870] [2871] [2872] [2873] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1 ,deriv=2) Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2874] [2875] [2876] [2877] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] [2880] [2881] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702 []\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 6729--6729 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2891] [2892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422 []\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 7441--7441 [] \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 [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] Underfull \vbox (badness 10000) has occurred while \output is active [2913] [2914] Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2915] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\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 8717--8720 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2916] [2917] [2918] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937 []\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 8938--8938 [] \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 8941--8941 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2919] [2920] [2921] Underfull \hbox (badness 1629) in paragraph at lines 9099--9104 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2922] [2923] [2924] [2925] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2926] [2927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2928] [2929] [2930] [2931] Underfull \vbox (badness 10000) has occurred while \output is active [2932] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2933] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \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 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2934] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\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 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2935] Underfull \hbox (badness 10000) in paragraph at lines 9939--9942 []\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 9939--9942 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2936] [2937] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2938] [2939] [2940] [2941] Underfull \hbox (badness 1946) in paragraph at lines 10247--10254 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2942] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2943] [2944] [2945] [2946] [2947] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2948] [2949] [2950] [2951] [2952] [2953] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985 []\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 10998--11002 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2954] Underfull \hbox (badness 10000) in paragraph at lines 11038--11042 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2955] [2956] [2957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2958] Underfull \hbox (badness 1803) in paragraph at lines 11267--11271 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11279--11291 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2959] [2960] [2961] Underfull \vbox (badness 10000) has occurred while \output is active [2962] Underfull \hbox (badness 6876) in paragraph at lines 11491--11497 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2963] [2964] Underfull \hbox (badness 10000) in paragraph at lines 11649--11650 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2965] [2966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2967] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2968] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 \T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m /n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or [2969] [2970] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2972] [2973] [2974] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2975] [2976] [2977] [2978] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2979] Underfull \hbox (badness 10000) in paragraph at lines 12468--12470 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2980] [2981] Underfull \vbox (badness 10000) has occurred while \output is active [2982] Underfull \hbox (badness 10000) in paragraph at lines 12627--12630 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12627--12630 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12627--12630 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 12754--12760 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2985] [2986] [2987] Underfull \vbox (badness 10000) has occurred while \output is active [2988] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2989] Underfull \hbox (badness 10000) in paragraph at lines 13071--13079 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [2990] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2991] [2992] [2993] [2994] Underfull \hbox (badness 3396) in paragraph at lines 13358--13361 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2995] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2996] [2997] [2998] [2999] Underfull \hbox (badness 10000) in paragraph at lines 13627--13630 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13627--13630 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3000] Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3006] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3007] [3008] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3009] [3010] Underfull \hbox (badness 4846) in paragraph at lines 14294--14297 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3031] [3032] [3033] [3034] [3035] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3036] [3037] [3038]) (./nlme-pkg.tex Chapter 25. [3039] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3040] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3041] [3042] [3043] [3044] [3045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3046] [3047] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3056] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3057] [3058] [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3064] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3070] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3071] Underfull \hbox (badness 1132) in paragraph at lines 2145--2147 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3072] [3073] Underfull \hbox (badness 4168) in paragraph at lines 2256--2262 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 2844--2848 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3135] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3136] Underfull \hbox (badness 2057) in paragraph at lines 6243--6254 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3137] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3138] [3139] [3140] [3141] Underfull \hbox (badness 7133) in paragraph at lines 6557--6561 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3142] Underfull \hbox (badness 10000) in paragraph at lines 6656--6662 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3143] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3145] [3146] [3147] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3148] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7039--7041 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3149] [3150] [3151] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3152] [3153] [3154] Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7406--7414 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3155] [3156] [3157] Underfull \hbox (badness 3354) in paragraph at lines 7644--7646 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8208--8230 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3166] [3167] [3168] [3169] [3170] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3171] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3184] Underfull \hbox (badness 6300) in paragraph at lines 9417--9420 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3189] Underfull \hbox (badness 10000) in paragraph at lines 9706--9709 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9750--9753 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9750--9753 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] Underfull \hbox (badness 7291) in paragraph at lines 10214--10216 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3198] [3199] [3200] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3201] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3202] [3203] [3204] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3205] [3206] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10797--10802 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3207] Underfull \hbox (badness 8075) in paragraph at lines 10819--10823 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3208] [3209] [3210] [3211] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3212] [3213] [3214] [3215] [3216] [3217] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3218] [3219] [3220] [3221] [3222] [3223] Underfull \hbox (badness 6268) in paragraph at lines 11906--11916 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 12167--12173 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3228] [3229] [3230] [3231] [3232] Underfull \hbox (badness 6876) in paragraph at lines 12489--12491 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3233] [3234] Underfull \hbox (badness 2452) in paragraph at lines 12645--12652 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3235] Underfull \hbox (badness 10000) in paragraph at lines 12710--12716 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3245] [3246] [3247] [3248] [3249] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3250] Underfull \hbox (badness 10000) in paragraph at lines 13691--13694 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3251] Underfull \hbox (badness 1838) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13734--13741 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3252] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13798--13801 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13826--13829 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13826--13829 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3253] Underfull \hbox (badness 10000) in paragraph at lines 13906--13909 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3254] Underfull \hbox (badness 1472) in paragraph at lines 13931--13938 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3255] Underfull \hbox (badness 10000) in paragraph at lines 14000--14002 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3256] [3257] [3258] [3259] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3260] [3261] [3262] [3263] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] Underfull \hbox (badness 1009) in paragraph at lines 15834--15843 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3283] [3284] [3285] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3286] [3287] [3288] [3289] [3290] Underfull \hbox (badness 10000) in paragraph at lines 16316--16322 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3291] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3292] [3293] [3294] [3295] [3296] [3297] [3298] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1867) in paragraph at lines 17171--17180 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3304] Underfull \hbox (badness 1521) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat ion of variance Underfull \hbox (badness 10000) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat ions per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 1694) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and [3305] [3306] [3307] [3308] Underfull \hbox (badness 10000) in paragraph at lines 17482--17489 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3309] [3310] [3311] [3312] [3313] [3314] [3315] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3316] Underfull \hbox (badness 3579) in paragraph at lines 18055--18060 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3317] Underfull \hbox (badness 3579) in paragraph at lines 18119--18124 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3318] Underfull \hbox (badness 3579) in paragraph at lines 18182--18187 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3319] Underfull \hbox (badness 1577) in paragraph at lines 18243--18245 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18245--18250 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3320] Underfull \hbox (badness 3579) in paragraph at lines 18308--18313 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3321] Underfull \hbox (badness 3579) in paragraph at lines 18380--18385 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3322] [3323] Underfull \hbox (badness 1009) in paragraph at lines 18526--18535 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3324] [3325] Underfull \hbox (badness 1009) in paragraph at lines 18658--18667 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \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} [3335] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3336] [3337] [3338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3340] [3341] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3342]) (./rpart-pkg.tex Chapter 27. [3343] [3344] [3345] [3346] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3347] [3348] [3349] [3350] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3351] [3352] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3353] [3354] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3355] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3356] [3357] [3358] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3359] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3360] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3361] [3362] [3363] [3364] [3365] [3366] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3367] [3368] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3369] [3370] [3371]) (./spatial-pkg.tex [3372] Chapter 28. [3373] [3374] [3375] [3376] [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391]) (./survival-pkg.tex [3392] Chapter 29. [3393] [3394] 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.[] [3395] [3396]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} [3397] [3398] 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)[] [3399] 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)[] [3400] [3401] Underfull \vbox (badness 10000) has occurred while \output is active [3402] 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"),[] [3403] [3404] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3405] [3406] [3407] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3408] [3409] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3410]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3411] 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"),[] [3412] [3413] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] [3414] [3415] [3416] [3417] [3418] Underfull \hbox (badness 1337) in paragraph at lines 1799--1803 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3419] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3420] [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3427] [3428] [3429] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3430] [3431] [3432] [3433] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3434] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3435] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3437] [3438] Underfull \vbox (badness 10000) has occurred while \output is active [3439] Underfull \vbox (badness 10000) has occurred while \output is active [3440] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3441] [3442] [3443] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3446] Underfull \vbox (badness 10000) has occurred while \output is active [3447] [3448] [3449] [3450] [3451] [3452] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3453] [3454] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3455] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3458] [3459] Underfull \hbox (badness 1852) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3460] [3461] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3462] [3463] [3464] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3465] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3466] [3467] [3468] [3469] [3470] Underfull \vbox (badness 2126) has occurred while \output is active [3471] [3472] [3473] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5560--5563 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3474] [3475] [3476] [3477] [3478] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3479] [3480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3481] [3482] [3483] [3484] [3485] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3486] [3487] [3488] [3489] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3490] [3491] [3492] Underfull \hbox (badness 1253) in paragraph at lines 6915--6918 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3493] [3494] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 7041--7050 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3495] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3496] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3497] Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3498] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3499] [3500] [3501] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3502] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3503] [3504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3505] [3506] [3507] Underfull \hbox (badness 3058) in paragraph at lines 7969--7974 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3509] [3510] [3511] [3512] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3513] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3514] [3515] Underfull \hbox (badness 2035) in paragraph at lines 8597--8604 \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 8597--8604 \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 8597--8604 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3516] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3517] [3518] [3519] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3520] [3521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 [] \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 8965--8965 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3522] [3523] [3524] [3525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267 []\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 9268--9268 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3526] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274 [] \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 9276--9276 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3527] [3528] [3529] [3530] [3531] [3532] [3533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3534] [3535] [3536]) (./fullrefman.ind [3537] [3538] [3539] [3540] [3541] [3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550] [3551] [3552] [3553] [3554] [3555] [3556] [3557] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2205--2207 []| \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 2207--2209 []| \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 2209--2211 []| \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 2211--2213 []| \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 2213--2215 []| \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 2215--2217 []| \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 2217--2219 []| \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 2219--2221 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2221--2223 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2223--2225 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2225--2227 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2227--2229 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2229--2231 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2231--2233 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3558] [3559] [3560] [3561] [3562] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2771--2773 []| \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 2773--2775 []| \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 2775--2777 []| \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 2777--2779 []| \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 2779--2781 []| \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 2781--2783 []| \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 2783--2785 []| \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 2785--2787 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2787--2789 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2789--2791 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2791--2793 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , [3563] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2793--2795 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2795--2797 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2797--2799 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3564] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2934--2936 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572] Overfull \hbox (62.8567pt too wide) in paragraph at lines 3939--3941 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3941--3943 []\T1/pcr/m/n/10 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13729--13731 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13731--13733 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13733--13735 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 13735--13737 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13737--13739 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13739--13741 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13741--13743 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13743--13745 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13745--13747 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13749--13751 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13751--13753 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13753--13755 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13755--13757 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13757--13759 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3633] [3634] [3635] [3636] Overfull \hbox (50.8567pt too wide) in paragraph at lines 14533--14535 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14539--14541 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 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wide) in paragraph at lines 14605--14607 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14607--14609 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3637] [3638] [3639] [3640] [3641] Overfull \hbox (52.01662pt too wide) in paragraph at lines 15599--15601 \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 , [3642] [3643] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16156--16158 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 16175--16177 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16177--16179 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16183--16185 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method [3644] Overfull \hbox (14.8567pt too wide) in paragraph at 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in paragraph at lines 16575--16577 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16579--16581 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16581--16583 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method [3647] Overfull \hbox (32.8567pt too wide) in paragraph at lines 16583--16585 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16603--16605 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16605--16607 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16607--16609 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 16609--16611 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16613--16615 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16617--16619 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16621--16623 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3648] Overfull \hbox (46.01662pt too wide) in paragraph at lines 16824--16826 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 16850--16852 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3649] [3650] [3651] [3652] [3653] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18124--18126 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18127--18129 \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 , [3654] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18129--18131 \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 18131--18133 \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 18133--18135 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18135--18137 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18137--18139 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18139--18141 \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 18141--18143 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18143--18145 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18147--18149 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18149--18151 \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 18151--18153 \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 18153--18155 \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 18155--18157 \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 18157--18159 \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 , [3655] [3656] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18507--18509 \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 18579--18581 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3657] [3658] [3659] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19043--19045 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19052--19054 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19054--19056 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19056--19058 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19058--19060 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19070--19072 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19080--19082 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19095--19097 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19101--19103 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3660] Overfull \hbox (62.8567pt too wide) in paragraph at lines 19217--19219 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3661] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19424--19426 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19426--19428 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19428--19430 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19430--19432 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19434--19436 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19436--19438 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19438--19440 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19440--19442 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19442--19444 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19444--19446 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19446--19448 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19452--19454 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19456--19458 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19466--19468 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19470--19472 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19472--19474 []\T1/pcr/m/n/10 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[3] [4] Underfull \hbox (badness 6741) 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 \T1/pcr/m/n/10 1 + x != 1\T1/ptm/m/n/10 . Underfull \hbox (badness 4805) in paragraph at lines 135--141 \T1/ptm/m/n/10 It equals \T1/pcr/m/n/10 double.base ^ ulp.digits \T1/ptm/m/n/10 if ei-ther \T1/pcr/m/n/10 double.base \T1/ptm/m/n/10 is Underfull \hbox (badness 4316) in paragraph at lines 135--141 \T1/ptm/m/n/10 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-er- wise, it is \T1/pcr/m/n/10 (double.base ^ Underfull \hbox (badness 5050) in paragraph at lines 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 . It Underfull \hbox (badness 1028) in paragraph at lines 141--149 \T1/ptm/m/n/10 equals \T1/pcr/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt m/m/n/10 if \T1/pcr/m/n/10 double.base Underfull \hbox (badness 2980) in paragraph at lines 141--149 \T1/ptm/m/n/10 is 2 or \T1/pcr/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth- er-wise, it is \T1/pcr/m/n/10 (double.base Underfull \hbox (badness 1394) in paragraph at lines 141--149 \T1/pcr/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/pcr/m /n/10 1.110223e-16\T1/ptm/m/n/10 . As Underfull \hbox (badness 1668) in paragraph at lines 152--159 []\T1/ptm/m/n/10 the largest nor-mal-ized floating-point num-ber. Typ-i-cally, it is equal to [5] [6] [7] Underfull \hbox (badness 10000) in paragraph at lines 339--342 [][][]\T1/pcr/m/n/10 R.version[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 Sys. info[][][] \T1/ptm/m/n/10 give more de-tails about the OS. In par-tic-u-lar, [8] [9] [10] 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 (4.38043pt too wide) in paragraph at lines 873--873 []\T1/pcr/m/n/9 mtext(paste("mean(all.equal(x1, x2*(1 + eps_k))) {100 x} Mean rel.diff.=",[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 891--891 []\T1/pcr/m/n/10 all.names(expr, functions = TRUE, max.names = -1L, unique = F ALSE) [16] [17] [18] [19] [20] Underfull \hbox (badness 1838) in paragraph at lines 1178--1181 []\T1/ptm/m/n/10 If the calls to \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec- tors of dif-fer-ent lengths, \T1/pcr/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis t of length [21] [22] [23] [24] [25] [26] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1670--1670 [] \T1/pcr/m/n/10 cut.names = FALSE, col.names = names(x), fix.em pty.names = TRUE,[] [27] Underfull \hbox (badness 1303) in paragraph at lines 1698--1701 []\T1/ptm/m/n/10 logical or in-te-ger; in-di-cat-ing if col-umn names with more than 256 (or [28] [29] Underfull \hbox (badness 10000) in paragraph at lines 1816--1818 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 Date \T1/ptm/m/n/10 ob-ject, or some-thing wh ich can be co-erced by [30] [31] Overfull \hbox (112.38031pt too wide) in paragraph at lines 1953--1953 []\T1/pcr/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] Underfull \hbox (badness 10000) in paragraph at lines 1991--1993 []\T1/ptm/m/n/10 If [][]\T1/pcr/m/n/10 is.object[][][](x) \T1/ptm/m/n/10 is tru e and it has a [][]\T1/pcr/m/n/10 class[][][] \T1/ptm/m/n/10 for which an [32] [33] [34] [35] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2261--2261 []\T1/pcr/m/n/9 (now <- as.POSIXlt(Sys.time())) # the current datetime, as cla ss "POSIXlt"[] [36] [37] Underfull \hbox (badness 10000) in paragraph at lines 2389--2391 []\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci ently) by Underfull \hbox (badness 10000) in paragraph at lines 2392--2397 [][][]\T1/pcr/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le ngth re-sults, so at-tempt-ing to split via [38] Underfull \hbox (badness 1107) in paragraph at lines 2460--2462 []\T1/ptm/m/n/10 There are no re-stric-tions on the name given as \T1/pcr/m/n/1 0 x\T1/ptm/m/n/10 : it can be a non-syntactic name (see [39] [40] Overfull \hbox (36.78088pt too wide) in paragraph at lines 2627--2627 []\T1/pcr/m/n/10 attach(what, pos = 2L, name = deparse(substitute(what), backt ick=FALSE), [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] Overfull \hbox (31.3804pt too wide) in paragraph at lines 3295--3295 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", nus), col = nus + 2, lwd = 1, bty="n")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3326--3326 []\T1/pcr/m/n/9 plot(range(x0), c(1e-40, 1), log = "xy", xlab = "x", ylab = "" , type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3327--3327 [] \T1/pcr/m/n/9 main = "Bessel Functions J_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] [51] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3334--3334 []\T1/pcr/m/n/9 plot(range(x0), 10^c(-100, 80), log = "xy", xlab = "x", ylab = "", type = "n",[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 3335--3335 [] \T1/pcr/m/n/9 main = "Bessel Functions K_nu(x) near 0\n log - log sc ale") ; axis(2, at=1)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3338--3338 []\T1/pcr/m/n/9 legend("topright", legend = paste("nu=", paste(nus, nus + 0.5, sep = ", ")),[] [52] [53] [54] [55] [56] [57] Underfull \hbox (badness 10000) in paragraph at lines 3771--3773 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [58] [59] [60] [61] Overfull \hbox (102.78088pt too wide) in paragraph at lines 4012--4012 [] \T1/pcr/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...) , recursive=recursive) [62] [63] [64] Underfull \hbox (badness 4927) in paragraph at lines 4267--4271 []\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 4267--4271 \T1/ptm/m/n/10 of class \T1/pcr/m/n/10 "[][]NativeSymbolInfo[][][]"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "[][]RegisteredNativeSymbol[][][]" \T1/ptm/m/n/10 or [65] [66] [67] Underfull \hbox (badness 4595) in paragraph at lines 4411--4414 []\T1/ptm/m/n/10 is ICU avail-able for col-la-tion? See the help on [][]Com-par -i-son[][][] and [68] [69] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4566--4566 []\T1/pcr/m/n/9 cat(paste(letters, 100* 1:26), fill = TRUE, labels = paste0("{ ", 1:10, "}:"))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 4590--4590 [] \T1/pcr/m/n/10 stringsAsFactors = default.stringsAsFactors(), factor.e xclude = NA)[] Underfull \hbox (badness 1199) in paragraph at lines 4596--4602 []\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 4607--4610 []\T1/ptm/m/n/10 (only for data frame method:) log-i-cal in-di-cat-ing if uniqu e and valid [70] [71] [72] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4780--4780 []\T1/pcr/m/n/9 rbind(1:4, c = 2, "a++" = 10, dd, deparse.level = 1) # 3 rowna mes (default)[] [73] [74] [75] Underfull \hbox (badness 2521) in paragraph at lines 5033--5035 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [76] [77] [78] [79] [80] [81] Underfull \hbox (badness 10000) in paragraph at lines 5430--5438 []\T1/ptm/m/n/10 When a generic func-tion \T1/pcr/m/n/10 fun \T1/ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 1796) in paragraph at lines 5993--6001 []\T1/ptm/m/n/10 Collation of char-ac-ter strings is a com-plex topic. 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Underfull \hbox (badness 1635) in paragraph at lines 6367--6370 []\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 6371--6374 []\T1/ptm/m/n/10 Restarts are used for es-tab-lish-ing re-cov-ery pro-to-cols. They can be es-tab-lished us-ing [95] Underfull \hbox (badness 1308) in paragraph at lines 6402--6410 []\T1/ptm/m/n/10 One ad-di-tional field that can be spec-i-fied for a restart i s \T1/pcr/m/n/10 interactive\T1/ptm/m/n/10 . This should [96] [97] Overfull \hbox (30.78088pt too wide) in paragraph at lines 6556--6556 []\T1/pcr/m/n/10 unz(description, filename, open = "", encoding = getOption("e ncoding"))[] [98] Overfull \hbox (89.35893pt too wide) in paragraph at lines 6598--6600 []\T1/ptm/m/n/10 character string, par-tially matched to \T1/pcr/m/n/10 c("defa ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 6746--6749 []\T1/ptm/m/n/10 A note on `\T1/pcr/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo st gen-eral form (from RFC1738) is Underfull \hbox (badness 2057) in paragraph at lines 6746--6749 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 file://host/path/to/file\T1/ptm/m/n/10 ', but \T 1/phv/m/n/10 R \T1/ptm/m/n/10 only ac-cepts the form with an empty \T1/pcr/m/n/ 10 host [101] [102] Underfull \hbox (badness 1406) in paragraph at lines 6928--6934 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \ T1/pcr/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re- move Underfull \hbox (badness 2173) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 a Byte Or-der Mark if present (which it of-ten is for files and web-pages gen-er-ated by Underfull \hbox (badness 2134) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it is not re c-om-mended) when writ-ing Underfull \hbox (badness 2452) in paragraph at lines 6928--6934 \T1/ptm/m/n/10 it should be writ-ten ex-plic-itly, e.g. by \T1/pcr/m/n/10 write Char("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 6948--6950 []\T1/ptm/m/n/10 It may be pos-si-ble to de-duce the cur-rent na-tive en-cod-in g from [103] Underfull \hbox (badness 1067) in paragraph at lines 6990--6997 \T1/ptm/m/n/10 pri-mary se-lec-tion (see [][]$\T1/pcr/m/n/10 http : / / standar ds . freedesktop . org / clipboards-[]spec / [104] [105] Underfull \vbox (badness 10000) has occurred while \output is active [106] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7182--7182 []\T1/pcr/m/n/9 A <- read.table(con <- file("students", encoding = "UCS-2LE")) ; close(con)[] [107] Underfull \hbox (badness 1231) in paragraph at lines 7307--7313 \T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the first el-e- [108] [109] [110] [111] Underfull \hbox (badness 10000) in paragraph at lines 7518--7520 []\T1/ptm/m/n/10 The cur-rent eval-u-a-tion depth (in-clud-ing two calls for th e call to [112] [113] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7663--7663 []\T1/pcr/m/n/9 curlGetHeaders("http://bugs.r-project.org") ## this redirect s to https://[] [114] [115] [116] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7901--7901 []\T1/pcr/m/n/9 tm <- seq(as.POSIXct("2012-06-01 06:00"), by = "6 hours", leng th.out = 24)[] [117] [118] Underfull \hbox (badness 8132) in paragraph at lines 8002--8006 []\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 8002--8006 \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 8021--8031 []\T1/pcr/m/n/10 data.frame \T1/ptm/m/n/10 con-verts each of its ar-gu-ments to a data frame by call-ing Underfull \hbox (badness 1975) in paragraph at lines 8021--8031 [][]\T1/pcr/m/n/10 as.data.frame[][][](optional = TRUE)\T1/ptm/m/n/10 . As that is a generic func-tion, meth-ods can be [119] Overfull \hbox (4.63962pt too wide) in paragraph at lines 8053--8057 []\T1/pcr/m/n/10 default.stringsAsFactors \T1/ptm/m/n/10 is a util-ity that tak es [][]\T1/pcr/m/n/10 getOption[][][]("stringsAsFactors") [120] [121] [122] [123] [124] [125] Underfull \hbox (badness 1629) in paragraph at lines 8539--8551 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 5578) in paragraph at lines 8539--8551 \T1/pcr/m/n/10 = "UTC") \T1/ptm/m/n/10 may give \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 , and hence \T1/pcr/m/n/10 as.POSIXct("1969-12-31 23:59:59",tz = [126] [127] [128] Underfull \hbox (badness 10000) in paragraph at lines 8801--8802 [][][]$\T1/pcr/m/n/10 https : / / www . debian . org / doc / debian-[]policy / index . html # [129] [130] [131] Underfull \hbox (badness 10000) in paragraph at lines 8987--8991 []\T1/pcr/m/n/10 .Defunct \T1/ptm/m/n/10 is called from de-funct func-tions. Fu nc-tions should be listed in [132] [133] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9078--9078 []\T1/pcr/m/n/9 ### Promises in an environment [for advanced users]: -------- -------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9080--9080 []\T1/pcr/m/n/9 e <- (function(x, y = 1, z) environment())(cos, "y", {cat(" HO !\n"); pi+2})[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9105--9105 [] \T1/pcr/m/n/10 backtick = mode(expr) %in% c("call", "expression", "( ", "function"),[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 9106--9106 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "sh owAttributes"),[] [134] [135] Underfull \hbox (badness 5403) in paragraph at lines 9224--9226 []\T1/pcr/m/n/10 ..deparseOpts \T1/ptm/m/n/10 is the [][]\T1/pcr/m/n/10 charact er[][][] \T1/ptm/m/n/10 vec-tor of pos-si-ble de-pars-ing op-tions used by Underfull \hbox (badness 6063) in paragraph at lines 9243--9245 []\T1/ptm/m/n/10 Surround un-eval-u-ated ex-pres-sions, but not [][]\T1/pcr/m/n /10 formula[][][]\T1/ptm/m/n/10 s, with [136] [137] [138] Underfull \hbox (badness 1603) in paragraph at lines 9454--9457 []\T1/ptm/m/n/10 a nu-meric value. The mod-u-lus (ab-so-lute value) of the de-t er-mi-nant if [139] [140] [141] [142] [143] [144] [145] [146] [147] Underfull \hbox (badness 1917) in paragraph at lines 10060--10065 []\T1/pcr/m/n/10 provideDimnames(x) \T1/ptm/m/n/10 pro-vides \T1/pcr/m/n/10 dim names \T1/ptm/m/n/10 where ``miss-ing'', such that its re-sult has Overfull \hbox (36.7804pt too wide) in paragraph at lines 10115--10115 []\T1/pcr/m/n/9 strd(provideDimnames(N, base= list(letters[-(1:9)], tail(LETTE RS)))) # recycling[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10116--10116 []\T1/pcr/m/n/9 strd(provideDimnames(A, base= list(c("AA","BB")))) # recycling on both levels[] [148] [149] Underfull \hbox (badness 1168) in paragraph at lines 10218--10223 \T1/ptm/m/n/10 code anal-y-sis as a di-rec-tive to sup-press check-ing of \T1/p cr/m/n/10 x\T1/ptm/m/n/10 . Cur-rently this is only used by [150] Underfull \hbox (badness 10000) in paragraph at lines 10257--10263 []\T1/pcr/m/n/10 ...elt(n) \T1/ptm/m/n/10 is a func-tional way to get \T1/pcr/m /n/10 .. \T1/ptm/m/n/10 and ba-si-cally the same as Underfull \hbox (badness 5403) in paragraph at lines 10264--10267 []\T1/pcr/m/n/10 ...length() \T1/ptm/m/n/10 re-turns the num-ber of ex-pres-sio ns in \T1/pcr/m/n/10 ...\T1/ptm/m/n/10 . This is the same as [151] [152] Underfull \hbox (badness 2828) in paragraph at lines 10423--10427 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / IEEE _ 754-[]19 85$[][]\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Underfull \hbox (badness 10000) in paragraph at lines 10423--10427 \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 _ Overfull \hbox (42.78088pt too wide) in paragraph at lines 10456--10456 [] \T1/pcr/m/n/10 control = c("keepNA", "keepInteger", "niceNames", "showA ttributes"))[] [153] [154] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10529--10529 []\T1/pcr/m/n/9 ## Write an ASCII version of the \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 base\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 function mean() to our temp file, ..[] [155] [156] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10673--10673 []\T1/pcr/m/n/9 aq <- transform(airquality, Month = factor(Month, labels = mon th.abb[5:9])) [157] [158] [159] Underfull \hbox (badness 6396) in paragraph at lines 10862--10870 []\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len t method def-i-ni-tions for Underfull \hbox (badness 10000) in paragraph at lines 10871--10873 []\T1/pcr/m/n/10 duplicated(x,fromLast = TRUE) \T1/ptm/m/n/10 is equiv-a-lent t o but faster than [160] [161] [162] Underfull \hbox (badness 10000) in paragraph at lines 11088--11091 []\T1/ptm/m/n/10 Do not use \T1/pcr/m/n/10 dyn.unload \T1/ptm/m/n/10 on a DLL l oaded by [][]\T1/pcr/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 : use [163] [164] [165] [166] [167] [168] [169] [170] [171] Underfull \hbox (badness 5288) in paragraph at lines 11786--11788 []\T1/ptm/m/n/10 The path to the de-fault browser. Used to set the de-fault val ue of [172] Underfull \hbox (badness 3039) in paragraph at lines 11796--11801 []\T1/ptm/m/n/10 Optional. The path to Ghostscript, used by [][]\T1/pcr/m/n/10 dev2bitmap[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 bitmap[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 10000) in paragraph at lines 11856--11858 []\T1/ptm/m/n/10 (and more). Op-tional. Set-tings for [173] [174] Underfull \hbox (badness 4569) in paragraph at lines 11978--11982 []\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been passed as an ar-gu-ment Underfull \hbox (badness 2401) in paragraph at lines 11978--11982 \T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller' s en-vi-ron-ment, i.e., one needs [175] [176] Underfull \hbox (badness 10000) in paragraph at lines 12093--12095 []\T1/ptm/m/n/10 a frame in the call-ing list. Equiv-a-lent to giv-ing \T1/pcr/ m/n/10 where \T1/ptm/m/n/10 as [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12934--12934 []\T1/pcr/m/n/9 ## "avector" := vector that keeps attributes. Could provide a constructor[] [188] [189] [190] [191] [192] [193] Underfull \hbox (badness 2221) in paragraph at lines 13380--13389 \T1/ptm/m/n/10 en-tries. If ar-gu-ment \T1/pcr/m/n/10 ordered \T1/ptm/m/n/10 is true (or \T1/pcr/m/n/10 ordered() \T1/ptm/m/n/10 is used) the re-sult has clas s Underfull \hbox (badness 1635) in paragraph at lines 13380--13389 \T1/pcr/m/n/10 c("ordered","factor")\T1/ptm/m/n/10 . Un-doc-u-ment-edly for a l ong time, \T1/pcr/m/n/10 factor(x) \T1/ptm/m/n/10 loses all [194] [195] [196] [197] Underfull \hbox (badness 2253) in paragraph at lines 13641--13643 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see [198] [199] Underfull \hbox (badness 2573) in paragraph at lines 13756--13758 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/pcr/m /n/10 PATH \T1/ptm/m/n/10 and \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/pcr /m/n/10 fsep = [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13906--13908 []\T1/ptm/m/n/10 logical: should file dates be pre-served where pos-si-ble? See [202] [203] Underfull \hbox (badness 10000) in paragraph at lines 14015--14019 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14026--14029 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . Overfull \hbox (47.58038pt too wide) in paragraph at lines 14047--14047 [] \T1/pcr/m/n/9 # |--> (TRUE,FALSE) : ok for A but not B as it exists already[] [204] Overfull \hbox (30.78088pt too wide) in paragraph at lines 14070--14070 []\T1/pcr/m/n/10 dir.create(path, showWarnings = TRUE, recursive = FALSE, mode = "0777")[] [205] Underfull \hbox (badness 10000) in paragraph at lines 14162--14165 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ex ists[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 unlink[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 basename[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 14172--14172 []\T1/pcr/m/n/9 f <- list.files(".", all.files = TRUE, full.names = TRUE, recu rsive = TRUE)[] [206] Underfull \hbox (badness 10000) in paragraph at lines 14238--14241 []\T1/pcr/m/n/10 packageNotFoundError \T1/ptm/m/n/10 cre-ates an er-ror con-di- tion ob-ject of class Overfull \hbox (20.58041pt too wide) in paragraph at lines 14255--14255 []\T1/pcr/m/n/9 ## will not give an error, maybe a warning about *all* locatio ns it is found:[] [207] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14284--14284 []\T1/pcr/m/n/10 findInterval(x, vec, rightmost.closed = FALSE, all.inside = F ALSE, Underfull \hbox (badness 1472) in paragraph at lines 14308--14315 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 findInterval \T1/ptm/m/n/10 finds the in-dex of one vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 in an-other, \T1/pcr /m/n/10 vec\T1/ptm/m/n/10 , where Underfull \hbox (badness 7273) in paragraph at lines 14308--14315 \T1/ptm/m/n/10 the lat-ter must be non-decreasing. Where this is triv-ial, equi v-a-lent to \T1/pcr/m/n/10 apply( Underfull \hbox (badness 3965) in paragraph at lines 14316--14320 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [208] [209] [210] Overfull \hbox (0.78088pt too wide) in paragraph at lines 14479--14479 [] \T1/pcr/m/n/10 .C(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING) Overfull \hbox (0.78088pt too wide) in paragraph at lines 14480--14480 [] \T1/pcr/m/n/10 .Fortran(.NAME, ..., NAOK = FALSE, DUP = TRUE, PACKAGE, ENCO DING)[] [211] [212] [213] Overfull \hbox (63.78036pt too wide) in paragraph at lines 14711--14711 []\T1/pcr/m/n/9 ## formals returns a pairlist. Arguments with no default have type symbol (aka name).[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 14714--14714 []\T1/pcr/m/n/9 ## formals returns NULL for primitive functions. Use it in co mbination with[] [214] Underfull \hbox (badness 1168) in paragraph at lines 14798--14802 []\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 14798--14802 \T1/ptm/m/n/10 tor should be en-coded in sci-en-tific for-mat, or an in-te-ger penalty (see [215] Underfull \hbox (badness 6944) in paragraph at lines 14896--14899 [][][]\T1/pcr/m/n/10 formatC[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 paste[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 sprintf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 prettyNum[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 toString[][][]\T1/ptm/m/n/10 , [216] Overfull \hbox (4.38043pt too wide) in paragraph at lines 14921--14921 []\T1/pcr/m/n/9 z <- list(a = letters[1:3], b = (-pi+0i)^((-2:2)/2), c = c(1,1 0,100,1000),[] [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 15059--15061 []\T1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 is used for ``pret-ti-fy-ing'' (pos -si-bly for-mat-ted) num-bers, also in Overfull \hbox (48.78088pt too wide) in paragraph at lines 15079--15079 [] \T1/pcr/m/n/10 decimal.mark = getOption("OutDec"), input.d.mark = decimal.mark,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15085--15085 []\T1/pcr/m/n/10 .format.zeros(x, zero.print, nx = suppressWarnings(as.numeric (x)),[] [219] Underfull \hbox (badness 2790) in paragraph at lines 15092--15095 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] \T1/pcr/m/n/10 complex[][][] \T1/ptm/m/n/10 only for Underfull \hbox (badness 1024) in paragraph at lines 15123--15130 []\T1/pcr/m/n/10 "f" \T1/ptm/m/n/10 gives num-bers in the usual \T1/pcr/m/n/10 xxx.xxx \T1/ptm/m/n/10 for-mat; \T1/pcr/m/n/10 "e" \T1/ptm/m/n/10 and \T1/pcr/m /n/10 "E" \T1/ptm/m/n/10 give [220] Underfull \hbox (badness 10000) in paragraph at lines 15198--15200 []\T1/ptm/m/n/10 This works via \T1/pcr/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic h calls Underfull \hbox (badness 4954) in paragraph at lines 15198--15200 \T1/pcr/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times in this Underfull \hbox (badness 10000) in paragraph at lines 15220--15225 []\T1/ptm/m/n/10 For num-bers, \T1/pcr/m/n/10 formatC() \T1/ptm/m/n/10 calls \T 1/pcr/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls Underfull \hbox (badness 2818) in paragraph at lines 15226--15228 []\T1/ptm/m/n/10 If you set \T1/pcr/m/n/10 format \T1/ptm/m/n/10 it over-rides the set-ting of \T1/pcr/m/n/10 mode\T1/ptm/m/n/10 , so \T1/pcr/m/n/10 formatC(1 23.45,mode = [221] Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 []\T1/pcr/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b ers on the dec-i-mal point, so Underfull \hbox (badness 10000) in paragraph at lines 15232--15236 \T1/pcr/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi ves \T1/pcr/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 15237--15245 []\T1/pcr/m/n/10 prettyNum \T1/ptm/m/n/10 is the util-ity func-tion for pret-ti -fy-ing \T1/pcr/m/n/10 x\T1/ptm/m/n/10 . \T1/pcr/m/n/10 x \T1/ptm/m/n/10 can be com-plex (or [222] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15345--15345 []\T1/pcr/m/n/9 fc <- formatC(1.234 + 10^(0:8), format = "fg", width = 11, big .mark = "\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ")[] Underfull \vbox (badness 10000) has occurred while \output is active [223] Overfull \hbox (42.18039pt too wide) in paragraph at lines 15367--15367 []\T1/pcr/m/n/9 doLC <- FALSE # <= R warns, so change to TRUE manually if you want see the effect[] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16184--16184 []\T1/pcr/m/n/9 utils::tail(getLoadedDLLs(), 2) # the last 2 loaded ones, stil l a DLLInfoList[] [236] Underfull \hbox (badness 2418) in paragraph at lines 16293--16297 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \ T1/pcr/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/pcr/m/n/10 CallRoutine\T1/ptm/m/n/10 , Underfull \hbox (badness 6510) in paragraph at lines 16300--16303 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 name \T1/ptm/m/n/10 con-tains only one sym-b ol name and \T1/pcr/m/n/10 unlist \T1/ptm/m/n/10 is \T1/pcr/m/n/10 TRUE\T1/ptm/ m/n/10 , then the sin-gle [237] Underfull \hbox (badness 2326) in paragraph at lines 16335--16342 [][][]\T1/pcr/m/n/10 getDLLRegisteredRoutines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 is.loaded[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .C[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 .Fortran[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Exte rnal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 .Call[][][]\T1/ptm/m/n/10 , [238] [239] [240] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16581--16581 []\T1/pcr/m/n/10 grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = F ALSE, [241] Underfull \hbox (badness 1867) in paragraph at lines 16606--16613 []\T1/ptm/m/n/10 character string con-tain-ing a [][]reg-u-lar ex-pres-sion[][] [] (or char-ac-ter string for [242] [243] [244] [245] Overfull \hbox (20.58041pt too wide) in paragraph at lines 16875--16875 [] \T1/pcr/m/n/9 nms <- nms[is.na(match(nms, c("F","T")))] # <-- work around "checking hack"[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 16904--16904 []\T1/pcr/m/n/9 name.rex <- "(?[[:upper:]][[:lower:]]+) (?[[:uppe r:]][[:lower:]]+)"[] Underfull \vbox (badness 10000) has occurred while \output is active [246] Overfull \hbox (0.78088pt too wide) in paragraph at lines 16955--16955 [] \T1/pcr/m/n/10 value = FALSE, fixed = FALSE, all = FALSE, invert = F ALSE)[] [247] [248] [249] [250] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17320--17320 []\T1/pcr/m/n/9 (ii <- grouping(x <- c(1, 1, 3:1, 1:4, 3), y <- c(9, 9:1), z < - c(2, 1:9))) [251] [252] [253] [254] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17574--17574 []\T1/pcr/m/n/10 iconv(x, from = "", to = "", sub = NA, mark = TRUE, toRaw = F ALSE) [255] [256] [257] [258] Underfull \hbox (badness 2435) in paragraph at lines 17837--17839 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/pcr/m/n/10 http : / / www . unicode . org / reports / tr35 / [259] Underfull \hbox (badness 2285) in paragraph at lines 17903--17905 []\T1/ptm/m/n/10 The ICU user guide chap-ter on col-la-tion ([][]$\T1/pcr/m/n/1 0 http : / / userguide . icu-[]project . org / Overfull \hbox (9.78043pt too wide) in paragraph at lines 17911--17911 []\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 17921--17921 [] \T1/pcr/m/n/9 icuSetCollate(locale = "da_DK", case_first = "default"); p rint(sort(x))[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 17941--17941 []\T1/pcr/m/n/10 identical(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.se t = TRUE, [260] [261] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18075--18075 []\T1/pcr/m/n/9 ### For functions ("closure"s): ------------------------------ ----------------[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 18081--18081 []\T1/pcr/m/n/9 identical(f, g) # TRUE, as bytecode is ignored by default[] [262] Overfull \hbox (25.98041pt too wide) in paragraph at lines 18084--18084 []\T1/pcr/m/n/9 ## GLM families contain several functions, some of which share an environment:[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 op <- options(keep.source = TRUE) # and so, these have differi ng "srcref" :[] [263] [264] Overfull \hbox (4.38043pt too wide) in paragraph at lines 18217--18217 []\T1/pcr/m/n/9 ## This is a (not atypical) case where it is better *not* to u se ifelse(),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18225--18225 []\T1/pcr/m/n/9 ## example of different return modes (and \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 test\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 alone determining length):[] [265] [266] [267] Underfull \hbox (badness 10000) in paragraph at lines 18430--18432 []\T1/ptm/m/n/10 how some er-rors are han-dled and re-ported, e.g. see [][]\T1/ pcr/m/n/10 stop[][][] \T1/ptm/m/n/10 and [268] Underfull \hbox (badness 4217) in paragraph at lines 18514--18523 [][][]\T1/pcr/m/n/10 length[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 length<-[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 dimnames<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dim[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 dim<-[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nam es[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 names<-[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 2057) in paragraph at lines 18529--18545 [][][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.c omplex[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.double[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.logi cal[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [269] [270] [271] [272] [273] [274] Underfull \hbox (badness 4699) in paragraph at lines 18948--18951 []\T1/pcr/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type s (\T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , [275] [276] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19071--19071 []\T1/pcr/m/n/10 ISOdate(year, month, day, hour = 12, min = 0, sec = 0, tz = " GMT")[] [277] [278] Underfull \hbox (badness 4739) in paragraph at lines 19206--19208 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [279] Overfull \hbox (36.7804pt too wide) in paragraph at lines 19255--19255 []\T1/pcr/m/n/9 isSymmetric(D3) # FALSE (as row and co lumn names differ)[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 19256--19256 []\T1/pcr/m/n/9 isSymmetric(D3, check.attributes=FALSE) # TRUE (as names are not checked)[] [280] [281] [282] [283] [284] [285] [286] [287] [288] Underfull \hbox (badness 1975) in paragraph at lines 19834--19837 []\T1/ptm/m/n/10 The value of the in-ter-nal eval-u-a-tion of a top-level \T1/p hv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sion is al-ways as-signed to [289] [290] [291] [292] [293] [294] Underfull \hbox (badness 1077) in paragraph at lines 20229--20234 []\T1/ptm/m/n/10 In late 2017 a \T1/pcr/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l a-tion was seen di-vided into two li-braries, \T1/pcr/m/n/10 libcurl \T1/ptm/m/ n/10 and [295] Underfull \hbox (badness 10000) in paragraph at lines 20243--20250 [][][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 http : / / curl . haxx . se / [296] Underfull \hbox (badness 10000) in paragraph at lines 20317--20321 []\T1/ptm/m/n/10 By de-fault \T1/pcr/m/n/10 R_LIBS \T1/ptm/m/n/10 is un-set, an d \T1/pcr/m/n/10 R_LIBS_USER \T1/ptm/m/n/10 is set to di-rec-tory [297] [298] Underfull \hbox (badness 10000) in paragraph at lines 20466--20470 []\T1/ptm/m/n/10 To sup-press mes-sages dur-ing the load-ing of pack-ages use Underfull \hbox (badness 1454) in paragraph at lines 20466--20470 [][]\T1/pcr/m/n/10 suppressPackageStartupMessages[][][]\T1/ptm/m/n/10 : this wi ll sup-press all mes-sages from \T1/phv/m/n/10 R \T1/ptm/m/n/10 it-self Underfull \hbox (badness 1221) in paragraph at lines 20471--20478 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 library \T1/ptm/m/n/10 is called with no \T1 /pcr/m/n/10 package \T1/ptm/m/n/10 or \T1/pcr/m/n/10 help \T1/ptm/m/n/10 ar-gu- ment, it lists all avail-able pack- [299] [300] Underfull \hbox (badness 10000) in paragraph at lines 20602--20609 [][][]\T1/pcr/m/n/10 attach[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 detach[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 search[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/ m/n/10 objects[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 autoload[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 requireNamespace[][][]\T1/ptm/m/n/10 , [301] Underfull \hbox (badness 10000) in paragraph at lines 20723--20727 []\T1/ptm/m/n/10 Do not use [][]\T1/pcr/m/n/10 dyn.unload[][][] \T1/ptm/m/n/10 on a DLL loaded by \T1/pcr/m/n/10 library.dynam\T1/ptm/m/n/10 : use [302] Underfull \hbox (badness 5161) in paragraph at lines 20793--20798 []\T1/ptm/m/n/10 A small num-ber of files (some of the API header files) are di s-tributed un-der the Underfull \hbox (badness 6592) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 LESSER GNU GEN-ERAL PUB-LIC LI-CENSE, ver-sion 2.1 or later. A c opy of Underfull \hbox (badness 5133) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 this li-cense is in file `\T1/pcr/m/n/10 $R_SHARE_DIR/licenses/L GPL-2.1\T1/ptm/m/n/10 ' and can be viewed Underfull \hbox (badness 10000) in paragraph at lines 20793--20798 \T1/ptm/m/n/10 by \T1/pcr/m/n/10 RShowDoc("LGPL-2.1")\T1/ptm/m/n/10 . Ver-sion 3 of the li-cense can be dis-played by [303] [304] [305] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20960--20960 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 20964--20964 [] \T1/pcr/m/n/10 ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)[] [306] Underfull \hbox (badness 3343) in paragraph at lines 21020--21024 [][][]\T1/pcr/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 file.ac cess[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 files[][][] \T1/ptm/m/n/10 for many more file han-dling func-tions and [307] Overfull \hbox (4.38043pt too wide) in paragraph at lines 21106--21106 [] \T1/pcr/m/n/9 identical(L$b, e$b)) # "$" working for environments as for lists[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21117--21117 [] \T1/pcr/m/n/9 df = data.frame(x = rnorm(20), y = rbinom(20, 1, pr = 0.2))),[] [308] [309] Overfull \hbox (9.78043pt too wide) in paragraph at lines 21228--21228 []\T1/pcr/m/n/9 ## This however annihilates all objects in .GlobalEnv with the same names ![] Overfull \hbox (74.58035pt too wide) in paragraph at lines 21231--21231 []\T1/pcr/m/n/9 attach("all.rda") # safer and will warn about masked objects w / same name in .GlobalEnv[] Underfull \hbox (badness 6380) in paragraph at lines 21276--21281 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup- [310] [311] Underfull \hbox (badness 2564) in paragraph at lines 21367--21370 []\T1/ptm/m/n/10 Almost all the out-put rou-tines used by \T1/phv/m/n/10 R \T1/ ptm/m/n/10 it-self un-der Win-dows ig-nore the set-ting of Overfull \hbox (4.38043pt too wide) in paragraph at lines 21397--21397 []\T1/pcr/m/n/9 Sys.setlocale("LC_TIME", "de_DE.UTF-8") # Linux, macOS, other Unix-alikes[] [312] [313] Underfull \hbox (badness 1400) in paragraph at lines 21565--21569 [][][]\T1/pcr/m/n/10 raw[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 or `number-like' vec-tors (i.e., of types [][]\T1/pcr/m/n/10 do uble[][][] \T1/ptm/m/n/10 (class [314] [315] [316] Underfull \hbox (badness 2469) in paragraph at lines 21735--21741 []\T1/pcr/m/n/10 as.logical \T1/ptm/m/n/10 at-tempts to co-erce its ar-gu-ment to be of log-i-cal type. For [][]\T1/pcr/m/n/10 factor[][][]\T1/ptm/m/n/10 s, Underfull \hbox (badness 10000) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 this uses the [][]\T1/pcr/m/n/10 levels[][][] \T1/ptm/m/n/10 (la -bels). Like [][]\T1/pcr/m/n/10 as.vector[][][] \T1/ptm/m/n/10 it strips at-tri butes in-clud-ing Underfull \hbox (badness 4531) in paragraph at lines 21735--21741 \T1/ptm/m/n/10 names. Char-ac-ter strings \T1/pcr/m/n/10 c("T","TRUE","True","t rue") \T1/ptm/m/n/10 are re-garded as true, [317] [318] [319] [320] [321] [322] [323] [324] [325] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22362--22362 []\T1/pcr/m/n/9 zN <- c(complex(real = NA , imaginary = r ), complex(real = r , imaginary = NA ),[] Overfull \hbox (52.98038pt too wide) in paragraph at lines 22363--22363 [] \T1/pcr/m/n/9 complex(real = r , imaginary = NaN), complex(real = N aN, imaginary = r ))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 22366--22366 []\T1/pcr/m/n/9 zM ##--> many "NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s" (= 1) and th e four non-NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s (3 different ones, at 7,9,10)[] [326] [327] Underfull \hbox (badness 1655) in paragraph at lines 22490--22494 []\T1/ptm/m/n/10 `function' on this help page means an in-ter-preted func-tion (also known as a `clo-sure'): [328] [329] [330] [331] Underfull \hbox (badness 2277) in paragraph at lines 22739--22742 []\T1/ptm/m/n/10 For ma-trix \T1/ptm/m/it/10 cross\T1/ptm/m/n/10 products, [][] \T1/pcr/m/n/10 crossprod[][][]() \T1/ptm/m/n/10 and \T1/pcr/m/n/10 tcrossprod() \T1/ptm/m/n/10 are typ-i-cally prefer-able. [332] [333] [334] [335] [336] [337] [338] [339] Underfull \hbox (badness 1484) in paragraph at lines 23304--23312 []\T1/ptm/m/n/10 The address-space limit is 2Gb un-der 32-bit Win-dows un-less the OS's de-fault has been Underfull \hbox (badness 1152) in paragraph at lines 23304--23312 \T1/ptm/m/n/10 changed to al-low more (up to 3Gb). See [][]$\T1/pcr/m/n/10 http s : / / docs . microsoft . com / en-[]gb / [340] [341] Overfull \hbox (0.78088pt too wide) in paragraph at lines 23381--23381 [] \T1/pcr/m/n/10 by.x = by, by.y = by, all = FALSE, all.x = all, all.y = all,[] [342] [343] [344] [345] [346] [347] [348] Underfull \hbox (badness 1448) in paragraph at lines 23886--23894 \T1/pcr/m/n/10 anyNA(recursive = FALSE) \T1/ptm/m/n/10 works the same way as \T 1/pcr/m/n/10 is.na\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 anyNA(recursive = [349] [350] Underfull \hbox (badness 3849) in paragraph at lines 24000--24005 []\T1/pcr/m/n/10 as.name \T1/ptm/m/n/10 first co-erces its ar-gu-ment in-ter-na lly to a char-ac-ter vec-tor (so meth-ods for [351] Underfull \hbox (badness 7308) in paragraph at lines 24077--24083 []\T1/ptm/m/n/10 For an [][]\T1/pcr/m/n/10 environment[][][] env\T1/ptm/m/n/10 , \T1/pcr/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond- ing Underfull \hbox (badness 10000) in paragraph at lines 24077--24083 \T1/ptm/m/n/10 list, i.e., \T1/pcr/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are also given by Underfull \hbox (badness 1210) in paragraph at lines 24077--24083 [][]\T1/pcr/m/n/10 ls[][][](env,all.names = TRUE,sorted = FALSE)\T1/ptm/m/n/10 . If the en-vi-ron-ment is used as a hash Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 []\T1/ptm/m/n/10 It is pos-si-ble to up-date just part of the names at-tribute via the gen-eral rules: Underfull \hbox (badness 10000) in paragraph at lines 24087--24090 \T1/ptm/m/n/10 see the ex-am-ples. This works be-cause the ex-pres-sion there i s eval-u-ated as \T1/pcr/m/n/10 z [352] [353] Underfull \hbox (badness 10000) in paragraph at lines 24240--24242 []\T1/ptm/m/n/10 character string: par-tial match-ing to one of [354] [355] [356] Underfull \hbox (badness 6188) in paragraph at lines 24459--24462 []\T1/ptm/m/n/10 optional [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 even- tu-ally to be passed to \T1/pcr/m/n/10 print()\T1/ptm/m/n/10 , used by [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2197) in paragraph at lines 24943--24947 []\T1/ptm/m/n/10 Loading a names-pace should where pos-si-ble be silent, with s tartup mes-sages given by Underfull \hbox (badness 4048) in paragraph at lines 24943--24947 \T1/pcr/m/n/10 .onAttach\T1/ptm/m/n/10 . These mes-sages (and any es-sen-tial o nes from \T1/pcr/m/n/10 .onLoad\T1/ptm/m/n/10 ) should use [364] Underfull \hbox (badness 2846) in paragraph at lines 24957--24961 []\T1/ptm/m/n/10 Uses of \T1/pcr/m/n/10 library \T1/ptm/m/n/10 with ar-gu-ment \T1/pcr/m/n/10 help \T1/ptm/m/n/10 to dis-play ba-sic in-for-ma-tion about the pack- Underfull \hbox (badness 1990) in paragraph at lines 24957--24961 \T1/ptm/m/n/10 age should use \T1/pcr/m/n/10 format \T1/ptm/m/n/10 on the com-p uted pack-age in-for-ma-tion ob-ject and pass this to Overfull \hbox (12.78088pt too wide) in paragraph at lines 24999--24999 []\T1/pcr/m/n/10 attachNamespace(ns, pos = 2L, depends = NULL, exclude, includ e.only) Overfull \hbox (0.78088pt too wide) in paragraph at lines 25003--25003 [] \T1/pcr/m/n/10 keep.parse.data = getOption("keep.parse.data.pk gs"))[] [365] Underfull \hbox (badness 10000) in paragraph at lines 25051--25057 []\T1/pcr/m/n/10 loadNamespace \T1/ptm/m/n/10 does not at-tach the name space i t loads to the search path. Underfull \hbox (badness 1168) in paragraph at lines 25051--25057 \T1/pcr/m/n/10 attachNamespace \T1/ptm/m/n/10 can be used to at-tach a frame co n-tain-ing the ex-ported val-ues of a Underfull \hbox (badness 10000) in paragraph at lines 25064--25066 []\T1/pcr/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m ore ef-fi-cient than \T1/pcr/m/n/10 pkg %in% [366] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25115--25115 [] \T1/pcr/m/n/9 ## The string "foo" and the symbol \TS1/pcr/m/n/9 '\T1/pcr/m/ n/9 foo\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 can be used interchangably here:[] [367] [368] [369] Underfull \hbox (badness 8189) in paragraph at lines 25308--25314 []\T1/ptm/m/n/10 The de-fault method for \T1/pcr/m/n/10 is.numeric \T1/ptm/m/n/ 10 re-turns \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 if its ar-gu-ment is of [][]mode [][][] [370] [371] [372] Underfull \hbox (badness 1694) in paragraph at lines 25530--25533 []\T1/ptm/m/n/10 a char-ac-ter vec-tor with suit-able nu-meric ver-sion strings (see `De-tails'); [373] [374] [375] Underfull \hbox (badness 1603) in paragraph at lines 25777--25779 []\T1/ptm/m/n/10 date ob-jects or char-ac-ter vec-tors. (Char-ac-ter vec-tors a re con-verted by [376] [377] Overfull \hbox (1.28088pt too wide) in paragraph at lines 25904--25912 \T1/pcr/m/n/10 c("datasets","utils","grDevices","graphics","stats","methods")\T 1/ptm/m/n/10 . [378] [379] Underfull \hbox (badness 3271) in paragraph at lines 26111--26114 []\T1/ptm/m/n/10 default PDF viewer. The de-fault is set from the en-vi-ron-men t vari-able [380] [381] [382] Underfull \hbox (badness 3138) in paragraph at lines 26411--26417 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/pcr/m/ n/10 setRepositories[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 e.g. the de-fault `\T1/pcr/m/n/10 "https://bioconductor.org"\T1/ ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 2088) in paragraph at lines 26411--26417 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\ T1/ptm/m/n/10 '. Can be set by [383] Underfull \hbox (badness 1194) in paragraph at lines 26424--26427 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/pcr/m/n/10 create.post[][ ][] \T1/ptm/m/n/10 (and hence[][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/n/10 and Underfull \hbox (badness 1389) in paragraph at lines 26450--26452 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 26470--26476 []\T1/ptm/m/n/10 logical: should per-directory pack-age lock-ing be used by Underfull \hbox (badness 3826) in paragraph at lines 26485--26490 []\T1/ptm/m/n/10 Used by [][]\T1/pcr/m/n/10 install.packages[][][] \T1/ptm/m/n/ 10 (and in-di-rectly Underfull \hbox (badness 1009) in paragraph at lines 26503--26506 []\T1/ptm/m/n/10 default email-ing method used by [][]\T1/pcr/m/n/10 create.pos t[][][] \T1/ptm/m/n/10 and hence [][]\T1/pcr/m/n/10 bug.report[][][] \T1/ptm/m/ n/10 and [384] Underfull \hbox (badness 10000) in paragraph at lines 26519--26522 []\T1/ptm/m/n/10 The de-fault type of pack-ages to be down-loaded and in-stalle d -- see Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 []\T1/pcr/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma -cOS build), Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/pcr/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "both" \T1/ptm/m/n/10 (the de-fault for CRAN ma- Underfull \hbox (badness 10000) in paragraph at lines 26527--26532 \T1/ptm/m/n/10 cOS builds). (\T1/pcr/m/n/10 "mac.binary.mavericks"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "mac.binary.leopard"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 []\T1/ptm/m/n/10 URLs of the repos-i-to-ries for use by [][]\T1/pcr/m/n/10 upda te.packages[][][]\T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 2384) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 c(CRAN="@CRAN@")\T1/ptm/m/n/10 , a value that causes some util-i -ties to prompt for a CRAN Underfull \hbox (badness 2837) in paragraph at lines 26541--26548 \T1/ptm/m/n/10 mir-ror. To avoid this do set the CRAN mir-ror, by some-thing li ke \T1/pcr/m/n/10 local({r Underfull \hbox (badness 10000) in paragraph at lines 26541--26548 \T1/pcr/m/n/10 <-getOption("repos"); r["CRAN"] <-"http://my.local.cran"; [385] [386] [387] [388] Underfull \vbox (badness 10000) has occurred while \output is active [389] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26885--26885 []\T1/pcr/m/n/9 system.time(o <- sort.list(xx, method = "radix")) # 0.007 sec, 300X faster[] Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 []\T1/ptm/m/n/10 The outer prod-uct of the ar-rays \T1/pcr/m/n/10 X \T1/ptm/m/n /10 and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 is the ar-ray \T1/pcr/m/n/10 A \T1/ptm/ m/n/10 with di-men-sion Underfull \hbox (badness 10000) in paragraph at lines 26898--26902 \T1/pcr/m/n/10 c(dim(X),dim(Y)) \T1/ptm/m/n/10 where el-e-ment \T1/pcr/m/n/10 A [c(arrayindex.x,arrayindex.y)] = [390] [391] Underfull \hbox (badness 10000) in paragraph at lines 27045--27048 []\T1/pcr/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 str2lang(s ) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of Underfull \hbox (badness 1062) in paragraph at lines 27045--27048 \T1/pcr/m/n/10 parse(text=s,keep.source=FALSE) \T1/ptm/m/n/10 and can there-for e be re-garded as trans-form-ing [392] [393] [394] Underfull \hbox (badness 10000) in paragraph at lines 27314--27320 [][][]\T1/pcr/m/n/10 toString[][][] \T1/ptm/m/n/10 typ-i-cally calls \T1/pcr/m/ n/10 paste(*,collapse=",")\T1/ptm/m/n/10 . String ma-nip-u-la-tion with Underfull \hbox (badness 2495) in paragraph at lines 27314--27320 [][]\T1/pcr/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 substr [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 nchar[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 strsplit[][][]\T1/ptm/m/n/10 ; fur-ther, [][]\T1/pcr/m/n/10 cat[][][] \T1/ptm/m/n/10 which con-cate-nates and [395] Overfull \hbox (42.18039pt too wide) in paragraph at lines 27336--27336 []\T1/pcr/m/n/9 ## Notice that the recycling rules make every input as long as the longest input.[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27348--27348 []\T1/pcr/m/n/9 paste("1st", "2nd", "3rd", collapse = ", ") # probably not wha t you wanted[] [396] [397] [398] [399] [400] [401] [402] Underfull \hbox (badness 1817) in paragraph at lines 27782--27786 []\T1/ptm/m/n/10 This func-tion is al-most never used: \TS1/pcr/m/n/10 `\T1/pcr /m/n/10 name\TS1/pcr/m/n/10 ` \T1/ptm/m/n/10 or, more care-fully, [][]\T1/pcr/m /n/10 get[][][](name,envir = [403] Underfull \hbox (badness 1796) in paragraph at lines 27850--27853 []\T1/ptm/m/n/10 character string (or \T1/pcr/m/n/10 NULL\T1/ptm/m/n/10 ) in-di -cat-ing [][]\T1/pcr/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put, see [404] [405] [406] Underfull \hbox (badness 10000) in paragraph at lines 28050--28053 []\T1/ptm/m/n/10 Option \T1/pcr/m/n/10 width \T1/ptm/m/n/10 con-trols the print -ing of vec-tors, ma-tri-ces and ar-rays, and op-tion [407] [408] [409] [410] [411] [412] [413] [414] [415] [416] Overfull \hbox (25.98041pt too wide) in paragraph at lines 28727--28727 [] \T1/pcr/m/n/9 c1 = rep(c(1,0,0), 2), c2 = rep(c(0,1,0), 2), c3 = rep(c(0,0,1),2))[] [417] [418] [419] [420] Overfull \hbox (15.18042pt too wide) in paragraph at lines 28993--28993 []\T1/pcr/m/n/9 (nn <- "\u0126\u0119\u1114\u022d\u2001\u03e2\u0954\u0f3f\u13d3 \u147b\u203c")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29004--29004 []\T1/pcr/m/n/9 n2 <- "\U0126\U0119\U1114\U022d\U2001\U03e2\U0954\U0f3f\U13d3\ U147b\U203c"[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29010--29010 []\T1/pcr/m/n/9 ## https://cran.r-project.org/doc/manuals/r-release/R-lang.htm l#Literal-constants[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29011--29011 []\T1/pcr/m/n/9 ## and bug 16098 https://bugs.r-project.org/bugzilla3/show_bug .cgi?id=16098[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 29014--29014 []\T1/pcr/m/n/9 ## nul characters (for terminating strings in C) are not allow ed (parse errors)[] [421] Underfull \hbox (badness 7415) in paragraph at lines 29089--29093 []\T1/ptm/m/n/10 Do \T1/ptm/m/it/10 not \T1/ptm/m/n/10 use \T1/pcr/m/n/10 R.ver sion$os \T1/ptm/m/n/10 to test the plat-form the code is run-ning on: use [422] Overfull \hbox (42.18039pt too wide) in paragraph at lines 29110--29110 []\T1/pcr/m/n/9 mtext(R.version.string, side = 1, line = 4, adj = 1) # a usefu l bottom-right note[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 29156--29156 []\T1/pcr/m/n/10 set.seed(seed, kind = NULL, normal.kind = NULL, sample.kind = NULL)[] [423] [424] Underfull \hbox (badness 3713) in paragraph at lines 29279--29290 []\T1/pcr/m/n/10 normal.kind \T1/ptm/m/n/10 can be \T1/pcr/m/n/10 "Kinderman-Ra mage"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Buggy Kinderman-Ramage" \T1/ptm/m/n/10 (n ot [425] Underfull \hbox (badness 1248) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 uni-form pseudo-random num-ber gen-er-a-tor, \T1/ptm/m/it/10 ACM Trans-ac-tions on Mod-el-ing and Com-puter Underfull \hbox (badness 10000) in paragraph at lines 29423--29430 \T1/ptm/m/n/10 Now see [][]$\T1/pcr/m/n/10 http : / / www . math . sci . hirosh ima-[]u . ac . jp / ~m-[]mat / MT / VERSIONS / [426] [427] Underfull \hbox (badness 1533) in paragraph at lines 29541--29544 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [428] [429] Overfull \hbox (42.78088pt too wide) in paragraph at lines 29686--29686 [] \T1/pcr/m/n/10 ties.method = c("average", "first", "last", "random", "m ax", "min"))[] [430] Underfull \hbox (badness 1038) in paragraph at lines 29704--29715 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/pcr/m/n/10 NA\ T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [431] [432] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29848--29848 []\T1/pcr/m/n/9 rapply(X, function(x) x, how = "replace") -> X.; stopifnot(ide ntical(X, X.))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29850--29850 []\T1/pcr/m/n/9 rapply(X, deparse, control = "all") # passing extras. argument of deparse()[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 29851--29851 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "list")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29852--29852 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29853--29853 []\T1/pcr/m/n/9 rapply(X, nchar, classes = "character", h ow = "unlist")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 29860--29860 []\T1/pcr/m/n/9 rapply(E, nchar, classes = "character", deflt = NA_integer_, h ow = "unlist")[] [433] [434] [435] [436] [437] Underfull \hbox (badness 4048) in paragraph at lines 30207--30212 []\T1/ptm/m/n/10 Either an ob-ject whose mode will give the mode of the vec-tor to Underfull \hbox (badness 4582) in paragraph at lines 30207--30212 \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 30207--30212 \T1/ptm/m/n/10 one of \T1/pcr/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 " double"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "int"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , [438] [439] [440] [441] [442] [443] [444] [445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30748--30748 []\T1/pcr/m/n/9 ## or examine the object via a connection, which will be opene d as needed.[] [446] [447] [448] [449] [450] [451] [452] Underfull \hbox (badness 7558) in paragraph at lines 31250--31254 []\T1/pcr/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/pcr/m/n/10 gregexpr \T1/ptm/m/n /10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1968) in paragraph at lines 31260--31262 []\T1/ptm/m/n/10 This help page is based on the TRE doc-u-men-ta-tion and the P OSIX stan-dard, and the Underfull \hbox (badness 5417) in paragraph at lines 31265--31268 [][][]\T1/pcr/m/n/10 grep[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 apropos[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 browseEnv[][][]\T1/ptm/m/n/10 , [][]\T1/pc r/m/n/10 glob2rx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 help.search[][][]\T1/ ptm/m/n/10 , [][]\T1/pcr/m/n/10 list.files[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/ n/10 ls[][][] \T1/ptm/m/n/10 and [453] Underfull \hbox (badness 10000) in paragraph at lines 31269--31271 []\T1/ptm/m/n/10 The TRE doc-u-men-ta-tion at [][]$\T1/pcr/m/n/10 http : / / la urikari . net / tre / documentation / Underfull \hbox (badness 10000) in paragraph at lines 31272--31274 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/pcr/m/n/10 http : / / p ubs . opengroup . org / onlinepubs / [454] [455] [456] [457] [458] Underfull \hbox (badness 10000) in paragraph at lines 31677--31681 [][][]\T1/pcr/m/n/10 TRUE[][][] [][]FALSE[][][] [][]NULL[][][] [][]Inf[][][] [] []NaN[][][] [][]NA[][][] [][]NA_integer_[][][] [][]NA_real_[][][] [][]NA_comple x_[][][] [459] [460] [461] [462] [463] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32021--32021 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"))[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32024--32024 [] \T1/pcr/m/n/10 units = c("secs", "mins", "hours", "days", "months", "y ears"),[] [464] [465] [466] [467] [468] [469] [470] Overfull \hbox (54.78088pt too wide) in paragraph at lines 32408--32408 [] \T1/pcr/m/n/10 useHash = (!replace && is.null(prob) && size <= n/ 2 && n > 1e7))[] [471] [472] [473] [474] [475] [476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 32843--32843 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, skipNul = FALSE)[] [477] Underfull \hbox (badness 1158) in paragraph at lines 32947--32952 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i t ap-plies to all fields; oth-er-wise, if [478] Underfull \hbox (badness 10000) in paragraph at lines 32974--32980 []\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac- ters Underfull \hbox (badness 1762) in paragraph at lines 32974--32980 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal and hex-adec-i-mal rep-re-sen-ta-tions [479] [480] Overfull \hbox (15.18042pt too wide) in paragraph at lines 33132--33132 []\T1/pcr/m/n/9 cat("TITLE extra line", "2 3 5 7", "11 13 17", file = "ex.data ", sep = "\n") [481] [482] [483] Underfull \hbox (badness 8151) in paragraph at lines 33392--33395 []\T1/ptm/m/n/10 The fourth form gen-er-ates the in-te-ger se-quence \T1/pcr/m/ n/10 1,2,...,length(along.with)\T1/ptm/m/n/10 . [484] [485] [486] [487] Underfull \hbox (badness 1210) in paragraph at lines 33627--33629 []\T1/ptm/m/n/10 Note that \T1/pcr/m/n/10 sequence <-function(nvec) unlist(lapp ly(nvec,seq_len)) \T1/ptm/m/n/10 and it [488] [489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500] [501] Overfull \hbox (66.78088pt too wide) in paragraph at lines 34564--34564 [] \T1/pcr/m/n/10 method = c("auto", "shell", "quick", "radix"), index .return = FALSE)[] [502] [503] [504] Overfull \hbox (6.78088pt too wide) in paragraph at lines 34816--34816 [] \T1/pcr/m/n/10 print. = TRUE, echo = TRUE, max.deparse.length = Inf,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 34818--34818 [] \T1/pcr/m/n/10 deparseCtrl = c("keepInteger", "showAttributes" , "keepNA"),[] [505] Underfull \hbox (badness 4954) in paragraph at lines 34861--34867 [][][]\T1/pcr/m/n/10 character[][][] \T1/ptm/m/n/10 vec-tor, passed as \T1/pcr/ m/n/10 control \T1/ptm/m/n/10 to [][]\T1/pcr/m/n/10 deparse[][][]()\T1/ptm/m/n/ 10 , see also Underfull \hbox (badness 5050) in paragraph at lines 34861--34867 [][]\T1/pcr/m/n/10 .deparseOpts[][][]\T1/ptm/m/n/10 . In \T1/phv/m/n/10 R \T1/p tm/m/n/10 ver-sion <= 3.3.x, this was hard-coded to [506] Overfull \hbox (20.58041pt too wide) in paragraph at lines 34972--34972 []\T1/pcr/m/n/9 ## (all should look "as if on top level", e.g. non-assignments should print:)[] [507] [508] [509] [510] [511] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35300--35300 []\T1/pcr/m/n/9 ### Calculate \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 z-scores\TS1/pcr/m /n/9 ' \T1/pcr/m/n/9 by group (standardize to mean zero, variance one)[] [512] Overfull \hbox (4.38043pt too wide) in paragraph at lines 35315--35315 []\T1/pcr/m/n/9 ## Notice that assignment form is not used since a variable is being added[] [513] [514] [515] [516] [517] [518] Overfull \hbox (12.78088pt too wide) in paragraph at lines 35756--35756 []\T1/pcr/m/n/10 srcfile(filename, encoding = getOption("encoding"), Enc = "un known") Overfull \hbox (12.78088pt too wide) in paragraph at lines 35757--35757 []\T1/pcr/m/n/10 srcfilecopy(filename, lines, timestamp = Sys.time(), isFile = FALSE)[] [519] [520] [521] Overfull \hbox (63.78036pt too wide) in paragraph at lines 36021--36021 []\T1/pcr/m/n/9 startsWith(search(), "package:") # typically at least two FALS E, nowadays often three [522] Underfull \hbox (badness 6110) in paragraph at lines 36105--36115 []\T1/ptm/m/n/10 A func-tion \T1/pcr/m/n/10 .First \T1/ptm/m/n/10 (and [][]\T1/ pcr/m/n/10 .Last[][][]\T1/ptm/m/n/10 ) can be de-fined in ap-pro-pri-ate `\T1/p cr/m/n/10 .Rprofile\T1/ptm/m/n/10 ' or Underfull \hbox (badness 2635) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' files or have been saved in `\T1/pcr/m/n/10 .RData\T1/ptm/m/n/10 '. If you want a dif-fer-ent Underfull \hbox (badness 1237) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set of pack-ages than the de-fault ones when you start, in-sert a call to [][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 in the Underfull \hbox (badness 1231) in paragraph at lines 36105--36115 \T1/pcr/m/n/10 = character()) \T1/ptm/m/n/10 will at-tach no ex-tra pack-ages o n startup (only the \T1/ptm/b/n/10 base \T1/ptm/m/n/10 pack-age) (or Underfull \hbox (badness 1112) in paragraph at lines 36105--36115 \T1/ptm/m/n/10 set \T1/pcr/m/n/10 R_DEFAULT_PACKAGES=NULL \T1/ptm/m/n/10 as an en-vi-ron-ment vari-able be-fore run-ning \T1/phv/m/n/10 R\T1/ptm/m/n/10 ). Us- ing [523] Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/pcr/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1496) in paragraph at lines 36149--36155 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/pcr/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be Underfull \hbox (badness 1460) in paragraph at lines 36161--36168 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/pcr/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 36161--36168 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment [524] [525] [526] [527] Overfull \hbox (60.78088pt too wide) in paragraph at lines 36438--36438 [] \T1/pcr/m/n/10 assert <- function(exprs) eval.parent(substitute(stopifnot(e xprs = exprs))) [528] [529] [530] [531] [532] [533] [534] [535] Overfull \hbox (0.78088pt too wide) in paragraph at lines 37000--37000 [] \T1/pcr/m/n/10 add the string to the left of the match to the ou tput.[] [536] [537] [538] [539] Overfull \hbox (6.78088pt too wide) in paragraph at lines 37248--37248 [] \T1/pcr/m/n/10 exdent = 0, prefix = "", simplify = TRUE, initial = p refix)[] [540] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37292--37292 []\T1/pcr/m/n/9 x <- paste(readLines(file.path(R.home("doc"), "THANKS")), coll apse = "\n")[] [541] [542] [543] [544] [545] [546] Overfull \hbox (52.98038pt too wide) in paragraph at lines 37726--37726 []\T1/pcr/m/n/9 ## In fact, you can pass vectors into several arguments, and e verything gets added.[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 37729--37729 []\T1/pcr/m/n/9 ## If there are missing values, the sum is unknown, i.e., also missing, ....[] [547] Underfull \hbox (badness 10000) in paragraph at lines 37780--37787 []\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 37780--37787 \T1/pcr/m/n/10 summary.default\T1/ptm/m/n/10 ) or [][]\T1/pcr/m/n/10 format[][] []() \T1/ptm/m/n/10 (for \T1/pcr/m/n/10 summary.data.frame\T1/ptm/m/n/10 ). [548] Overfull \hbox (4.38043pt too wide) in paragraph at lines 37833--37833 []\T1/pcr/m/n/9 summary(attenu, digits = 4) #-> summary.data.frame(...), defau lt precision [549] [550] [551] [552] Overfull \hbox (31.3804pt too wide) in paragraph at lines 38134--38134 [] \T1/pcr/m/n/9 cat(ch,":", switch(EXPR = ch, a =, A = 1, b = 2:3, "Otherw ise: last"),"\n")[] [553] Underfull \vbox (badness 10000) has occurred while \output is active [554] [555] Overfull \hbox (4.38043pt too wide) in paragraph at lines 38299--38299 []\T1/pcr/m/n/9 ## whether HOST is set will be shell-dependent e.g. Solaris\TS 1/pcr/m/n/9 ' \T1/pcr/m/n/9 csh does not. [556] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38337--38337 []\T1/pcr/m/n/9 if(.Platform$OS.type == "unix") ## on Unix-alikes such Linux, macOS, FreeBSD:[] Underfull \hbox (badness 4792) in paragraph at lines 38386--38391 []\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 38386--38391 \T1/pcr/m/n/10 Sys.glob("*.RData") \T1/ptm/m/n/10 may or may not match `\T1/pcr /m/n/10 .RData\T1/ptm/m/n/10 ' but will not usu-ally match [557] Underfull \hbox (badness 2452) in paragraph at lines 38476--38479 \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 38476--38479 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 getlogin(2)\T1/ptm/m/n/10 , and the user nam es from \T1/pcr/m/n/10 getpwuid(getuid()) \T1/ptm/m/n/10 and [558] [559] [560] Underfull \hbox (badness 10000) in paragraph at lines 38664--38668 []\T1/pcr/m/n/10 sys.status() \T1/ptm/m/n/10 re-turns a list with com-po-nents \T1/pcr/m/n/10 sys.calls\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sys.parents \T1/ptm/m/n /10 and Underfull \hbox (badness 1584) in paragraph at lines 38679--38682 []\T1/pcr/m/n/10 sys.call \T1/ptm/m/n/10 re-turns a call, \T1/pcr/m/n/10 sys.fu nction \T1/ptm/m/n/10 a func-tion def-i-ni-tion, and \T1/pcr/m/n/10 sys.frame \ T1/ptm/m/n/10 and [561] [562] Overfull \hbox (25.98041pt too wide) in paragraph at lines 38811--38811 []\T1/pcr/m/n/9 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths ), keepNA=TRUE))[] [563] Overfull \hbox (20.58041pt too wide) in paragraph at lines 38881--38881 []\T1/pcr/m/n/9 print(Sys.setenv(R_TEST = "testit", "A+C" = 123)) # \TS1/pcr/ m/n/9 `\T1/pcr/m/n/9 A+C\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 could also be used [564] [565] [566] Underfull \hbox (badness 1082) in paragraph at lines 39025--39028 []\T1/ptm/m/n/10 logical. If \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee p their source in-clud-ing com-ments, see [567] [568] Underfull \hbox (badness 1038) in paragraph at lines 39216--39219 []\T1/ptm/m/n/10 a log-i-cal (not \T1/pcr/m/n/10 NA\T1/ptm/m/n/10 ) in-di-cat-i ng whether mes-sages writ-ten to `\T1/pcr/m/n/10 stdout\T1/ptm/m/n/10 ' or [569] [570] [571] [572] [573] [574] Underfull \hbox (badness 1442) in paragraph at lines 39579--39583 \T1/ptm/m/n/10 con-sider it to be piped or redi-rected: \T1/pcr/m/n/10 stdout = TRUE \T1/ptm/m/n/10 uses a pipe whereas \T1/pcr/m/n/10 stdout = [575] [576] [577] Underfull \hbox (badness 4096) in paragraph at lines 39825--39828 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 ftable[][][] \T1/ptm/m/n/10 for print-i ng (and more) of mul-ti-di-men-sional ta-bles. [][]\T1/pcr/m/n/10 margin.table[ ][][]\T1/ptm/m/n/10 , [578] [579] Underfull \hbox (badness 7888) in paragraph at lines 39939--39943 []\T1/ptm/m/n/10 On 64-bit plat-forms \T1/pcr/m/n/10 bin \T1/ptm/m/n/10 can hav e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/pcr/m/n/10 length(bin) > [580] [581] Overfull \hbox (63.78036pt too wide) in paragraph at lines 40093--40093 [] \T1/pcr/m/n/9 matrix(c(1L, 2L, NA, 3L), 2, dimnames = list(c("1" , "2"), c("A", "B")))),[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 40095--40095 [] \T1/pcr/m/n/9 array(list(\TS1/pcr/m/n/9 `\T1/pcr/m/n/9 2\TS1/pcr /m/n/9 ` \T1/pcr/m/n/9 = structure(c(2, 5.75, 9.5, 13.25, 17), .Names = nq),[] [582] Overfull \hbox (58.38037pt too wide) in paragraph at lines 40097--40097 [] \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 4\TS1/pcr/m/n/9 ` \T1/pcr/m/n /9 = NULL, \TS1/pcr/m/n/9 `\T1/pcr/m/n/9 5\TS1/pcr/m/n/9 ` \T1/pcr/m/n/9 = NULL ), dim=4, dimnames=list(as.character(2:5)))))[] Underfull \hbox (badness 10000) in paragraph at lines 40110--40112 []\T1/pcr/m/n/10 removeTaskCallback \T1/ptm/m/n/10 un-registers a func-tion tha t was reg-is-tered ear-lier via [583] Underfull \hbox (badness 10000) in paragraph at lines 40190--40193 [][][]\T1/pcr/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [ ][]$https : / / developer . [584] [585] Underfull \hbox (badness 3872) in paragraph at lines 40308--40311 []\T1/ptm/m/n/10 Duncan Tem-ple Lang (2001) \T1/ptm/m/it/10 Top-level Task Call -backs in R\T1/ptm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / developer . [586] Underfull \hbox (badness 5475) in paragraph at lines 40374--40378 [][][]\T1/pcr/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 r emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 taskCallbackManager[ ][][]\T1/ptm/m/n/10 \ [][]$\T1/pcr/m/n/10 https : / / [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 40792--40799 \T1/ptm/m/n/10 is also known as `\T1/pcr/m/n/10 GB\T1/ptm/m/n/10 ', `\T1/pcr/m/ n/10 GB-Eire\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 Europe/Belfast\T1/ptm/m/n/10 ', ` \T1/pcr/m/n/10 Europe/Guernsey\T1/ptm/m/n/10 ', Underfull \hbox (badness 4467) in paragraph at lines 40848--40857 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 OlsonNames \T1/ptm/m/n/10 re-turn s the time-zone names known to the cur-rently se- Underfull \hbox (badness 3954) in paragraph at lines 40848--40857 \T1/ptm/m/n/10 lected Ol-son/IANA database. The system-specific lo-ca-tion in t he file sys-tem varies, Underfull \hbox (badness 10000) in paragraph at lines 40858--40866 []\T1/ptm/m/n/10 Where \T1/phv/m/n/10 R \T1/ptm/m/n/10 was con-fig-ured with op -tion `\T1/pcr/m/n/10 --with-internal-tzcode\T1/ptm/m/n/10 ' (the de- Underfull \hbox (badness 10000) in paragraph at lines 40858--40866 \T1/ptm/m/n/10 fault on ma-cOS and Win-dows: rec-om-mended on So-laris), the da tabase at Underfull \hbox (badness 2503) in paragraph at lines 40858--40866 \T1/pcr/m/n/10 file.path(R.home("share"),"zoneinfo") \T1/ptm/m/n/10 is used by de-fault: file `\T1/pcr/m/n/10 VERSION\T1/ptm/m/n/10 ' [593] Underfull \hbox (badness 1337) in paragraph at lines 40924--40932 \T1/ptm/m/n/10 a file `\T1/pcr/m/n/10 localtime\T1/ptm/m/n/10 ', usu-ally un-de r `\T1/pcr/m/n/10 /etc\T1/ptm/m/n/10 ' (but pos-si-bly un-der `\T1/pcr/m/n/10 / usr/local/etc\T1/ptm/m/n/10 ' or Underfull \hbox (badness 10000) in paragraph at lines 40933--40936 []\T1/ptm/m/n/10 `Because the time zone iden-ti-fier is ex-tracted from the sym -link tar-get name of [594] Underfull \hbox (badness 3460) in paragraph at lines 40987--40990 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][ ] \T1/ptm/m/n/10 and [][]$\T1/pcr/m/n/10 https : / / data . iana . org / Underfull \hbox (badness 4429) in paragraph at lines 40991--40993 [][][]$\T1/pcr/m/n/10 https : / / data . iana . org / time-[]zones / theory . h tml$[][] \T1/ptm/m/n/10 for the `rules' of the Ol- Overfull \hbox (31.3804pt too wide) in paragraph at lines 41000--41000 []\T1/pcr/m/n/9 ## typically some acronyms/aliases such as "UTC", "NZ", "MET", "Eire", ..., but[] [595] [596] [597] Underfull \hbox (badness 10000) in paragraph at lines 41217--41219 []\T1/ptm/m/n/10 Using [][]\T1/pcr/m/n/10 setBreakpoint[][][] \T1/ptm/m/n/10 (f rom pack-age \T1/ptm/b/n/10 utils\T1/ptm/m/n/10 ) may be an al-ter-na-tive, cal l-ing [598] [599] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41339--41339 []\T1/pcr/m/n/9 trace(pt, tracer = quote(cat(sprintf("tracing pt(*, ncp = %.15 g)\n", ncp))),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 41341--41341 []\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 [600] [601] [602] [603] [604] Underfull \hbox (badness 6542) in paragraph at lines 41703--41705 []\T1/pcr/m/n/10 cospi(x)\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sinpi(x)\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 tanpi(x)\T1/ptm/m/n/10 , com-pute \T1/pcr/m/n/10 cos(pi*x )\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sin(pi*x)\T1/ptm/m/n/10 , and [605] [606] Overfull \hbox (30.78088pt too wide) in paragraph at lines 41822--41822 []\T1/pcr/m/n/10 trimws(x, which = c("both", "left", "right"), whitespace = "[ \t\r\n]") [607] Underfull \hbox (badness 1708) in paragraph at lines 41890--41898 []\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 41890--41898 \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 4859) in paragraph at lines 41920--41925 [][][]\T1/pcr/m/n/10 options[][][] \T1/ptm/m/n/10 for set-ting er-ror han-dlers and sup-press-ing the print-ing of er-ror mes-sages; [608] Underfull \hbox (badness 3895) in paragraph at lines 41982--41994 []\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 41982--41994 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/main/util.c\T1/ptm/m/n/10 '. Cur-rent val-ue s are the vec-tor types \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , [609] [610] [611] [612] [613] Overfull \hbox (9.78043pt too wide) in paragraph at lines 42305--42305 []\T1/pcr/m/n/9 ll <- list(as.name("sinc"), quote( a + b ), 1:10, letters, exp ression(1+x))[] [614] [615] [616] [617] [618] [619] Overfull \hbox (4.38043pt too wide) in paragraph at lines 42772--42772 []\T1/pcr/m/n/9 (xx <- intToUtf8(x, , TRUE)) # will only display in some local es and fonts[] [620] Overfull \hbox (20.58041pt too wide) in paragraph at lines 42781--42781 []\T1/pcr/m/n/9 system(paste("od -x", foo)) # 2-byte units, correct on little- endian platform[] [621] Underfull \hbox (badness 1803) in paragraph at lines 42906--42909 []\T1/ptm/m/n/10 The atomic modes are \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "integer"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "numeric" \T1/ptm/m/n/1 0 (syn-onym \T1/pcr/m/n/10 "double"\T1/ptm/m/n/10 ), [622] Underfull \hbox (badness 3471) in paragraph at lines 42910--42917 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 mode = "any"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 is.vector \T1/ptm/m/n/10 may re-turn \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 for the atomic modes, [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 and [623] [624] [625] Underfull \hbox (badness 3668) in paragraph at lines 43125--43127 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di- ately, even if [626] Overfull \hbox (36.78088pt too wide) in paragraph at lines 43229--43229 [] \T1/pcr/m/n/10 header = ngettext(n, "Warning message:\n", "Warning mes sages:\n"),[] [627] Overfull \hbox (4.38043pt too wide) in paragraph at lines 43304--43304 []\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 43312--43312 []\T1/pcr/m/n/9 x <- 1:36; for(n in 1:13) for(m in 1:12) A <- matrix(x, n,m) # There were 105 warnings ...[] [628] [629] Underfull \hbox (badness 6220) in paragraph at lines 43442--43447 []\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 43442--43447 \T1/ptm/m/n/10 to be used for con-struct-ing dim-names for \T1/pcr/m/n/10 array Ind() \T1/ptm/m/n/10 (and hence, [630] Underfull \hbox (badness 10000) in paragraph at lines 43463--43468 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/pcr/m /n/10 x \T1/ptm/m/n/10 is an [][]\T1/pcr/m/n/10 array[][][] \T1/ptm/m/n/10 (has a [][]\T1/pcr/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is Underfull \hbox (badness 4229) in paragraph at lines 43463--43468 \T1/pcr/m/n/10 arrayInd(which(x),dim(x),dimnames(x))\T1/ptm/m/n/10 , namely a m a-trix whose rows each [631] Underfull \hbox (badness 2818) in paragraph at lines 43553--43559 []\T1/ptm/m/n/10 For a [][]\T1/pcr/m/n/10 logical[][][] \T1/ptm/m/n/10 vec-tor \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with both \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 val-ues, \T1/pcr/m/n/10 which.min(x) \T1/ ptm/m/n/10 and [632] Overfull \hbox (15.18042pt too wide) in paragraph at lines 43588--43588 []\T1/pcr/m/n/9 ## Find the first occurrence, i.e. the first TRUE, if there is at least one:[] [633] Underfull \hbox (badness 1622) in paragraph at lines 43682--43684 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/pcr/m/n/10 http : / / developer . [634] [635] [636] [637] [638] Underfull \hbox (badness 2846) in paragraph at lines 44045--44049 []\T1/pcr/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [639] Overfull \hbox (4.38043pt too wide) in paragraph at lines 44085--44085 []\T1/pcr/m/n/9 .packages(all.available = TRUE) # return all available as char acter vector[] Underfull \hbox (badness 3209) in paragraph at lines 44106--44110 []\T1/pcr/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard ' reg-exps, in-clud-ing el-e-ments named [640]) (./compiler-pkg.tex Chapter 2. [641] Underfull \hbox (badness 2884) in paragraph at lines 105--119 []\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 105--119 \T1/ptm/m/n/10 rently four op-tions: \T1/pcr/m/n/10 optimize\T1/ptm/m/n/10 , \T 1/pcr/m/n/10 suppressAll\T1/ptm/m/n/10 , \T1/pcr/m/n/10 suppressUndefined\T1/pt m/m/n/10 , and [642] [643] [644]) (./datasets-pkg.tex Chapter 3. [645] [646] [647] [648] [649] 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,[] [650] 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 [651] [652] [653] [654] [655] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [656] [657] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [658] [659] 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. [660] [661] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [662] [663] [664] [665] [666] 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)")[] [667] [668] 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 [669] [670] [671] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [672] 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)[] [673] [674] 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]]))))[] [675] [676] [677] [678] Overfull \hbox (48.81013pt 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","nfGroup edData","groupedData","data.frame") [679] [680] [681] Overfull \vbox (4.29591pt too high) has occurred while \output is active [682] [683] [684] [685] [686] Overfull \hbox (48.81013pt too wide) in paragraph at lines 2717--2720 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [687] Overfull \vbox (13.87083pt too high) has occurred while \output is active [688] Underfull \vbox (badness 2376) has occurred while \output is active [689] [690] Overfull \vbox (12.25539pt too high) has occurred while \output is active [691] [692] Overfull \vbox (17.12102pt too high) has occurred while \output is active [693] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3146--3146 []\T1/pcr/m/n/9 pairs(quakes, main = "Fiji Earthquakes, N = 1000", cex.main = 1.2, pch = ".")[] [694] [695] [696] [697] [698] [699] [700] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3603--3603 [] \T1/pcr/m/n/9 ## The yearly series *is* close to the averages of t he monthly one:[] [701] [702] Overfull \hbox (48.81013pt too wide) in paragraph at lines 3751--3754 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("nfnGroupedData","nfGroup edData","groupedData","data.frame") [703] Overfull \vbox (10.49593pt too high) has occurred while \output is active [704] Overfull \vbox (15.49593pt too high) has occurred while \output is active [705] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3960--3960 [] \T1/pcr/m/n/9 xlab = "ToothGrowth data: length vs dose, given type of supplement")[] Underfull \hbox (badness 10000) in paragraph at lines 3989--3992 []\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 3998--4000 []\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 3998--4000 \T1/pcr/m/n/10 20110523225828 / http : / / www . ltrr . arizona . edu / ~hallma n / sitephotos / [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719]) (./grDevices-pkg.tex [720] Chapter 4. [721] [722] [723] [724] Underfull \hbox (badness 1365) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/pcr/m/n/10 c(mi,ma,n.)\T1/ptm /m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 4752) in paragraph at lines 298--303 []\T1/ptm/m/n/10 Apart from that, [][]\T1/pcr/m/n/10 axisTicks[][][]() \T1/ptm/ m/n/10 just calls the C func-tion \T1/pcr/m/n/10 CreateAtVector() \T1/ptm/m/n/1 0 in [725] [726] Underfull \hbox (badness 10000) in paragraph at lines 379--387 []\T1/ptm/m/n/10 The two `hinges' are ver-sions of the first and third quar-til e, i.e., close to Underfull \hbox (badness 1748) in paragraph at lines 379--387 \T1/ptm/m/n/10 and dif-fer for even $\OML/cmm/m/it/10 n$\T1/ptm/m/n/10 . Wherea s the quar-tiles only equal ob-ser-va-tions for \T1/pcr/m/n/10 n %% 4 == 1 [727] [728] Overfull \hbox (6.78088pt too wide) in paragraph at lines 515--515 []\T1/pcr/m/n/10 cairo_pdf(filename = if(onefile) "Rplots.pdf" else "Rplot%03d .pdf",[] [729] [730] [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5175) in paragraph at lines 1120--1122 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [738] [739] Underfull \hbox (badness 10000) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 For the white points [][]$\T1/pcr/m/n/10 http : / / www . efg2 . com / Lab / Graphics / Colors / Overfull \hbox (25.98041pt too wide) in paragraph at lines 1280--1280 []\T1/pcr/m/n/9 zapsmall(lab <- convertColor(cols, from = "sRGB", to = "Lab", scale.in = 255))[] [740] Underfull \hbox (badness 1173) in paragraph at lines 1322--1325 []\T1/pcr/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col- ors that will be used in plot-ting, call-ing [741] [742] [743] [744] [745] [746] [747] [748] Underfull \hbox (badness 1565) in paragraph at lines 1810--1815 []\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 1810--1815 \T1/ptm/m/n/10 sys-tem: see [][]\T1/pcr/m/n/10 postscript[][][] \T1/ptm/m/n/10 for how to set this up. Win-dows users may pre-fer to use [749] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1893--1893 []\T1/pcr/m/n/10 dev2bitmap(file, type = "png16m", height = 7, width = 7, res = 72,[] Underfull \hbox (badness 1184) in paragraph at lines 1934--1944 []\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 1934--1944 \T1/pcr/m/n/10 "tiffg4"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffgray"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tifflzw"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiffpack"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "tiff12nc"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "tiff24nc"\T1/p tm/m/n/10 , [750] [751] Underfull \hbox (badness 10000) in paragraph at lines 2046--2048 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [752] [753] Underfull \hbox (badness 6758) in paragraph at lines 2224--2227 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [754] [755] Underfull \hbox (badness 2326) in paragraph at lines 2341--2351 \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 2341--2351 \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 2341--2351 \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 2341--2351 \T1/pcr/m/n/10 setGraphicsEventHandlers \T1/ptm/m/n/10 or \T1/pcr/m/n/10 setGra phicsEventEnv \T1/ptm/m/n/10 on one or more graph-ics [756] [757] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2444--2444 []\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 [758] Overfull \hbox (72.78088pt too wide) in paragraph at lines 2560--2560 []\T1/pcr/m/n/10 gray.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE) Overfull \hbox (72.78088pt too wide) in paragraph at lines 2561--2561 []\T1/pcr/m/n/10 grey.colors(n, start = 0.3, end = 0.9, gamma = 2.2, alpha = N ULL, rev = FALSE)[] [759] [760] [761] [762] [763] Underfull \hbox (badness 10000) in paragraph at lines 2828--2829 Underfull \vbox (badness 10000) has occurred while \output is active [764] [765] [766] [767] [768] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3161--3161 []\T1/pcr/m/n/10 colorConverter(toXYZ, fromXYZ, name, white = NULL, vectorized = FALSE)[] [769] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3245--3245 []\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 3246--3246 []\T1/pcr/m/n/9 (hex <- convertColor(luv, from = "Luv", to = hexcolor, scale. out = NULL))[] [770] [771] Underfull \hbox (badness 10000) in paragraph at lines 3384--3389 []\T1/pcr/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas ed on the inter-quartile range Underfull \hbox (badness 1264) in paragraph at lines 3384--3389 \T1/ptm/m/n/10 ([][]\T1/pcr/m/n/10 IQR[][][](signif(x,5))\T1/ptm/m/n/10 ) un-le ss that's zero where it uses in-creas-ingly more ex-treme sym- [772] [773] [774] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3545--3545 []\T1/pcr/m/n/10 hcl.colors(n, palette = "viridis", alpha = NULL, rev = FALSE, fixup = TRUE) Underfull \hbox (badness 8170) in paragraph at lines 3571--3574 []\T1/ptm/m/n/10 the type of palettes to list: \T1/pcr/m/n/10 "qualitative"\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 "sequential"\T1/ptm/m/n/10 , [775] Underfull \hbox (badness 10000) in paragraph at lines 3655--3659 \T1/pcr/m/n/10 wikipedia . org / w / index . php ? title = HCL _ color _ space & oldid = 883465135$[][]\T1/ptm/m/n/10 . [776] [777] Underfull \hbox (badness 5260) in paragraph at lines 3785--3788 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a C in-te-ger for-mat such as [778] [779] [780] [781] [782] Underfull \hbox (badness 5939) in paragraph at lines 4113--4118 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 onefile\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fa mily\T1/ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fonts\ T1/ptm/m/n/10 , [783] [784] [785] [786] [787] [788] Underfull \hbox (badness 10000) in paragraph at lines 4514--4519 [][][]$\T1/pcr/m/n/10 https : / / www . adobe . com / content / dam / acom / en / devnet / actionscript / Underfull \hbox (badness 3612) in paragraph at lines 4514--4519 \T1/pcr/m/n/10 pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in dec-i-m al, oc-tal and hex at [][]$\T1/pcr/m/n/10 http : / / www . stat . [789] [790] Overfull \hbox (60.78088pt too wide) in paragraph at lines 4629--4629 [] \T1/pcr/m/n/10 compression = c("none", "rle", "lzw", "jpeg", "zip", "lz w+p", "zip+p"),[] [791] [792] Underfull \hbox (badness 1348) in paragraph at lines 4828--4831 []\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, [][]$\T1/pcr/m/n/10 https : / / ww w . iso . org / standard / 34342 . html$[][]\T1/ptm/m/n/10 . See also [793] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4852--4852 []\T1/pcr/m/n/9 ## Not run: dev.print(png, file = "myplot.png", width = 1024, height = 768)[] Underfull \hbox (badness 7522) in paragraph at lines 4892--4898 []\T1/ptm/m/n/10 For use with \T1/pcr/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv e a \T1/pcr/m/n/10 printf \T1/ptm/m/n/10 for-mat such as [794] Underfull \hbox (badness 1112) in paragraph at lines 4923--4927 []\T1/ptm/m/n/10 as `\T1/pcr/m/n/10 "CP1250.enc"\T1/ptm/m/n/10 ' (Cen-tral Eu-r o-pean), \T1/pcr/m/n/10 "CP1251.enc" [795] Underfull \hbox (badness 1755) in paragraph at lines 5065--5067 []\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East Asian lan-guages -- see [796] [797] [798] Underfull \hbox (badness 7344) in paragraph at lines 5245--5247 []\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 5256--5260 [][][]\T1/pcr/m/n/10 postscriptFonts[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 D evices[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 check.options[][][] \T1/ptm /m/n/10 which is called from both [799] [800] Underfull \hbox (badness 1552) in paragraph at lines 5380--5389 \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 5380--5389 \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 5380--5389 \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 5390--5392 []\T1/ptm/m/n/10 There are also map-pings for \T1/pcr/m/n/10 "ComputerModern"\T 1/ptm/m/n/10 , \T1/pcr/m/n/10 "ComputerModernItalic" \T1/ptm/m/n/10 and Underfull \hbox (badness 4686) in paragraph at lines 5422--5428 \T1/pcr/m/n/10 "Japan1"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Japan1HeiMin"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Japan1GothicBBB"\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 "Jap an1Ryumin" \T1/ptm/m/n/10 for [801] Underfull \hbox (badness 10000) in paragraph at lines 5448--5455 []\T1/pcr/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/pcr /m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu / [802] [803] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5549--5549 []\T1/pcr/m/n/9 ## time ranges in diverse scales:% also in ../../../../tests/r eg-tests-1c.R[] [804] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5661--5661 []\T1/pcr/m/n/10 quartz.save(file, type = "png", device = dev.cur(), dpi = 100 , ...)[] [805] [806] Underfull \hbox (badness 10000) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Calling \T1/pcr/m/n/10 quartz() \T1/ptm/m/n/10 sets [][]\T1/pc r/m/n/10 .Device[][][] \T1/ptm/m/n/10 to \T1/pcr/m/n/10 "quartz" \T1/ptm/m/n/10 for on-screen de-vices and to [807] [808] [809] [810] [811] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6112--6112 []\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 6125--6128 []\T1/pcr/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red /green/blue) into HSV space [812] [813] [814] [815] [816] [817] Overfull \hbox (0.78088pt too wide) in paragraph at lines 6458--6458 []\T1/pcr/m/n/10 windows(width, height, pointsize, record, rescale, xpinch, yp inch, Overfull \hbox (0.78088pt too wide) in paragraph at lines 6465--6465 []\T1/pcr/m/n/10 win.metafile(filename = "", width = 7, height = 7, pointsize = 12,[] [818] [819] [820] [821] Underfull \hbox (badness 10000) in paragraph at lines 6728--6733 []\T1/ptm/m/n/10 arguments \T1/pcr/m/n/10 width\T1/ptm/m/n/10 , \T1/pcr/m/n/10 height\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pointsize\T1/ptm/m/n/10 , \T1/pcr/m/n/10 record\T1/ptm/m/n/10 , \T1/pcr/m/n/10 rescale\T1/ptm/m/n/10 , Underfull \hbox (badness 1803) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 xpinch\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ypinch\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 bg\T1/ptm/m/n/10 , \T1/pcr/m/n/10 canvas\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 gamma\T1/ptm/m/n/10 , \T1/pcr/m/n/10 xpos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 y pos\T1/ptm/m/n/10 , \T1/pcr/m/n/10 buffered\T1/ptm/m/n/10 , Underfull \hbox (badness 2941) in paragraph at lines 6728--6733 \T1/pcr/m/n/10 restoreConsole\T1/ptm/m/n/10 , \T1/pcr/m/n/10 clickToConfirm\T1/ ptm/m/n/10 , \T1/pcr/m/n/10 title\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fillOddEven \T 1/ptm/m/n/10 and [822] Overfull \hbox (36.7804pt too wide) in paragraph at lines 6833--6833 []\T1/pcr/m/n/9 windows() # make sure we have the right device type (availabl e on Windows only)[] [823] Underfull \hbox (badness 5954) in paragraph at lines 6872--6875 []\T1/ptm/m/n/10 The \T1/phv/m/n/10 R \T1/ptm/m/n/10 func-tion is a wrap-per fo r two de-vices, one based on Xlib ([][]$\T1/pcr/m/n/10 https : [824] Underfull \hbox (badness 1189) in paragraph at lines 6947--6949 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [825] Underfull \hbox (badness 10000) in paragraph at lines 7045--7047 []\T1/pcr/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK lan-guages and [826] Underfull \hbox (badness 10000) in paragraph at lines 7084--7091 []\T1/ptm/m/n/10 Problems with in-cor-rect ren-der-ing of sym-bols (e.g., of \T 1/pcr/m/n/10 quote(pi) \T1/ptm/m/n/10 and Underfull \hbox (badness 2469) in paragraph at lines 7084--7091 \T1/pcr/m/n/10 expression(10^degree)\T1/ptm/m/n/10 ) have been seen on Linux sy s-tems which have the Wine [827] Underfull \hbox (badness 5607) in paragraph at lines 7168--7172 []\T1/pcr/m/n/10 type = "Xlib" \T1/ptm/m/n/10 sup-ports `True-Color', `Pseu-do- Color', `GrayScale', \T1/pcr/m/n/10 StaticGray \T1/ptm/m/n/10 and Overfull \hbox (20.58041pt too wide) in paragraph at lines 7214--7214 [] \T1/pcr/m/n/9 function(...) grDevices::X11.options(width = 8, height = 6, xpos = 0,[] [828] [829] Underfull \hbox (badness 5637) in paragraph at lines 7345--7351 \T1/pcr/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Helvetica" \T1/ptm/m/n /10 (the de-fault), \T1/pcr/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/10 , [830] Underfull \hbox (badness 1721) in paragraph at lines 7378--7381 []\T1/ptm/m/n/10 Windows users can make use of Win-FIG ([][]$\T1/pcr/m/n/10 htt p : / / www . schmidt-[]web-[]berlin . de / [831] [832] Underfull \hbox (badness 1231) in paragraph at lines 7546--7548 []\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/pcr/m/n/10 n umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of [833] [834] [835]) (./graphics-pkg.tex [836] Chapter 5. Underfull \hbox (badness 4647) in paragraph at lines 16--18 []\T1/ptm/m/n/10 For a com-plete list of func-tions with in-di-vid-ual help pag es, use \T1/pcr/m/n/10 library(help = [837] [838] [839] Underfull \hbox (badness 3792) in paragraph at lines 177--180 []\T1/ptm/m/n/10 For each \T1/pcr/m/n/10 i\T1/ptm/m/n/10 , an ar-row is drawn b e-tween the point \T1/pcr/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the point [840] 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- [841] [842] [843] Overfull \hbox (6.05087pt too wide) in paragraph at lines 450--450 [] \T1/pcr/m/n/10 gap.axis <- if(perpendicular(side, las)) 0.25 else 1[] Underfull \hbox (badness 4048) in paragraph at lines 482--488 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 at = NULL\T1/ptm/m/n/10 , pretty tick mark lo-ca-tions are com-puted in-ter-nally (the same way [844] [845] Overfull \hbox (47.58038pt too wide) in paragraph at lines 580--580 []\T1/pcr/m/n/9 ## now shrink the window (in x- and y-direction) and observe t he axis labels drawn[] [846] Underfull \hbox (badness 10000) in paragraph at lines 694--698 []\T1/ptm/m/n/10 numeric vec-tor of length three, de-fault-ing to [][]\T1/pcr/m /n/10 par[][][]("xaxp") \T1/ptm/m/n/10 or Underfull \hbox (badness 3250) in paragraph at lines 694--698 [][]\T1/pcr/m/n/10 par[][][]("yaxp") \T1/ptm/m/n/10 de-pend-ing on the \T1/pcr/ m/n/10 side \T1/ptm/m/n/10 ar-gu-ment (\T1/pcr/m/n/10 par("xaxp") \T1/ptm/m/n/1 0 if [847] [848] Overfull \hbox (4.38043pt too wide) in paragraph at lines 781--781 [] \T1/pcr/m/n/9 axp = c(get_axp(usr.i), n = 3), log = TRUE, n intLog = 5))[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 818--818 [] \T1/pcr/m/n/10 add = FALSE, ann = !add && par("ann"), args.legend = NULL, ...)[] [849] [850] [851] Underfull \hbox (badness 10000) in paragraph at lines 960--964 [][][]\T1/pcr/m/n/10 plot[][][](...,type = "h")\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 dotchart[][][]\T1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 hist[][][] \T1/ptm/m/n/10 for bars of a \T1/ptm/m/it/10 con-tin-u-ous \T1/ptm/m/n/10 vari-able. Overfull \hbox (106.98032pt too wide) in paragraph at lines 977--977 [] \T1/pcr/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend = TRUE)[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 979--979 []\T1/pcr/m/n/9 (xt <- xtabs(Freq ~ Survived + Class + Sex, d.Titanic, subset = Age=="Adult"))[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 981--981 []\T1/pcr/m/n/9 mosaicplot(xt[,,"Male"], main = "mosaicplot(Freq ~ Class + Sur vived, *)", color=TRUE)[] [852] [853] [854] [855] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1265--1265 []\T1/pcr/m/n/9 # *add* notches (somewhat funny here <--> warning "notches .. outside hinges"):[] [856] [857] [858] Underfull \hbox (badness 1024) in paragraph at lines 1427--1435 \T1/pcr/m/n/10 col.main\T1/ptm/m/n/10 , \T1/pcr/m/n/10 sub\T1/ptm/m/n/10 , \T1/ pcr/m/n/10 cex.sub\T1/ptm/m/n/10 , \T1/pcr/m/n/10 col.sub\T1/ptm/m/n/10 , \T1/p cr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr/m/n/10 ylab\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 cex.lab\T1/ptm/m/n/10 , and Underfull \hbox (badness 3375) in paragraph at lines 1461--1463 []\T1/ptm/m/n/10 whisker line type (de-fault: \T1/pcr/m/n/10 "dashed"\T1/ptm/m/ n/10 ), [859] [860] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1531--1531 []\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 1532--1532 []\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 1538--1538 []\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 1539--1539 [] \T1/pcr/m/n/9 medlwd = 3, medcol = "white", whisklty = 3, outl ty = 1, outpch = NA)[] [861] [862] [863] [864] Underfull \hbox (badness 10000) in paragraph at lines 1839--1845 [][][]\T1/pcr/m/n/10 contourLines[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fill ed.contour[][][] \T1/ptm/m/n/10 for color-filled con-tours, [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 (and [865] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1876--1876 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1885--1885 []\T1/pcr/m/n/9 plot(x = 0, y = 0, type = "n", xlim = rx, ylim = ry, xlab = "" , ylab = "")[] [866] [867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1970--1970 []\T1/pcr/m/n/10 coplot(formula, data, given.values, panel = points, rows, col umns, [868] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2099--2099 []\T1/pcr/m/n/9 coplot(lat ~ long | depth, data = quakes, given.v = given.dept h, rows = 1)[] [869] Overfull \hbox (9.78043pt too wide) in paragraph at lines 2104--2104 []\T1/pcr/m/n/9 coplot(ll.dm, data = quakes, number = c(4, 7), show.given = c( TRUE, FALSE))[] [870] [871] [872] [873] Overfull \hbox (78.78088pt too wide) in paragraph at lines 2378--2378 [] \T1/pcr/m/n/10 color.palette = function(n) hcl.colors(n, "YlO rRd", rev = TRUE),[] Underfull \hbox (badness 1009) in paragraph at lines 2390--2397 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [874] Underfull \hbox (badness 7273) in paragraph at lines 2472--2476 [][][]\T1/pcr/m/n/10 contour[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 image[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hcl.colors[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 gray.colors[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 palette[][][]\T 1/ptm/m/n/10 ; [][]\T1/pcr/m/n/10 contourplot[][][] \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 2485--2485 []\T1/pcr/m/n/9 filled.contour(x, y, volcano, color = function(n) hcl.colors(n , "terrain"),[] [875] [876] [877] [878] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2719--2719 []\T1/pcr/m/n/9 ## maybe change the desired number of tick marks: par(lab = c (mx, my, 7))[] [879] [880] [881] Underfull \hbox (badness 1226) in paragraph at lines 2880--2884 \T1/pcr/m/n/10 1)\T1/ptm/m/n/10 , they are the rel-a-tive fre-quen-cies \T1/pcr /m/n/10 counts/n \T1/ptm/m/n/10 and in gen-eral sat-isfy Overfull \hbox (15.18042pt too wide) in paragraph at lines 2933--2933 []\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 2937--2937 []\T1/pcr/m/n/9 length(hh$breaks) ## typically 1 million -- though 1e6 was "a suggestion only"[] [882] Underfull \hbox (badness 10000) in paragraph at lines 2989--2992 [][][]\T1/ptm/m/n/10 graphical pa-ram-e-ters[][][], or ar-gu-ments to [][]\T1/p cr/m/n/10 hist.default[][][] \T1/ptm/m/n/10 such as [883] [884] [885] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3194--3194 []\T1/pcr/m/n/9 identifyPch <- function(x, y = NULL, n = length(x), plot = FAL SE, pch = 19, ...)[] Overfull \hbox (79.98035pt too wide) in paragraph at lines 3199--3199 [] \T1/pcr/m/n/9 ans <- identify(x[!sel], y[!sel], labels = which(!sel) , n = 1, plot = plot, ...)[] [886] [887] Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 useRaster \T1/ptm/m/n/10 is not spec-i-fied, raster im-ages are used when the Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 [][]\T1/pcr/m/n/10 getOption[][][]("preferRaster") \T1/ptm/m/n/10 is true, the grid is reg-u-lar and ei-ther Underfull \hbox (badness 10000) in paragraph at lines 3338--3343 [][]\T1/pcr/m/n/10 dev.capabilities[][][]("rasterImage")$rasterImage \T1/ptm/m/ n/10 is \T1/pcr/m/n/10 "yes" \T1/ptm/m/n/10 or it is [888] [889] [890] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3524--3524 []\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 3543--3543 [] \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 3547--3547 [] \T1/pcr/m/n/10 text.font = NULL, merge = do.lines && has.pch, trace = FALSE,[] [891] [892] [893] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3724--3724 [] \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 3725--3725 [] \T1/pcr/m/n/9 legend(3, y.leg[i], leg.txt, pch = "sSvV", col = c(1, 3), ce x = cexv[i])[] [894] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3764--3764 [] \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 [895] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3816--3816 []\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 3824--3824 []\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 3826--3826 []\T1/pcr/m/n/9 legend("topright", "(x,y)", pch=1, title= "topright, inset = .02",inset = .02)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3834--3834 [] \T1/pcr/m/n/9 plot(1, type = "n", axes = FALSE, ann = FALSE); title(paste ("text.font =",i))[] [896] Underfull \hbox (badness 10000) in paragraph at lines 3897--3901 [][][]\T1/pcr/m/n/10 lines.formula[][][] \T1/ptm/m/n/10 for the for-mula method ; [][]\T1/pcr/m/n/10 points[][][]\T1/ptm/m/n/10 , par-tic-u-larly for \T1/pcr/m /n/10 type %in% [897] Overfull \hbox (6.78088pt too wide) in paragraph at lines 4008--4008 [] \T1/pcr/m/n/10 log = "", ..., add = FALSE, verbose = getOption("verb ose"))[] [898] [899] [900] [901] Underfull \hbox (badness 3930) in paragraph at lines 4215--4217 []\T1/ptm/m/n/10 The mag-ni-fi-ca-tion to be used for axis an-no-ta-tion, as a mul-ti-ple of [902] [903] [904] [905] Underfull \hbox (badness 1286) in paragraph at lines 4526--4529 \T1/ptm/m/n/10 which draws the ti-tle. You may want to spec-ify \T1/pcr/m/n/10 oma \T1/ptm/m/n/10 when chang-ing [906] Underfull \hbox (badness 3229) in paragraph at lines 4534--4539 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4631--4631 []\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 4636--4636 [] \T1/pcr/m/n/9 main = "Lengths and Widths in [log]", line.main=1.5, oma =c(2,2,3,2))[] [908] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4680--4680 []\T1/pcr/m/n/9 pairs(swiss, panel = panel.smooth, lwd = 2, cex = 1.5, col = " blue") # hmm...[] [909] Underfull \hbox (badness 1264) in paragraph at lines 4754--4767 \T1/ptm/m/n/10 func-tions such as [][]\T1/pcr/m/n/10 plot.default[][][]\T1/ptm/ m/n/10 , [][]\T1/pcr/m/n/10 plot.window[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 points[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lines[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 abline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 axis[][][]\T1 /ptm/m/n/10 , [910] [911] Underfull \hbox (badness 10000) in paragraph at lines 4891--4897 []\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/pcr/m/n /10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units. [912] Underfull \hbox (badness 10000) in paragraph at lines 5022--5025 [913 ] Underfull \hbox (badness 10000) in paragraph at lines 5083--5085 Underfull \vbox (badness 10000) has occurred while \output is active [914] [915 ] [916] Underfull \hbox (badness 10000) in paragraph at lines 5273--5275 []\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/pcr/m/n/10 lty = 2 :6\T1/ptm/m/n/10 ) cor-re-spond to [917] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5329--5329 []\T1/pcr/m/n/9 c(prof.pilots = 16, lawyers = 11, farmers = 10, salesmen = 9, physicians = 9,[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5330--5330 [] \T1/pcr/m/n/9 mechanics = 6, policemen = 6, managers = 6, engineers = 5, t eachers = 4,[] [918] [919] [920] [921] [922] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5695--5695 []\T1/pcr/m/n/9 pie(c(Sky = 78, "Sunny side of pyramid" = 17, "Shady side of p yramid" = 5),[] [923] Overfull \hbox (47.58038pt too wide) in paragraph at lines 5696--5696 [] \T1/pcr/m/n/9 init.angle = 315, col = c("deepskyblue", "yellow", "yellow 3"), border = FALSE)[] Underfull \hbox (badness 1360) in paragraph at lines 5747--5751 []\T1/ptm/m/n/10 All other \T1/pcr/m/n/10 type\T1/ptm/m/n/10 s give a warn-ing or an er-ror; us-ing, e.g., \T1/pcr/m/n/10 type = [924] [925] [926] [927] [928] [929] [930] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6181--6181 []\T1/pcr/m/n/9 plot(weight ~ group, data = PlantGrowth) # numeric v ector ~ factor[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6187--6187 []\T1/pcr/m/n/9 plot(PlantGrowth$group, axes = FALSE, main = "no axes") # ext remely silly[] [931] [932] [933] [934] [935] [936] Underfull \hbox (badness 10000) in paragraph at lines 6614--6616 []\T1/ptm/m/n/10 background (fill) color for the open plot sym-bols 21:25: see [937] [938] Underfull \hbox (badness 1028) in paragraph at lines 6708--6710 []\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 6751--6752 [][] [939 ] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6845--6845 []\T1/pcr/m/n/9 plot(x, sin(x), type = "o", pch = 21, bg = par("bg"), col = "b lue", cex = .6,[] [940] Overfull \hbox (31.3804pt too wide) in paragraph at lines 6876--6876 [] \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 [941] [942] Underfull \hbox (badness 10000) in paragraph at lines 6998--7000 []\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 7025--7025 [] \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 7031--7031 []\T1/pcr/m/n/9 yy <- c(c(0, cumsum(stats::rnorm(n))), rev(c(0, cumsum(stats:: rnorm(n)))))[] [943] Underfull \hbox (badness 2600) in paragraph at lines 7091--7093 []\T1/ptm/m/n/10 character value spec-i-fy-ing the path fill mode: ei-ther \T1/ pcr/m/n/10 "winding" \T1/ptm/m/n/10 or [944] [945] [946] [947] Overfull \hbox (9.78043pt too wide) in paragraph at lines 7323--7323 []\T1/pcr/m/n/9 rect(100+i, 300+i, 150+i, 380+i, col = rainbow(11, start = 0.7 , end = 0.1))[] [948] [949] [950] [951] [952] [953] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7710--7710 []\T1/pcr/m/n/9 Lab.palette <- colorRampPalette(c("blue", "orange", "red"), sp ace = "Lab")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7714--7714 []\T1/pcr/m/n/9 ## label the 20 very lowest-density points,the "outliers" (wit h obs.number):[] [954] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7726--7726 []\T1/pcr/m/n/9 pairs(y, panel = function(...) smoothScatter(..., nrpoints = 0 , add = TRUE),[] [955] [956] [957] [958] [959] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8075--8075 []\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 8078--8078 []\T1/pcr/m/n/9 stars(USJudgeRatings, locations = c(0, 0), scale = FALSE, radi us = FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8082--8082 [] \T1/pcr/m/n/9 draw.segments = TRUE, col.segments = 0, col.stars = 1:10 , key.loc = 0:1,[] [960] [961] [962] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8253--8253 []\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 8254--8254 []\T1/pcr/m/n/10 strheight(s, units = "user", cex = NULL, font = NULL, vfont = NULL, ...)[] [963] [964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8358--8358 []\T1/pcr/m/n/10 sunflowerplot(formula, data = NULL, xlab = NULL, ylab = NULL, ...,[] Underfull \hbox (badness 2080) in paragraph at lines 8369--8374 []\T1/ptm/m/n/10 integer vec-tor of length \T1/pcr/m/n/10 n\T1/ptm/m/n/10 . \T1 /pcr/m/n/10 number[i] \T1/ptm/m/n/10 = num-ber of repli-cates for [965] Underfull \hbox (badness 1112) in paragraph at lines 8417--8421 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 number[i] == 1\T1/ptm/m/n/10 , a (slightly en-larged) usual plot-ting sym-bol (\T1/pcr/m/n/10 pch\T1/ptm/m/n/10 ) is drawn . For [966] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8477--8477 []\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 8492--8492 []\T1/pcr/m/n/9 sunflowerplot(rnorm(100), rnorm(100), number = rpois(n = 100, lambda = 2),[] [967] [968] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8623--8623 []\T1/pcr/m/n/9 text(x, y, apply(format(round(z3, digits = 2)), 1, paste, coll apse = ","),[] [969] [970] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8808--8808 [] \T1/pcr/m/n/9 "Le français, c\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 est façile: Règles, Liberté, Egalité, Fraternité...")[] [971] Underfull \hbox (badness 10000) in paragraph at lines 8836--8838 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color Underfull \hbox (badness 10000) in paragraph at lines 8838--8840 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color Underfull \hbox (badness 1584) in paragraph at lines 8870--8876 []\T1/ptm/m/n/10 The po-si-tions of \T1/pcr/m/n/10 xlab\T1/ptm/m/n/10 , \T1/pcr /m/n/10 ylab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sub \T1/ptm/m/n/10 are \T1/pcr/m /n/10 line \T1/ptm/m/n/10 (de-fault for \T1/pcr/m/n/10 xlab \T1/ptm/m/n/10 and \T1/pcr/m/n/10 ylab \T1/ptm/m/n/10 be-ing [972]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.unit s}) has been already used, duplicate ignored \relax l.8918 \HeaderA{units}{Graphical Units}{units} [973] Underfull \hbox (badness 1205) in paragraph at lines 8983--8985 []\T1/ptm/m/n/10 vectors con-tain-ing the co-or-di-nates of the ver-tices of th e poly-gon. See [974] [975] Overfull \hbox (25.98041pt too wide) in paragraph at lines 9102--9102 []\T1/pcr/m/n/9 arrows(res$x[nr-3], res$y[nr-3], res$x[nr], res$y[nr], code = 2, length = 0.1)[] [976]) (./grid-pkg.tex Chapter 6. [977] [978] [979] [980] [981] [982] [983] [984] Underfull \hbox (badness 10000) in paragraph at lines 476--482 \T1/ptm/m/n/10 (i.e., pop or up any view-ports that were pushed; again, see, fo r ex-am-ple, Underfull \hbox (badness 1024) in paragraph at lines 476--482 \T1/pcr/m/n/10 grid:::postDrawDetails.frame\T1/ptm/m/n/10 ). Note that the de-f ault be-haviour for grobs is to [985] [986] [987] [988] [989] [990] [991] [992] [993] [994] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1117--1117 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="B"),[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1119--1119 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="C"),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1121--1121 [] \T1/pcr/m/n/9 just=c("left", "bottom" ), name="D")),[] Underfull \hbox (badness 1430) in paragraph at lines 1166--1171 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [995] [996] [997] [998] Underfull \hbox (badness 3219) in paragraph at lines 1380--1383 []\T1/ptm/m/n/10 Both func-tions cre-ate a cir-cle grob (a graph-i-cal ob-ject de-scrib-ing a cir-cle), but only [999] [1000] [1001] [1002] [1003] [1004] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1767--1767 [] \T1/pcr/m/n/9 do.call("grid.curve", c(list(x1=.25, y1=.25, x2=.75, y2=.75) , list(...)))[] [1005] [1006] [1007] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1981--1981 []\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 1982--1982 []\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 1983--1983 []\T1/pcr/m/n/9 grid.rect(width=.4, height=.4, x=.75, y=.25, gp=gpar(fill="whi te"), name="r3")[] [1008] Underfull \hbox (badness 2961) in paragraph at lines 2018--2023 []\T1/ptm/m/n/10 The meth-ods for grob and gTree call the generic hook func-tio ns \T1/pcr/m/n/10 preDrawDetails\T1/ptm/m/n/10 , [1009] Underfull \hbox (badness 1430) in paragraph at lines 2077--2082 []\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 2106--2109 []\T1/ptm/m/n/10 Both func-tions call \T1/pcr/m/n/10 editDetails \T1/ptm/m/n/10 to al-low a grob to per-form cus-tom ac-tions and [1010] [1011] [1012] Underfull \hbox (badness 2894) in paragraph at lines 2313--2320 []\T1/ptm/m/n/10 Both func-tions cre-ate a frame grob (a graph-i-cal ob-ject de -scrib-ing a frame), but only [1013] [1014] [1015] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2469--2469 []\T1/pcr/m/n/10 getGrob(gTree, gPath, strict = FALSE, grep = FALSE, global = FALSE)[] Underfull \hbox (badness 1430) in paragraph at lines 2481--2486 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1016] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2540--2540 []\T1/pcr/m/n/10 grid.grabExpr(expr, warn = 2, wrap = wrap.grobs, wrap.grobs = FALSE,[] [1017] [1018] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2692--2692 [] \T1/pcr/m/n/9 children=gList(grob(name="child", vp ="vp1::vp2")),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2724--2724 [] \T1/pcr/m/n/10 default.units = "npc", gp=gpar(col = "grey"), vp = NULL)[] [1019] [1020] [1021] [1022] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 [] \T1/pcr/m/n/9 pushViewport(viewport(layout=grid.layout(1, 1, widths=unit(1 , "inches"),[] [1023] [1024] [1025] [1026] [1027] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3281--3281 [] \T1/pcr/m/n/9 children=vpList(viewpor t(name="vp2"))))[] [1028] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3377--3377 []\T1/pcr/m/n/9 pushViewport(viewport(x=0, y=0, w=0.25, h=0.25, just=c("left", "bottom")))[] [1029] Underfull \hbox (badness 2799) in paragraph at lines 3411--3417 []\T1/ptm/m/n/10 There are two hooks called \T1/pcr/m/n/10 "before.grid.newpage " \T1/ptm/m/n/10 and \T1/pcr/m/n/10 "grid.newpage" \T1/ptm/m/n/10 (see [1030] [1031] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3503--3503 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3510--3510 [] \T1/pcr/m/n/10 force.width = FALSE, force.height = FALSE, border = NULL,[] [1032] [1033] [1034] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3711--3711 [] \T1/pcr/m/n/9 "Nested rectangles, outer clockwise, inner ant i-clockwise")[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3726--3726 [] \T1/pcr/m/n/9 "Overlapping rectangles, one clockwise, other anti-clockwise")[] Underfull \vbox (badness 10000) has occurred while \output is active [1035] Overfull \hbox (15.18042pt too wide) in paragraph at lines 3747--3747 []\T1/pcr/m/n/9 # Not specifying pathId will treat all points as part of the s ame path, thus[] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] Underfull \hbox (badness 1067) in paragraph at lines 4486--4489 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1048] Underfull \hbox (badness 1430) in paragraph at lines 4532--4537 []\T1/ptm/m/n/10 A boolean in-di-cat-ing whether the \T1/pcr/m/n/10 gPath \T1/p tm/m/n/10 should be treated as a reg-u- [1049] [1050] [1051] Underfull \hbox (badness 7256) in paragraph at lines 4731--4733 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] Underfull \hbox (badness 10000) in paragraph at lines 5368--5370 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 grid.legend()\T1/ptm/m/n/10 : all the ar-gu -ments above are passed to [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] Underfull \hbox (badness 6859) in paragraph at lines 6056--6062 []\T1/ptm/m/n/10 Certain arith-metic and sum-mary op-er-a-tions are de-fined fo r unit ob-jects. In par- Underfull \hbox (badness 10000) in paragraph at lines 6056--6062 \T1/ptm/m/n/10 tic-u-lar, it is pos-si-ble to add and sub-tract unit ob-jects ( e.g., \T1/pcr/m/n/10 unit(1,"npc") [1072] [1073] [1074] [1075] [1076] Underfull \hbox (badness 1867) in paragraph at lines 6366--6368 []\T1/ptm/m/n/10 This func-tion can be used to gen-er-ate a view-port path for use in \T1/pcr/m/n/10 downViewport \T1/ptm/m/n/10 or [1077] Underfull \hbox (badness 10000) in paragraph at lines 6403--6409 [][][]\T1/pcr/m/n/10 viewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pushView port[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 seekV iewport[][][]\T1/ptm/m/n/10 , [1078] [1079] Underfull \hbox (badness 1371) in paragraph at lines 6535--6538 []\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by do-ing some-thing like \T1/pcr/m/n/10 depth [1080] [1081] [1082] Overfull \hbox (25.98041pt too wide) in paragraph at lines 6739--6739 []\T1/pcr/m/n/9 invisible(lapply(trace, function(t) grid.lines(t$x, t$y, gp=gp ar(col="red"))))[] [1083]) (./methods-pkg.tex [1084] Chapter 7. [1085] [1086] 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 [1087] [1088] [1089] Underfull \hbox (badness 1348) in paragraph at lines 392--395 [][][]\T1/pcr/m/n/10 GroupGenericFunctions[][][] \T1/ptm/m/n/10 for other in-fo r-ma-tion about group generic func-tions; [][]Meth- [1090] [1091] 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[] [1092] 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 [1093] 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 [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] 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[] [1109] [1110] 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 [1111] [1112] [1113] Underfull \hbox (badness 1478) in paragraph at lines 2214--2219 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use \T1/pcr/m/n/10 where = [1114] [1115] Underfull \hbox (badness 10000) in paragraph at lines 2328--2332 []\T1/ptm/m/n/10 To see the ac-tual ta-ble (an [][]\T1/pcr/m/n/10 environment[] [][]\T1/ptm/m/n/10 ) used for meth-ods dis-patch, call 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}:[] [1116] [1117] [1118] 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 [1119] 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))[] [1120] [1121] [1122] 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:[] [1123] [1124] [1125] [1126] [1127] [1128] [1129] 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 [1130] [1131] 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 [1132] Underfull \hbox (badness 10000) in paragraph at lines 3634--3639 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 initialize \T1/ptm/m/n/10 method for these classes takes spe-cial ar-gu-ments Overfull \hbox (14.78088pt too wide) in paragraph at lines 3642--3651 [] [1133] [1134] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/pcr/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude = Underfull \hbox (badness 10000) in paragraph at lines 3809--3810 []\T1/pcr/m/n/10 setMethod("plot",c("Pos","missing"),function(x,y,...) { [1135] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/pcr/m/n/10 Currency <-setClass("Currency",slots = c(unit = Underfull \hbox (badness 6157) in paragraph at lines 3908--3912 []\T1/ptm/m/n/10 A call to [][]\T1/pcr/m/n/10 selectSuperClasses[][][](cl) \T1/ ptm/m/n/10 re-turns a list of su-per-classes, sim-i-larly to [1136] [1137] [1138] Underfull \hbox (badness 10000) in paragraph at lines 4135--4137 []\T1/pcr/m/n/10 signature(from = "ANY",to = "call")\T1/ptm/m/n/10 . A method e x-ists for [1139] [1140] [1141] 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,[] [1142] 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) [1143] [1144] [1145] Underfull \hbox (badness 2126) in paragraph at lines 4574--4582 []\T1/ptm/m/n/10 For ad-di-tional in-for-ma-tion see doc-u-men-ta-tion for the im-por-tant steps: ([][]\T1/pcr/m/n/10 setMethod[][][]()\T1/ptm/m/n/10 , [1146] [1147] [1148] Underfull \hbox (badness 10000) in paragraph at lines 4811--4820 []\T1/ptm/m/n/10 In prin-ci-ple, a generic func-tion could be any func-tion tha t eval-u-ates a call to [1149] [1150] [1151] [1152] 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[] [1153] 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 [1154] [1155] Underfull \hbox (badness 10000) in paragraph at lines 5355--5356 []\T1/pcr/m/n/10 unique.uncased <-function(x,incomparables = FALSE,...) [1156] [1157] 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 [1158] [1159] [1160] 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 [1161] [1162] [1163] [1164] [1165] [1166] 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 [1167] [1168] 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 [1169] 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 [1170] [1171] Underfull \hbox (badness 2875) in paragraph at lines 6647--6656 []\T1/ptm/m/n/10 Reference classes can have va-lid-ity meth-ods in the same sen se as any S4 class (see Underfull \hbox (badness 1436) in paragraph at lines 6647--6656 [][]\T1/pcr/m/n/10 setValidity[][][]\T1/ptm/m/n/10 ). Such meth-ods are of-ten a good idea; they will be called by call-ing [1172] Underfull \vbox (badness 10000) has occurred while \output is active [1173] [1174] [1175]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.S4}) has been already used, duplicate ignored \relax l.6973 \aliasA{S4}{S3Part}{S4} [1176] 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().[] [1177] [1178] 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")[] [1179]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 [1180] 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 , [1181] [1182] Underfull \hbox (badness 1694) in paragraph at lines 7472--7474 []\T1/ptm/m/n/10 name of the class or (more ef-fi-ciently) the class def-i-ni-t ion ob-ject (see 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 [1183] [1184] Underfull \hbox (badness 1019) in paragraph at lines 7663--7670 \T1/ptm/m/n/10 about it, you'll prob-a-bly agree that you wouldn't want the re- sult to be from some class [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] 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 [1196] 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(), [1197] 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 =,[] [1198] [1199] [1200] [1201] 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[] [1202] [1203] [1204] 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")[] [1205] [1206] [1207] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9429--9429 []\T1/pcr/m/n/9 ## Using a short form for the signature, which matches like fo rmal arguments[] [1208] [1209] [1210] [1211] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9737--9737 []\T1/pcr/m/n/9 ## Define a new generic function to compute the residual degre es of freedom[] [1212] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9847--9847 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9858--9858 []\T1/pcr/m/n/9 ## Not run: [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,1 0] [,11] [,12][] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] Underfull \hbox (badness 10000) in paragraph at lines 10556--10558 []\T1/ptm/m/n/10 Object of the orig-i-nal class; e.g., \T1/pcr/m/n/10 "function " \T1/ptm/m/n/10 for class 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 [1223] [1224] [1225]) (./parallel-pkg.tex [1226] Chapter 8. Underfull \hbox (badness 2418) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/pcr /m/n/10 "L\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[ ][][]: see [1227] Underfull \hbox (badness 4242) in paragraph at lines 96--98 []\T1/ptm/m/n/10 a vec-tor for \T1/pcr/m/n/10 clusterApply \T1/ptm/m/n/10 and \ T1/pcr/m/n/10 clusterApplyLB\T1/ptm/m/n/10 , a ma-trix for [1228] [1229] 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 [1230] [1231] [1232] Underfull \hbox (badness 10000) in paragraph at lines 443--445 []\T1/ptm/m/n/10 Character vec-tor of ad-di-tional ar-gu-ments for \T1/pcr/m/n/ 10 Rscript \T1/ptm/m/n/10 such as [1233] [1234] [1235] [1236] Underfull \hbox (badness 1917) in paragraph at lines 744--753 []\T1/pcr/m/n/10 mcfork \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1/pcr /m/n/10 "childProcess" \T1/ptm/m/n/10 to the mas-ter and of class Underfull \hbox (badness 1178) in paragraph at lines 744--753 \T1/pcr/m/n/10 "masterProcess" \T1/ptm/m/n/10 to the child: both the classes in -herit from class \T1/pcr/m/n/10 "process"\T1/ptm/m/n/10 . If [1237] [1238] Overfull \hbox (60.78088pt too wide) in paragraph at lines 837--837 [] \T1/pcr/m/n/10 mc.cleanup = TRUE, mc.allow.recursive = TRUE, affini ty.list = NULL)[] [1239] [1240] [1241] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1026--1026 []\T1/pcr/m/n/9 mclapply(list(A, A, A), first, mc.preschedule = FALSE, affinit y.list = affL)[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 1030--1030 []\T1/pcr/m/n/9 # To optimize the overall execution time elements of X are sch eduled to suitable CPUs[] [1242] Underfull \hbox (badness 5388) in paragraph at lines 1145--1150 []\T1/pcr/m/n/10 mcparallel \T1/ptm/m/n/10 re-turns an ob-ject of the class \T1 /pcr/m/n/10 "parallelJob" \T1/ptm/m/n/10 which in-her-its from [1243] Underfull \hbox (badness 10000) in paragraph at lines 1169--1177 []\T1/ptm/m/n/10 The be-haviour with \T1/pcr/m/n/10 mc.set.seed = TRUE \T1/ptm/ m/n/10 is dif-fer-ent only if Overfull \hbox (9.78043pt too wide) in paragraph at lines 1206--1206 []\T1/pcr/m/n/9 mccollect(p, wait = FALSE, 10) # will retrieve the result (sin ce it\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s fast)[] [1244] [1245] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1322--1322 [] \T1/pcr/m/n/9 as.integer(runif(N, 1, 12)), as.integer(runif (N, 1, 28)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1336--1336 []\T1/pcr/m/n/9 system.time(c <- unlist(mclapply(dates, as.POSIXct, format = "%Y-%m-%d")))[] [1246] Underfull \hbox (badness 1577) in paragraph at lines 1365--1368 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/pcr/m/n/10 .R andom.seed \T1/ptm/m/n/10 when the Underfull \hbox (badness 3375) in paragraph at lines 1411--1413 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 nextRNGStream \T1/ptm/m/n/10 and \T1/pcr/m/ n/10 nextRNGSubStream\T1/ptm/m/n/10 , a value which can be as-signed to [1247] [1248]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/pcr/m/n/10 \T1/ptm/ m/n/10 and William N. Ven-ables [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] Overfull \hbox (4.38043pt too wide) in paragraph at lines 495--495 []\T1/pcr/m/n/9 ispl <- polySpline(interpSpline( weight ~ height, women, bSpl ine = TRUE))[] [1257] Underfull \hbox (badness 1424) in paragraph at lines 594--596 []\T1/ptm/m/n/10 An in-te-ger be-tween 0 and \T1/pcr/m/n/10 splineOrder(object) -1 \T1/ptm/m/n/10 spec-i-fy-ing the [1258] [1259] Overfull \hbox (25.98041pt too wide) in paragraph at lines 709--709 []\T1/pcr/m/n/9 Matrix::drop0(zapsmall(6*splineDesign(knots = 1:40, x = 4:37, sparse = TRUE)))[] [1260] [1261] [1262]) (./stats-pkg.tex Chapter 10. [1263] Underfull \hbox (badness 1077) in paragraph at lines 71--74 []\T1/pcr/m/n/10 .MFclass() \T1/ptm/m/n/10 re-turns a char-ac-ter string, one o f \T1/pcr/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ordered"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "factor"\T1/ptm/m/n/10 , Overfull \hbox (69.18036pt too wide) in paragraph at lines 91--91 []\T1/pcr/m/n/9 (xl <- .getXlevels(terms(mf), mf)) # a list with one entry " $ Species" with 3 levels:[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 94--94 [] \T1/pcr/m/n/9 identical(.getXlevels(terms(mc), mc), xl[0]) # a empty named list, as no factors[] [1264] [1265] [1266] [1267] [1268] Overfull \hbox (20.58041pt too wide) in paragraph at lines 445--445 []\T1/pcr/m/n/9 add1(glm.D93, scope = ~outcome*treatment, test = "Rao") ## Pea rson Chi-square[] [1269] Overfull \hbox (6.78088pt too wide) in paragraph at lines 466--466 []\T1/pcr/m/n/10 addmargins(A, margin = seq_along(dim(A)), FUN = sum, quiet = FALSE) [1270] [1271] [1272] [1273] [1274] [1275] Underfull \hbox (badness 1024) in paragraph at lines 875--877 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/pcr/m/n/10 lm \T1/ptm/m/n/10 or \T1/pcr/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for [1276] [1277] [1278] [1279] [1280] [1281] [1282] [1283] [1284] Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 c("aov","lm") \T1/ptm/m/n/1 0 or for mul-ti-ple re-sponses of class Underfull \hbox (badness 10000) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("maov","aov","mlm","lm") \T1/ptm/m/n/10 or for mul-ti-ple er-r or strata of class Underfull \hbox (badness 2343) in paragraph at lines 1536--1540 \T1/pcr/m/n/10 c("aovlist","[][]listof[][][]")\T1/ptm/m/n/10 . There are [][]\T 1/pcr/m/n/10 print[][][] \T1/ptm/m/n/10 and [][]\T1/pcr/m/n/10 summary[][][] \T 1/ptm/m/n/10 meth-ods avail-able for [1285] [1286] [1287] [1288] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1737--1737 []\T1/pcr/m/n/9 (amy <- approx(x, y, xout = x)$y) # warning, can be avoided by specifying \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ties=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 :[ ] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299] [1300] [1301] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2726--2726 []\T1/pcr/m/n/10 ARMAacf(ar = numeric(), ma = numeric(), lag.max = r, pacf = F ALSE) [1302] [1303] [1304] [1305] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2966--2966 []\T1/pcr/m/n/9 lines(ave(breaks, wool, tension, FUN = median), type = "s", co l = "green")[] [1306] [1307] [1308] Underfull \hbox (badness 10000) in paragraph at lines 3175--3177 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Bartlett test of homoge neity of [1309] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3223--3223 []\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 3224--3224 []\T1/pcr/m/n/10 qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)[] [1310] [1311] [1312] [1313] [1314] [1315] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3615--3615 []\T1/pcr/m/n/9 plot (k, dbinom(k, n, pi/10, log = TRUE), type = "l", ylab = " log density",[] [1316] [1317] [1318] [1319] Overfull \hbox (12.78088pt too wide) in paragraph at lines 3893--3893 []\T1/pcr/m/n/10 Box.test(x, lag = 1, type = c("Box-Pierce", "Ljung-Box"), fit df = 0) [1320] [1321] [1322] [1323] [1324] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4182--4182 []\T1/pcr/m/n/10 pcauchy(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4183--4183 []\T1/pcr/m/n/10 qcauchy(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1325] [1326] [1327] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4421--4421 []\T1/pcr/m/n/9 chisq.test(x, p = p) # maybe doubtful , but is ok![] [1328] [1329] [1330] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4589--4589 [] \T1/pcr/m/n/9 plot(pp, sort(pchisq(rr <- rchisq(n, df = df, ncp = L), df = df, ncp = L)),[] [1331] Underfull \hbox (badness 3989) in paragraph at lines 4681--4688 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1332] [1333] [1334] [1335] [1336] [1337] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5066--5066 []\T1/pcr/m/n/9 constrOptim(c(-1.2,0.9), fr, grr, ui = rbind(c(-1,0), c(0,-1)) , ci = c(-1,-1))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5068--5068 []\T1/pcr/m/n/9 constrOptim(c(.5,0), fr, grr, ui = rbind(c(-1,0), c(1,-1)), ci = c(-0.9,0.1))[] [1338] [1339] [1340] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5289--5289 []\T1/pcr/m/n/9 ## using sparse contrasts: % useful, once model.matrix() works with these :[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5307--5307 []\T1/pcr/m/n/10 convolve(x, y, conj = TRUE, type = c("circular", "open", "fil ter")) Underfull \hbox (badness 2680) in paragraph at lines 5334--5336 []\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se- quences \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 is given by [1341] [1342] [1343] Underfull \hbox (badness 1436) in paragraph at lines 5517--5522 []\T1/ptm/m/n/10 an op-tional char-ac-ter string giv-ing a method for com-put-i ng co-vari-ances Underfull \hbox (badness 1377) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 in the pres-ence of miss-ing val-ues. This must be (an ab-bre-vi -a-tion of) Underfull \hbox (badness 1448) in paragraph at lines 5517--5522 \T1/ptm/m/n/10 one of the strings \T1/pcr/m/n/10 "everything"\T1/ptm/m/n/10 , \ T1/pcr/m/n/10 "all.obs"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "complete.obs"\T1/ptm/m/ n/10 , [1344] [1345] [1346] Overfull \hbox (0.78088pt too wide) in paragraph at lines 5715--5715 [] \T1/pcr/m/n/10 exact = NULL, conf.level = 0.95, continuity = FALSE, ...)[] [1347] [1348] [1349] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5882--5882 []\T1/pcr/m/n/10 cov.wt(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE, center = TRUE, [1350] [1351] [1352] Overfull \hbox (6.78088pt too wide) in paragraph at lines 6067--6067 []\T1/pcr/m/n/10 decompose(x, type = c("additive", "multiplicative"), filter = NULL) [1353] Overfull \hbox (84.78088pt too wide) in paragraph at lines 6175--6175 []\T1/pcr/m/n/10 reformulate(termlabels, response = NULL, intercept = TRUE, en v = parent.frame())[] [1354] Underfull \hbox (badness 10000) in paragraph at lines 6242--6247 []\T1/ptm/m/n/10 Apply func-tion \T1/pcr/m/n/10 FUN \T1/ptm/m/n/10 to each node of a [][]\T1/pcr/m/n/10 dendrogram[][][] \T1/ptm/m/n/10 re-cur-sively. When \T 1/pcr/m/n/10 y [1355] [1356] [1357] [1358] Underfull \hbox (badness 5954) in paragraph at lines 6438--6440 []\T1/ptm/m/n/10 logical in-di-cat-ing if a box around the plot should be drawn , see [1359] Underfull \hbox (badness 2503) in paragraph at lines 6520--6523 []\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 6524--6526 []\T1/pcr/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra m \T1/pcr/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also Underfull \hbox (badness 1655) in paragraph at lines 6527--6532 \T1/ptm/m/n/10 has \T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm /m/n/10 (and op-tional fur-ther ar-gu-ments) as branches. Note that be-fore \T1 /phv/m/n/10 R \T1/ptm/m/n/10 3.1.2, Underfull \hbox (badness 7238) in paragraph at lines 6563--6566 [][][]\T1/pcr/m/n/10 dendrapply[][][] \T1/ptm/m/n/10 for ap-ply-ing a func-tion to \T1/ptm/m/it/10 each \T1/ptm/m/n/10 node. [][]\T1/pcr/m/n/10 order.dendrogr am[][][] \T1/ptm/m/n/10 and [1360] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6598--6598 []\T1/pcr/m/n/9 plot(dend2$lower[[3]], nodePar = list(col = 4), horiz = TRUE, type = "tr")[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6613--6613 []\T1/pcr/m/n/9 ## merge() all parts back (using default \TS1/pcr/m/n/9 '\T1/p cr/m/n/9 height\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 instead of original one):[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6628--6628 []\T1/pcr/m/n/9 plot(d3, nodePar= nP, edgePar = list(col = "gray", lwd = 2), h oriz = TRUE)[] Underfull \vbox (badness 10000) has occurred while \output is active [1361] [1362] [1363] [1364] Overfull \hbox (4.38043pt too wide) in paragraph at lines 6872--6872 [] \T1/pcr/m/n/9 function(k) density(kernel = k, give.Rker n = TRUE))))[] [1365] [1366] [1367] [1368] [1369] [1370] Underfull \hbox (badness 10000) in paragraph at lines 7270--7274 \T1/pcr/m/n/10 "maximum"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "manhattan"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "canberra"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "binary" \T1/ptm/ m/n/10 or [1371] Underfull \hbox (badness 6493) in paragraph at lines 7369--7372 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T 1/pcr/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the [1372] [1373] Underfull \hbox (badness 10000) in paragraph at lines 7506--7509 []\T1/ptm/m/n/10 The CRAN task view on dis-tri-bu-tions, [][]$\T1/pcr/m/n/10 ht tps : / / CRAN . R-[]project . org / view = [1374] [1375] [1376] [1377] [1378] [1379] [1380] Underfull \hbox (badness 10000) in paragraph at lines 7918--7923 []\T1/ptm/m/n/10 Each row of the re-sult-ing ma-trix con-sists of se-quences \T 1/pcr/m/n/10 x[t]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 x[t-1]\T1/ptm/m/n/10 , ..., [1381] [1382] [1383] [1384] [1385] Underfull \hbox (badness 1210) in paragraph at lines 8273--8275 []\T1/ptm/m/n/10 Components of \T1/pcr/m/n/10 control \T1/ptm/m/n/10 can also b e sup-plied as named ar-gu-ments to [1386] [1387] [1388] [1389] [1390] [1391] [1392] Overfull \hbox (15.18042pt too wide) in paragraph at lines 8736--8736 []\T1/pcr/m/n/9 glm.qD93 <- glm(counts ~ outcome + treatment, d.AD, family = q uasipoisson())[] Underfull \vbox (badness 10000) has occurred while \output is active [1393] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8781--8781 []\T1/pcr/m/n/9 ## Not run: glm(y ~ x, family = quasi(variance = "mu^3", link = "log")) # fails[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 8784--8784 []\T1/pcr/m/n/9 glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit "), start = c(0,1))[] [1394] [1395] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8922--8922 []\T1/pcr/m/n/9 quantile(rel.err(qf(2*p - 1, df1 = 1, df2 = df), qt(p, df)^2), .90) # ~= 7e-9[] [1396] [1397] [1398] [1399] [1400] [1401] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9349--9349 [] \T1/pcr/m/n/9 dimnames = list(income = c("< 15k", "15-25k", "25-4 0k", "> 40k"),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 9350--9350 [] \T1/pcr/m/n/9 satisfaction = c("VeryD", "LittleD", "Mod erateS", "VeryS")))[] [1402] [1403] [1404] Underfull \hbox (badness 7291) in paragraph at lines 9529--9531 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Fligner-Killeen test of homogeneity of [1405] [1406] [1407] [1408] [1409] [1410] Underfull \hbox (badness 6944) in paragraph at lines 9990--9996 [][][]\T1/pcr/m/n/10 ftable.formula[][][] \T1/ptm/m/n/10 for the for-mula in-te r-face (which al-lows a \T1/pcr/m/n/10 data = . \T1/ptm/m/n/10 ar-gu-ment); [1411] [1412] [1413] Underfull \hbox (badness 3758) in paragraph at lines 10203--10206 []\T1/ptm/m/n/10 See also [][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Incomplete _ gamma _ function$[][]\T1/ptm/m/n/10 , or [1414] [1415] [1416] [1417] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10439--10439 [] \T1/pcr/m/n/10 x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL , ...)[] Underfull \hbox (badness 4518) in paragraph at lines 10465--10470 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1418] Underfull \hbox (badness 4132) in paragraph at lines 10504--10508 []\T1/ptm/m/n/10 the method to be used in fit-ting the model. The de-fault meth od Underfull \hbox (badness 1112) in paragraph at lines 10558--10564 []\T1/ptm/m/n/10 A spec-i-fi-ca-tion of the form \T1/pcr/m/n/10 first:second \T 1/ptm/m/n/10 in-di-cates the set of terms ob-tained by tak- [1419] Underfull \hbox (badness 10000) in paragraph at lines 10609--10612 []\T1/ptm/m/n/10 The generic ac-ces-sor func-tions [][]\T1/pcr/m/n/10 coefficie nts[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 effects\T1/ptm/m/n/10 , \T1/pcr/m/n/10 fitted.values \T1/ptm/m/n/10 and [1420] [1421] [1422] Underfull \hbox (badness 2142) in paragraph at lines 10825--10828 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ [1423] [1424] Underfull \hbox (badness 1708) in paragraph at lines 10906--10910 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: Underfull \hbox (badness 10000) in paragraph at lines 10948--10954 [][][]\T1/pcr/m/n/10 glm[][][] \T1/ptm/m/n/10 for com-put-ing \T1/pcr/m/n/10 gl m.obj\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 anova.glm[][][]\T1/ptm/m/n/10 ; the co r-re-spond-ing \T1/ptm/m/it/10 generic \T1/ptm/m/n/10 func-tions, [1425] Underfull \hbox (badness 1418) in paragraph at lines 10986--10991 \T1/pcr/m/n/10 "average" \T1/ptm/m/n/10 (= UP-GMA), \T1/pcr/m/n/10 "mcquitty" \ T1/ptm/m/n/10 (= WPGMA), \T1/pcr/m/n/10 "median" \T1/ptm/m/n/10 (= [1426] Underfull \hbox (badness 2635) in paragraph at lines 11119--11122 \T1/ptm/m/n/10 There are [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [][]\T1 /pcr/m/n/10 plot[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 identify \T1/ptm/m/n/1 0 (see [][]\T1/pcr/m/n/10 identify.hclust[][][]\T1/ptm/m/n/10 ) meth-ods and th e [1427] [1428] [1429] Underfull \hbox (badness 1694) in paragraph at lines 11302--11305 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1430] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11403--11403 []\T1/pcr/m/n/9 heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, Col SideColors = cc,[] [1431] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11436--11436 [] \T1/pcr/m/n/10 optim.start = c(alpha = 0.3, beta = 0.1, gamma = 0.1),[] Underfull \hbox (badness 10000) in paragraph at lines 11449--11453 []\T1/ptm/m/n/10 Character string to se-lect an \T1/pcr/m/n/10 "additive" \T1/p tm/m/n/10 (the de-fault) or [1432] [1433] [1434] Underfull \hbox (badness 7379) in paragraph at lines 11629--11632 []\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds [][]\T1/pcr/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq uiv-a-lent of [1435] [1436] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11768--11768 []\T1/pcr/m/n/9 identify(hci, function(k) barplot(table(iris[k,5]), col = 2:4) , DEV.FUN = nD)[] [1437]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat }) has been already used, duplicate ignored \relax l.11783 \aliasA{hat}{influence.measures}{hat} Overfull \hbox (0.78088pt too wide) in paragraph at lines 11836--11836 []\T1/pcr/m/n/10 cooks.distance(model, infl = lm.influence(model, do.coef = FA LSE),[] [1438] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11848--11848 []\T1/pcr/m/n/10 hatvalues(model, infl = lm.influence(model, do.coef = FALSE), ...)[] Underfull \hbox (badness 1062) in paragraph at lines 11901--11906 []\T1/ptm/m/n/10 The op-tional \T1/pcr/m/n/10 infl\T1/ptm/m/n/10 , \T1/pcr/m/n/ 10 res \T1/ptm/m/n/10 and \T1/pcr/m/n/10 sd \T1/ptm/m/n/10 ar-gu-ments are ther e to en-cour-age the use of these di- Underfull \hbox (badness 1052) in paragraph at lines 11918--11920 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1439] [1440] [1441] [1442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12168--12168 [] \T1/pcr/m/n/10 type = c("l", "p", "b", "o", "c"), legend = TRUE,[] [1443] [1444] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12261--12261 [] \T1/pcr/m/n/9 interaction.plot(agegp, tobgp, ncases/ncontrols, trace.label = "tobacco",[] [1445] [1446] [1447] [1448] Underfull \hbox (badness 10000) in paragraph at lines 12511--12513 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/pcr/m/n/10 solve.defa ult[][][] \T1/ptm/m/n/10 when \T1/pcr/m/n/10 SSinit = Underfull \hbox (badness 4739) in paragraph at lines 12534--12536 []\T1/ptm/m/n/10 the es-ti-mate at time $\OML/cmm/m/it/10 t \OMS/cmsy/m/n/10 ^^ @ \OT1/cmr/m/n/10 1$ \T1/ptm/m/n/10 of the state un-cer-tainty ma-trix $\OML/cm m/m/it/10 Q$ \T1/ptm/m/n/10 (not up-dated by [1449] Underfull \hbox (badness 2753) in paragraph at lines 12603--12605 []\T1/ptm/m/n/10 R bug re-port PR#14682 (2011-2013) [][]$\T1/pcr/m/n/10 https : / / bugs . r-[]project . org / bugzilla3 / [1450] [1451] [1452] [1453] Underfull \hbox (badness 6910) in paragraph at lines 12841--12843 []\T1/ptm/m/n/10 an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class \T1/pcr/m/ n/10 "kmeans"\T1/ptm/m/n/10 , typ-i-cally the re-sult \T1/pcr/m/n/10 ob \T1/ptm /m/n/10 of \T1/pcr/m/n/10 ob Underfull \hbox (badness 2894) in paragraph at lines 12847--12851 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method Underfull \hbox (badness 1038) in paragraph at lines 12847--12851 \T1/ptm/m/n/10 (\T1/pcr/m/n/10 "Hartigan-Wong"\T1/ptm/m/n/10 ): if pos-i-tive ( or true), trac-ing in-for-ma-tion on the [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13554--13554 []\T1/pcr/m/n/9 dimnames(cAS) <- list(paste("it =", format(1:10)), c("intercep t", "slope"))[] [1464] Underfull \hbox (badness 4518) in paragraph at lines 13597--13602 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1465] [1466] [1467] Underfull \hbox (badness 10000) in paragraph at lines 13796--13800 []\T1/ptm/m/n/10 More \T1/pcr/m/n/10 lm() \T1/ptm/m/n/10 ex-am-ples are avail-a ble e.g., in [][]\T1/pcr/m/n/10 anscombe[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/ 10 attitude[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 freeny[][][]\T1/ptm/m/n/10 , [1468] [1469] [1470] [1471] [1472] Underfull \hbox (badness 1163) in paragraph at lines 14129--14137 \T1/ptm/m/n/10 els, [][]\T1/pcr/m/n/10 influence[][][] \T1/ptm/m/n/10 (etc on t hat page) for re-gres-sion di-ag-nos-tics, [][]\T1/pcr/m/n/10 weighted.residual s[][][]\T1/ptm/m/n/10 , [1473] Underfull \hbox (badness 4518) in paragraph at lines 14249--14254 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1474] [1475] [1476] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14435--14435 []\T1/pcr/m/n/10 plogis(q, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14436--14436 []\T1/pcr/m/n/10 qlogis(p, location = 0, scale = 1, lower.tail = TRUE, log.p = FALSE)[] [1477] [1478] [1479] [1480] [1481] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14779--14779 []\T1/pcr/m/n/10 plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14780--14780 []\T1/pcr/m/n/10 qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE)[] [1482] [1483] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14873--14873 []\T1/pcr/m/n/10 lowess(x, y = NULL, f = 2/3, iter = 3, delta = 0.01 * diff(ra nge(x))) [1484] [1485] [1486] [1487] [1488] [1489] Underfull \hbox (badness 2726) in paragraph at lines 15279--15282 []\T1/ptm/m/n/10 character; one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cauchit"\T1/ptm/m/n/10 , \T1 /pcr/m/n/10 "cloglog"\T1/ptm/m/n/10 , [1490] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15373--15373 []\T1/pcr/m/n/9 stopifnot(all.equal(pfm, pf2)) ## was off (rel.diff. 0.0766) i n R <= 3.5.0[] [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] Overfull \hbox (31.3804pt too wide) in paragraph at lines 15998--15998 []\T1/pcr/m/n/9 a <- model.frame(cbind(ncases,ncontrols) ~ agegp + tobgp + alc gp, data = esoph) [1501] [1502] Underfull \hbox (badness 1490) in paragraph at lines 16136--16141 \T1/ptm/m/n/10 those spec-i-fied in \T1/pcr/m/n/10 ... \T1/ptm/m/n/10 which are re-cy-cled to the num-ber of data frame rows. Un-like [1503] Underfull \hbox (badness 1648) in paragraph at lines 16202--16204 []\T1/ptm/m/n/10 a data frame cre-ated with [][]\T1/pcr/m/n/10 model.frame[][][ ]\T1/ptm/m/n/10 . If an-other sort of ob-ject, Underfull \hbox (badness 2591) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 us-ing the data in \T1/pcr/m/n/10 data \T1/ptm/m/n/10 which must sup-ply vari-ables with the same names as would Underfull \hbox (badness 3930) in paragraph at lines 16217--16226 \T1/ptm/m/n/10 be cre-ated by a call to \T1/pcr/m/n/10 model.frame(object) \T1/ ptm/m/n/10 or, more pre-cisely, by eval-u-at-ing [1504] Overfull \hbox (15.18042pt too wide) in paragraph at lines 16287--16287 []\T1/pcr/m/n/9 model.matrix(~ a + b, dd, contrasts = list(a = "contr.sum", b = contr.poly))[] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] Overfull \hbox (9.78043pt too wide) in paragraph at lines 16845--16845 []\T1/pcr/m/n/9 stopifnot(all(na.omit(1:3) == 1:3)) # does not affect objects with no NA\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s[] [1514] [1515] [1516] Overfull \hbox (25.98041pt too wide) in paragraph at lines 17073--17073 []\T1/pcr/m/n/9 persp(x, size, dnb <- outer(x, size, function(x,s) dnbinom(x, s, prob = 0.4)),[] [1517] [1518] [1519] [1520] [1521] [1522] [1523] [1524] [1525] [1526] Underfull \vbox (badness 10000) has occurred while \output is active [1527] Underfull \vbox (badness 10000) has occurred while \output is active [1528] Overfull \hbox (15.18042pt too wide) in paragraph at lines 17833--17833 [] \T1/pcr/m/n/9 start = list(a = rep(b[2], 21), b = rep(b[3], 21 ), th = b[1]))[] [1529] [1530] [1531] Overfull \hbox (9.78043pt too wide) in paragraph at lines 17996--17996 []\T1/pcr/m/n/9 DN.srt <- sortedXyData(expression(log(conc)), expression(densi ty), DNase.2)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18043--18043 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1532] Overfull \hbox (20.58041pt too wide) in paragraph at lines 18090--18090 []\T1/pcr/m/n/9 DN.srt <- sortedXyData( expression(log(conc)), expression(dens ity), DNase.2 )[] [1533] [1534] [1535] [1536] [1537] [1538] [1539] [1540] Underfull \hbox (badness 1248) in paragraph at lines 18581--18584 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 1661) in paragraph at lines 18594--18598 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce [1541] Underfull \hbox (badness 1478) in paragraph at lines 18602--18606 \T1/ptm/m/n/10 if \T1/pcr/m/n/10 control$trace \T1/ptm/m/n/10 is pos-i-tive. De -faults to ev-ery 10 it-er-a-tions for \T1/pcr/m/n/10 "BFGS" \T1/ptm/m/n/10 and Underfull \hbox (badness 2042) in paragraph at lines 18660--18662 []\T1/ptm/m/n/10 indicates an er-ror from the \T1/pcr/m/n/10 "L-BFGS-B" \T1/ptm /m/n/10 method; see com-po-nent [1542] [1543] Overfull \hbox (15.18042pt too wide) in paragraph at lines 18766--18766 [] \T1/pcr/m/n/9 lower = rep(2, 25), upper = rep(4, 25)) # par[24] is *no t* at boundary[] Underfull \vbox (badness 10000) has occurred while \output is active [1544] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18809--18809 [] \T1/pcr/m/n/9 main = "initial solution of traveling salesman problem", axes = FALSE)[] Overfull \hbox (123.1803pt too wide) in paragraph at lines 18827--18827 []\T1/pcr/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (96.18033pt too wide) in paragraph at lines 18830--18830 []\T1/pcr/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 18850--18850 []\T1/pcr/m/n/10 optimize(f, interval, ..., lower = min(interval), upper = max (interval), Overfull \hbox (36.78088pt too wide) in paragraph at lines 18853--18853 []\T1/pcr/m/n/10 optimise(f, interval, ..., lower = min(interval), upper = max (interval),[] [1545] Underfull \hbox (badness 2564) in paragraph at lines 18888--18899 []\T1/ptm/m/n/10 The func-tion \T1/pcr/m/n/10 f \T1/ptm/m/n/10 is never eval-u- ated at two points closer to-gether than $\OML/cmm/m/it/10 ^^O$$\OMS/cmsy/m/n/1 0 j\OML/cmm/m/it/10 x[]\OMS/cmsy/m/n/10 j \OT1/cmr/m/n/10 + (\OML/cmm/m/it/10 t ol=\OT1/cmr/m/n/10 3)$\T1/ptm/m/n/10 , Underfull \hbox (badness 1082) in paragraph at lines 18888--18899 \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 ^^O$ \T1/ptm/m/n/10 is ap-prox-i-mately \T1/pcr/m/n/10 sqrt([][].Machine[][][]$double.eps) \T1/ptm/m/n/10 and $\OML/cmm /m/it/10 x[]$ \T1/ptm/m/n/10 is the fi-nal ab-scissa [1546] Overfull \hbox (9.78043pt too wide) in paragraph at lines 18951--18951 []\T1/pcr/m/n/9 f <- function(x) ifelse(x > -1, ifelse(x < 4, exp(-1/abs(x - 1)), 10), 10)[] [1547] [1548] [1549] Overfull \hbox (9.78043pt too wide) in paragraph at lines 19176--19176 []\T1/pcr/m/n/9 matplot(p, p.adj, ylab="p.adjust(p, meth)", type = "l", asp = 1, lty = 1:6,[] [1550] Underfull \hbox (badness 1337) in paragraph at lines 19252--19255 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1551] [1552] [1553] [1554] [1555] [1556] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19571--19571 [] \T1/pcr/m/n/10 par.fit = list(col = "red", cex = 1.5, pch = 13, lwd = 1.5),[] [1557] Overfull \hbox (24.78088pt too wide) in paragraph at lines 19659--19659 [] \T1/pcr/m/n/10 expression("Cook\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 s dist vs Leverage " * h[ii] / (1 - h[ii]))),[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 19661--19661 [] \T1/pcr/m/n/10 panel.smooth(x, y, iter=iter.smooth, ...) else points,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 19663--19663 [] \T1/pcr/m/n/10 ask = prod(par("mfcol")) < length(which) && dev.interact ive(),[] [1558] Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 []\T1/ptm/m/n/10 the num-ber of ro-bust-ness it-er-a-tions, the ar-gu-ment \T1/ pcr/m/n/10 iter \T1/ptm/m/n/10 in Underfull \hbox (badness 10000) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 panel.smooth[][][]()\T1/ptm/m/n/10 ; the de-fault uses no su ch it-er-a-tions for Underfull \hbox (badness 5260) in paragraph at lines 19709--19713 [][]\T1/pcr/m/n/10 glm[][][](*,family=binomial) \T1/ptm/m/n/10 fits which is pa r-tic-u-larly de-sir-able for [1559] Underfull \hbox (badness 3049) in paragraph at lines 19748--19752 []\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou rs of stan-dard-ized resid-u-als [1560] [1561] [1562] Overfull \hbox (0.78088pt too wide) in paragraph at lines 19996--19996 [] \T1/pcr/m/n/10 main = NULL, ci.col = "blue", ci.lty = 3, ...)[] [1563] Underfull \hbox (badness 1194) in paragraph at lines 20006--20009 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1564] Underfull \hbox (badness 1107) in paragraph at lines 20064--20066 []\T1/ptm/m/n/10 numeric vec-tor of ab-scissa val-ues at which to eval-u-ate \T 1/pcr/m/n/10 x\T1/ptm/m/n/10 . De-faults to Overfull \hbox (20.58041pt too wide) in paragraph at lines 20119--20119 []\T1/pcr/m/n/9 plot(sfun.2);plot(sfun.2, xval = tt, add = TRUE, col = "orange ") # all colors[] [1565] Overfull \hbox (31.3804pt too wide) in paragraph at lines 20126--20126 []\T1/pcr/m/n/9 legend(2.5, 1.9, paste("f =", c(0, 0.2, 1)), col = 1:3, lty = 1, y.intersp = 1)[] [1566] Overfull \hbox (20.58041pt too wide) in paragraph at lines 20220--20220 []\T1/pcr/m/n/9 title("plot(ts(..), axes=FALSE, ann=FALSE, frame.plot=TRUE, ma r..., oma...)")[] [1567] [1568] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20345--20345 [] \T1/pcr/m/n/9 ppois(10*(15:25), lambda = 100, lower.tail = FALSE) # no cancellation[] [1569] Underfull \hbox (badness 7740) in paragraph at lines 20408--20410 []\T1/ptm/m/n/10 the char-ac-ter string \T1/pcr/m/n/10 "Exact Poisson test" \T1 /ptm/m/n/10 or \T1/pcr/m/n/10 "Comparison of Overfull \hbox (6.78088pt too wide) in paragraph at lines 20456--20456 []\T1/pcr/m/n/10 poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE) [1570] [1571] Overfull \hbox (4.38043pt too wide) in paragraph at lines 20548--20548 [] \T1/pcr/m/n/9 zm <- zapsmall(polym ( 1:4, c(1, 4:6), degree = 3)) # or just poly():[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 20553--20553 []\T1/pcr/m/n/9 ## poly(, df) --- used to fail till July 14 (vive la F rance!), 2017:[] [1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581] [1582] [1583] [1584] Overfull \hbox (25.98041pt too wide) in paragraph at lines 21407--21407 [] \T1/pcr/m/n/9 all.equal(pz3$sdev, pZ$sdev, tol = 1e-15)) # exactly equal typically[] [1585] Underfull \hbox (badness 6859) in paragraph at lines 21474--21481 [][][]\T1/pcr/m/n/10 predict.glm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predi ct.lm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.loess[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 predict.nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pre dict.poly[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 21485--21491 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/pcr/m/n/10 predict.ar[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 , [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] Overfull \hbox (48.78088pt too wide) in paragraph at lines 22223--22223 [] \T1/pcr/m/n/10 subset = rep_len(TRUE, nrow(as.matrix(x))), fix_sign = TRUE, ...)[] [1598] [1599] [1600] [1601] [1602] Overfull \hbox (0.78088pt too wide) in paragraph at lines 22507--22507 [] \T1/pcr/m/n/10 has.Pvalue = nc >= 4L && length(cn <- colnames(x )) &&[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 22508--22508 [] \T1/pcr/m/n/10 substr(cn[nc], 1L, 3L) %in% c("Pr(" , "p-v"),[] [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 1337) in paragraph at lines 22834--22840 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1608] [1609] [1610] [1611] [1612] [1613] [1614] [1615] Overfull \hbox (133.98029pt too wide) in paragraph at lines 23399--23399 [] \T1/pcr/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty p, ...), quantile(x, prob, type=1)))[] [1616] [1617] Underfull \hbox (badness 1028) in paragraph at lines 23540--23543 []\T1/ptm/m/n/10 further ar-gu-ments to be passed to or from meth-ods; for \T1/ pcr/m/n/10 write() \T1/ptm/m/n/10 and [1618] [1619] Underfull \hbox (badness 10000) in paragraph at lines 23650--23653 []\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by [1620] Underfull \hbox (badness 7944) in paragraph at lines 23705--23707 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 reorder[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1621] Underfull \hbox (badness 7944) in paragraph at lines 23767--23769 []\T1/ptm/m/n/10 This, as [][]\T1/pcr/m/n/10 relevel[][][]()\T1/ptm/m/n/10 , is a spe-cial case of sim-ply call-ing [][]\T1/pcr/m/n/10 factor[][][](x,levels = [1622] [1623] Overfull \hbox (9.78043pt too wide) in paragraph at lines 23869--23869 []\T1/pcr/m/n/9 plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")[] [1624] [1625] [1626] Overfull \hbox (31.3804pt too wide) in paragraph at lines 24089--24089 []\T1/pcr/m/n/9 reshape(df, timevar = "visit", idvar = "id", direction = "wide ", v.names = "x")[] [1627] [1628] Underfull \hbox (badness 10000) in paragraph at lines 24235--24238 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/pcr/m/n/10 y = run med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/pcr/m/n/10 y[j] = [1629] Underfull \hbox (badness 2134) in paragraph at lines 24287--24291 [][][]\T1/pcr/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's end point rule and is called by de-fault from Overfull \hbox (9.78043pt too wide) in paragraph at lines 24300--24300 []\T1/pcr/m/n/9 plot(myNHT, type = "b", ylim = c(48, 60), main = "Running Medi ans Example")[] [1630] [1631] [1632] [1633] [1634] [1635] Underfull \vbox (badness 10000) has occurred while \output is active [1636] [1637] Underfull \hbox (badness 6268) in paragraph at lines 24777--24782 [][]\T1/pcr/m/n/10 SSasympOrig[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSbiexp [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSfol[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 SSfpl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSgompertz[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 SSlogis[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 SSmicmen[][][]\T1/ptm/m/n/10 , Overfull \hbox (58.38037pt too wide) in paragraph at lines 24805--24805 [] \T1/pcr/m/n/9 setNames(pars[c(".lin", "xmid", "scal")], nm = mCall[c("As ym", "xmid", "scal")])[] [1638] [1639] [1640] Underfull \hbox (badness 1867) in paragraph at lines 24982--24984 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/ptm/m/n/10 where \T1/pcr/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u se.fallback) \T1/ptm/m/n/10 and \T1/pcr/m/n/10 PP Underfull \hbox (badness 10000) in paragraph at lines 24995--24999 \T1/pcr/m/n/10 <-sum(!is.na([][]coef[][][](object))) \T1/ptm/m/n/10 -- where in older \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions this was [1641] Overfull \hbox (20.58041pt too wide) in paragraph at lines 25031--25031 []\T1/pcr/m/n/9 sigma(lm1) # ~= 7.165 = "Residual standard error" printed fr om summary(lm1)[] [1642] [1643] [1644] Underfull \hbox (badness 2495) in paragraph at lines 25221--25230 []\T1/ptm/m/n/10 For an in-verse gaus-sian GLM the model as-sumed is $\OML/cmm/ m/it/10 IG\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 ^^V[]; ^^Uw[]\OT1/cmr/m/n/10 )$ \T1 /ptm/m/n/10 (see [][]$\T1/pcr/m/n/10 https : / / en . [1645] Overfull \hbox (24.78088pt too wide) in paragraph at lines 25303--25303 [] \T1/pcr/m/n/10 twiceit = FALSE, endrule = c("Tukey", "copy"), do.ends = FALSE)[] Underfull \hbox (badness 1412) in paragraph at lines 25310--25312 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing the kind of smoother re-qui red; de-faults to [1646] Overfull \hbox (25.98041pt too wide) in paragraph at lines 25397--25397 []\T1/pcr/m/n/9 matlines(cbind(smooth(x, "3R"), smooth(x, "S"), smooth(x, "3RS S"), smooth(x)))[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 25422--25422 []\T1/pcr/m/n/10 smooth.spline(x, y = NULL, w = NULL, df, spar = NULL, lambda = NULL, cv = FALSE, Overfull \hbox (66.78088pt too wide) in paragraph at lines 25425--25425 [] \T1/pcr/m/n/10 control.spar = list(), tol = 1e-6 * IQR(x), kee p.stuff = FALSE)[] [1647] [1648] [1649] Overfull \hbox (18.78088pt too wide) in paragraph at lines 25648--25648 [] \T1/pcr/m/n/10 nx <- length(x) - sum(duplicated( round((x - mean(x)) / tol) ))[] Underfull \hbox (badness 2547) in paragraph at lines 25651--25657 []\T1/ptm/m/n/10 The de-fault \T1/pcr/m/n/10 all.knots = FALSE \T1/ptm/m/n/10 a nd \T1/pcr/m/n/10 nknots = .nknots.smspl\T1/ptm/m/n/10 , en-tails us-ing only [1650] Overfull \hbox (4.38043pt too wide) in paragraph at lines 25697--25697 []\T1/pcr/m/n/9 plot(dist ~ speed, data = cars, main = "data(cars) & smoothi ng splines")[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 25718--25718 []\T1/pcr/m/n/9 with(cars.spl$fit, min + range * knot[-c(1:3, nk+1 +1:3)]) # = = unique(cars$speed)[] [1651] Underfull \hbox (badness 1019) in paragraph at lines 25780--25785 \T1/ptm/m/n/10 ser-va-tions closer to the be-gin-ning/end than half the win-dow \T1/pcr/m/n/10 k\T1/ptm/m/n/10 . The first and last value [1652] [1653] Overfull \hbox (0.78088pt too wide) in paragraph at lines 25911--25911 []\T1/pcr/m/n/10 spec.ar(x, n.freq, order = NULL, plot = TRUE, na.action = na. fail, [1654] [1655] [1656] [1657] [1658] [1659] [1660] Overfull \hbox (36.78088pt too wide) in paragraph at lines 26290--26290 [] \T1/pcr/m/n/10 method = c("fmm", "periodic", "natural", "monoH.FC" , "hyman"),[] [1661] [1662] Overfull \hbox (69.18036pt too wide) in paragraph at lines 26471--26471 []\T1/pcr/m/n/9 set.seed(8); x <- sort(round(rnorm(30), 1)); y <- round(sin(pi * x) + rnorm(30)/10, 3)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 26477--26477 []\T1/pcr/m/n/9 plot(x, y, main = "spline(x,y, ties=list(\"ordered\", mean) f or when x has ties")[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26486--26486 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "monoH.FC")(x), add = TRUE, c ol = 3, n = 1001)[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 26487--26487 []\T1/pcr/m/n/9 curve(splinefun(x., y., method = "hyman") (x), add = TRUE, c ol = 4, n = 1001)[] Underfull \vbox (badness 10000) has occurred while \output is active [1663] Underfull \hbox (badness 2922) in paragraph at lines 26556--26561 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1664] Overfull \hbox (9.78043pt too wide) in paragraph at lines 26593--26593 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5.2), xlim = c(-.3, 5),[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 26596--26596 [] \T1/pcr/m/n/9 {f[phi](x) == phi[1] + (phi[2]-phi[1])*~e^ {-e^{phi[3]}*~x}}))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 26605--26605 [] \T1/pcr/m/n/9 c(0 , 1 ), 1, length = 0.08, angle = 25); text(0. 5, 1, quote(1))[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26606--26606 [] \T1/pcr/m/n/9 y0 <- 1 + 4*exp(-3/4) ; t.5 <- log(2) / exp(-3/4) ; AR2 <- 3 # (Asym + R0)/2[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 26610--26610 [] \T1/pcr/m/n/9 axis(2, at = c(1,AR2,5), labels= expression(phi[2], frac(phi [1]+phi[2],2), phi[1]),[] [1665] Underfull \hbox (badness 3240) in paragraph at lines 26664--26667 [][][]\T1/pcr/m/n/10 nls[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 selfStart[][] []\T1/ptm/m/n/10 ; \T1/pcr/m/n/10 example(SSasympOff) \T1/ptm/m/n/10 gives grap h show-ing the \T1/pcr/m/n/10 SSasympOff [1666] Overfull \hbox (36.7804pt too wide) in paragraph at lines 26685--26685 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOff(xx, Asym = 5, lrc = log( 0.4), c0 = 3/4)) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26688--26688 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(-.5,6), xlim = c(-1, 8),[] [1667] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26771--26771 [] \T1/pcr/m/n/9 stopifnot( all.equal(yy, SSasympOrig(xx, Asym = 5, lrc = log (log(2)))) )[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 26775--26775 [] \T1/pcr/m/n/9 plot(xx, yy, type = "l", axes = FALSE, ylim = c(0,5), xlim = c(-1/4, 5),[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 26785--26785 [] \T1/pcr/m/n/9 axis(2, at = 5*c(1/2,1), labels= expression(frac(phi[1],2), phi[1]), pos=0, las=1)[] Overfull \hbox (106.98032pt too wide) in paragraph at lines 26790--26790 [] \T1/pcr/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] [1668] Underfull \hbox (badness 2922) in paragraph at lines 26826--26832 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 26848--26848 []\T1/pcr/m/n/9 print(getInitial(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), dat a = Indo.1),[] [1669] Overfull \hbox (25.98041pt too wide) in paragraph at lines 26864--26864 [] \T1/pcr/m/n/9 legend("topright", c("y1+y2", "y1 = 3.5 * exp(-4*x)", "y2 = 1.5 * exp(-x)"),[] [1670] Overfull \hbox (30.78088pt too wide) in paragraph at lines 26978--26978 []\T1/pcr/m/n/10 Dose * exp(lKe+lKa-lCl) * (exp(-exp(lKe)*input) - exp(-exp(lK a)*input)) [1671] Underfull \hbox (badness 2922) in paragraph at lines 27040--27045 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1672] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27078--27078 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "A", phi[2] == "B", phi[3] == "xm id", phi[4] == "scal")))[] [1673] Underfull \hbox (badness 2922) in paragraph at lines 27127--27132 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27158--27158 []\T1/pcr/m/n/9 lines(x, do.call(SSgompertz, c(list(x=x), coef(fm1))), col = " red", lwd=2)[] [1674] Underfull \hbox (badness 2922) in paragraph at lines 27192--27197 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (25.98041pt too wide) in paragraph at lines 27217--27217 []\T1/pcr/m/n/9 ## Initial values are in fact the converged one here, "Number of iter...: 0" :[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 27221--27221 []\T1/pcr/m/n/9 fm2 <- update(fm1, control=nls.control(tol = 1e-9, warnOnly=TR UE), trace = TRUE)[] [1675] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27241--27241 [] \T1/pcr/m/n/9 mtext(quote(list(phi[1] == "Asym", phi[2] == "xmid", phi[3] == "scal")))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 27251--27251 [] \T1/pcr/m/n/9 segments(c(2,2.6,2.6), c(0, 2.5,3.5), # NB. SSlogis(x = xmid = 2) = 2.5[] Underfull \hbox (badness 2922) in paragraph at lines 27286--27291 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 input\ T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1676] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27308--27308 []\T1/pcr/m/n/9 print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 27326--27326 [] \T1/pcr/m/n/9 ann = FALSE, axes = FALSE, main = "Parameters in the SS micmen model")[] [1677] Underfull \hbox (badness 6493) in paragraph at lines 27378--27383 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/pcr/m/n/10 x\T1/p tm/m/n/10 . It is the value of the ex-pres-sion Overfull \hbox (4.38043pt too wide) in paragraph at lines 27405--27405 []\T1/pcr/m/n/9 getInitial(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] [1678] Overfull \hbox (4.38043pt too wide) in paragraph at lines 27407--27407 []\T1/pcr/m/n/9 fm1 <- nls(weight ~ SSweibull(Time, Asym, Drop, lrc, pwr), dat a = Chick.6)[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 27410--27410 []\T1/pcr/m/n/9 plot(weight ~ Time, Chick.6, xlim = c(0, 21), main = "SSweibul l() fit to Chick.6")[] Overfull \hbox (69.18036pt too wide) in paragraph at lines 27413--27413 []\T1/pcr/m/n/9 As <- coef(fm1)[["Asym"]]; abline(v = 0, h = c(As, As - coef(f m1)[["Drop"]]), lty = 3)[] [1679] [1680] [1681] [1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692] Underfull \hbox (badness 3396) in paragraph at lines 28337--28339 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.glm"\T1/ptm/m/n/10 , usu-ally, a re-sult of a call to [1693] [1694] [1695] Underfull \hbox (badness 2237) in paragraph at lines 28514--28516 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1696] [1697] Underfull \hbox (badness 2591) in paragraph at lines 28678--28680 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.nls"\T1/ptm/m/n/10 , usu-ally the re-sult of a call to [1698] Underfull \hbox (badness 2237) in paragraph at lines 28724--28727 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/p cr/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if [1699] Overfull \hbox (48.78088pt too wide) in paragraph at lines 28797--28797 []\T1/pcr/m/n/10 supsmu(x, y, wt =, span = "cv", periodic = FALSE, bass = 0, t race = FALSE) [1700] [1701] Underfull \hbox (badness 3407) in paragraph at lines 28905--28909 []\T1/ptm/m/n/10 character vec-tor, one shorter than (the \T1/ptm/m/it/10 aug-m ented\T1/ptm/m/n/10 , see \T1/pcr/m/n/10 corr \T1/ptm/m/n/10 be-low) [1702] [1703] Underfull \hbox (badness 1337) in paragraph at lines 29038--29042 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1704] [1705] [1706] [1707] Overfull \hbox (9.78043pt too wide) in paragraph at lines 29286--29286 []\T1/pcr/m/n/9 persp(tt, ncp, ptn, zlim = 0:1, r = 2, phi = 20, theta = 200, main = t.tit,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29314--29314 [] \T1/pcr/m/n/10 use.factor.levels = TRUE, smooth = NULL, ylim = "com mon",[] [1708] Underfull \hbox (badness 1616) in paragraph at lines 29340--29343 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1709] Overfull \hbox (20.58041pt too wide) in paragraph at lines 29419--29419 []\T1/pcr/m/n/9 termplot(model, partial.resid = TRUE, smooth = panel.smooth, s pan.smth = 1/4)[] [1710] Overfull \hbox (0.78088pt too wide) in paragraph at lines 29496--29496 []\T1/pcr/m/n/10 terms(x, specials = NULL, abb = NULL, data = NULL, neg.out = TRUE,[] [1711] [1712] Underfull \hbox (badness 2205) in paragraph at lines 29585--29590 []\T1/ptm/m/n/10 If a \T1/pcr/m/n/10 specials \T1/ptm/m/n/10 ar-gu-ment was giv en to [][]\T1/pcr/m/n/10 terms.formula[][][] \T1/ptm/m/n/10 there is a [1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721] Overfull \hbox (12.78088pt too wide) in paragraph at lines 30180--30180 []\T1/pcr/m/n/10 ptukey(q, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE) Overfull \hbox (12.78088pt too wide) in paragraph at lines 30181--30181 []\T1/pcr/m/n/10 qtukey(p, nmeans, df, nranges = 1, lower.tail = TRUE, log.p = FALSE)[] [1722] [1723] [1724] [1725] [1726] Overfull \hbox (30.78088pt too wide) in paragraph at lines 30481--30481 [] \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 30482--30482 [] \T1/pcr/m/n/10 tol = .Machine$double.eps^0.25, maxiter = 1000, trace = 0)[] [1727] [1728] Overfull \hbox (31.3804pt too wide) in paragraph at lines 30608--30608 []\T1/pcr/m/n/9 ##--- uniroot() with new interval extension + checking feature s: --------------[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 30617--30617 []\T1/pcr/m/n/9 ## where as \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 extendInt="yes"\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 simply first enlarges the search interval:[] Underfull \vbox (badness 10000) has occurred while \output is active [1729] [1730] [1731] Underfull \hbox (badness 1337) in paragraph at lines 30834--30838 []\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 [1732] [1733] [1734] [1735] [1736] [1737] [1738] [1739] [1740] Underfull \hbox (badness 1337) in paragraph at lines 31361--31365 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1741] [1742] [1743] [1744] [1745] [1746] Overfull \hbox (0.78088pt too wide) in paragraph at lines 31788--31788 []\T1/pcr/m/n/10 xtabs(formula = ~., data = parent.frame(), subset, sparse = F ALSE, [1747] Underfull \hbox (badness 6775) in paragraph at lines 31845--31850 []\T1/ptm/m/n/10 There is a \T1/pcr/m/n/10 summary \T1/ptm/m/n/10 method for co n-tin-gency ta-ble ob-jects cre-ated by \T1/pcr/m/n/10 table \T1/ptm/m/n/10 or [1748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 31908--31908 []\T1/pcr/m/n/9 ## The Female:Rejected combination has NA \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 Freq\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 (and NA prints \TS1/pcr/m/n/9 '\T1 /pcr/m/n/9 invisibly\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 as "")[] [1749]) (./stats4-pkg.tex [1750] Chapter 11. [1751] [1752] [1753] 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))[] [1754] [1755] [1756]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} [1757] [1758] [1759]) (./tcltk-pkg.tex [1760] Chapter 12. [1761] [1762] [1763] [1764] 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[] [1765] [1766] [1767] Underfull \vbox (badness 10000) has occurred while \output is active [1768] 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 [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] 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 [1780]) (./tools-pkg.tex Chapter 13. [1781] 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.[] [1782] 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 [1783] 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)[] [1784] 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 , [1785] 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 [1786] [1787] [1788] [1789] [1790] [1791] [1792] Overfull \vbox (7.18602pt too high) has occurred while \output is active [1793] [1794] Overfull \hbox (0.78088pt too wide) in paragraph at lines 906--906 []\T1/pcr/m/n/10 resaveRdaFiles(paths, compress = c("auto", "gzip", "bzip2", " xz"),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 961--961 []\T1/pcr/m/n/9 bad <- is.na(res$ASCII) | res$ASCII | (res$size > 1e4 & res$co mpress == "none")[] [1795] [1796] [1797] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1123--1123 [] \T1/pcr/m/n/10 outputs = FALSE, sources = FALS E, ...)[] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1124--1124 []\T1/pcr/m/n/10 check_packages_in_dir_details(dir, logs = NULL, drop_ok = TRU E, ...)[] Underfull \hbox (badness 1112) in paragraph at lines 1139--1149 \T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe n-den-cies (de-fault: Underfull \hbox (badness 3724) in paragraph at lines 1139--1149 \T1/pcr/m/n/10 getOption("repos")\T1/ptm/m/n/10 ), the types of re-verse de-pen -den-cies (de-fault: [1798] Underfull \hbox (badness 1014) in paragraph at lines 1163--1165 []\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 1169--1171 []\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 1206--1209 []\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 1206--1209 \T1/ptm/m/n/10 ing \T1/pcr/m/n/10 summarize_check_packages_in_dir_results \T1/p tm/m/n/10 and [1799] Underfull \hbox (badness 10000) in paragraph at lines 1214--1217 []\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 [1800] [1801] Underfull \hbox (badness 10000) in paragraph at lines 1363--1366 []\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 [1802] [1803] [1804] [1805] [1806] Overfull \hbox (0.78088pt too wide) in paragraph at lines 1686--1686 [] \T1/pcr/m/n/10 dependencies = c("Depends", "Imports", "Linking To"),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1689--1689 [] \T1/pcr/m/n/10 utils::installed.packages(lib.loc, fields = "En hances"))[] Underfull \hbox (badness 7981) in paragraph at lines 1696--1701 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 1696--1701 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1807] [1808] [1809]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSCMD}) has been already used, duplicate ignored \relax l.1900 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [1810] [1811] [1812] [1813] Underfull \hbox (badness 1142) in paragraph at lines 2168--2174 []\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 2202--2202 []\T1/pcr/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl ogo.svg}{options: width=100}",[] [1814] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2203--2203 [] \T1/pcr/m/n/9 "\\if{latex}{\\figure{Rlogo.pdf}{options: wi dth=0.5in}}}"),[] Underfull \hbox (badness 2359) in paragraph at lines 2230--2237 []\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 2230--2237 \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 2230--2237 \T1/ptm/m/n/10 pi-la-tions in sub-di-rec-to-ries of `\T1/pcr/m/n/10 src\T1/ptm/ m/n/10 '), e.g., by adding con-fig-ure code call-ing \T1/phv/m/n/10 R \T1/ptm/m /n/10 with [1815] Underfull \hbox (badness 1342) in paragraph at lines 2282--2288 \T1/ptm/m/n/10 This al-lows e.g. the trans-la-tions shipped in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.x.y to be up-dated to those cur-rently in [1816] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2358--2358 []\T1/pcr/m/n/10 recursive = FALSE, reverse = FALSE, verbose = getOption("verb ose"))[] Underfull \hbox (badness 7981) in paragraph at lines 2371--2377 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a sub-set of Overfull \hbox (20.55087pt too wide) in paragraph at lines 2371--2377 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . [1817] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2404--2404 []\T1/pcr/m/n/9 myPkgs <- c("MASS", "Matrix", "KernSmooth", "class", "cluster" , "codetools")[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 2413--2413 [] \T1/pcr/m/n/9 which = c("Depends", "Imports", "LinkingTo ", "Suggests"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 2430--2430 [] \T1/pcr/m/n/10 align = TRUE, character_only = TRUE, include_declarations = TRUE)[] [1818] [1819] [1820] [1821] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2705--2705 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macros", "system. Rd"),[] [1822] Underfull \hbox (badness 2486) in paragraph at lines 2750--2758 []\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion 3.2.0, User-d efined macros may be given in a sep-a-rate file us-ing [1823] [1824] [1825] [1826] [1827] Underfull \hbox (badness 1072) in paragraph at lines 3128--3130 []\T1/pcr/m/n/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-to r of links, as re-turned by [1828] [1829] [1830] [1831] [1832] Overfull \hbox (72.78088pt too wide) in paragraph at lines 3464--3464 [] \T1/pcr/m/n/10 macros = file.path(R.home("share"), "Rd", "macro s", "system.Rd"))[] [1833] [1834] [1835] [1836] Underfull \hbox (badness 4108) in paragraph at lines 3712--3719 []\T1/ptm/m/n/10 This func-tion starts the in-ter-nal HTTP server, which runs o n the loop-back in-ter-face [1837] [1838] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3812--3812 [] \T1/pcr/m/n/10 types = c("examples", "tests", "vignett es"),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3815--3815 []\T1/pcr/m/n/10 testInstalledBasic(scope = c("basic", "devel", "both", "inter net"))[] Underfull \hbox (badness 10000) in paragraph at lines 3832--3834 []\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 3849--3855 []\T1/pcr/m/n/10 testInstalledBasic \T1/ptm/m/n/10 runs the ba-sic tests, if in -stalled. This should be run with [1839] [1840] Underfull \hbox (badness 7832) in paragraph at lines 3971--3974 []\T1/ptm/m/n/10 Where sup-ported (\T1/pcr/m/n/10 texi2dvi \T1/ptm/m/n/10 5.0 a nd later; \T1/pcr/m/n/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion [1841] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4047--4047 [] \T1/pcr/m/n/10 depLevel = c("Depends", "Imports", "Sugg ests"))[] [1842] Underfull \hbox (badness 1137) in paragraph at lines 4073--4075 []\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal sys-tem, as from [1843] [1844] [1845] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4258--4258 [] \T1/pcr/m/n/10 "mac.binary", "win.binary"), verbose.level = as.integer(dry run),[] [1846] [1847] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4420--4420 []\T1/pcr/m/n/10 update_pkg_po(pkgdir, pkg = NULL, version = NULL, copyright, bugs) Underfull \hbox (badness 10000) in paragraph at lines 4431--4434 []\T1/ptm/m/n/10 optional char-ac-ter strings for the `\T1/pcr/m/n/10 Copyright \T1/ptm/m/n/10 ' and [1848] Underfull \hbox (badness 6859) in paragraph at lines 4447--4452 []\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 4455--4461 []\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 4455--4461 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in t he pack-age are ex-am-ined to cre-ate a file [1849] [1850] [1851] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4654--4654 [] \T1/pcr/m/n/10 verbose = FALSE, unpacked = FALSE, subdirs = F ALSE,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 4655--4655 [] \T1/pcr/m/n/10 latestOnly = TRUE, addFiles = FALSE, rds_compr ess = "xz")[] Underfull \hbox (badness 3240) in paragraph at lines 4667--4670 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to be used in the `\T 1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/10 ', Underfull \hbox (badness 1742) in paragraph at lines 4671--4681 \T1/pcr/m/n/10 "Package"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Version"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Priority"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Depends"\T1/ptm/m/ n/10 , \T1/pcr/m/n/10 "Imports"\T1/ptm/m/n/10 , Underfull \hbox (badness 1127) in paragraph at lines 4706--4712 []\T1/pcr/m/n/10 write_PACKAGES \T1/ptm/m/n/10 scans the named di-rec-tory for R pack-ages, ex-tracts in-for-ma-tion from Underfull \hbox (badness 1635) in paragraph at lines 4706--4712 \T1/ptm/m/n/10 each pack-age's `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file , and writes this in-for-ma-tion into the `\T1/pcr/m/n/10 PACKAGES\T1/ptm/m/n/1 0 ', [1852] Underfull \hbox (badness 1571) in paragraph at lines 4734--4738 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by Underfull \hbox (badness 2772) in paragraph at lines 4760--4765 \T1/ptm/m/n/10 and `\T1/pcr/m/n/10 PACKAGES.gz\T1/ptm/m/n/10 ' files. See [][]\ T1/pcr/m/n/10 update_PACKAGES[][][] \T1/ptm/m/n/10 for ef-fi-ciently up-dat-ing ex-ist-ing [1853] [1854] [1855]) (./utils-pkg.tex [1856] Chapter 14. Underfull \hbox (badness 1072) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T 1/pcr/m/n/10 insertions\T1/ptm/m/n/10 ', [1857] [1858] [1859] [1860] 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[] [1861] Overfull \hbox (24.05087pt too wide) in paragraph at lines 376--381 \T1/pcr/m/n/10 c("vertical","horizontal","cascade","minimize","restore") [1862] Underfull \hbox (badness 10000) in paragraph at lines 382--384 []\T1/ptm/m/n/10 a [][]\T1/pcr/m/n/10 list[][][] \T1/ptm/m/n/10 of win-dow han- dles, by de-fault pro-duced by [1863] Overfull \hbox (9.78043pt too wide) in paragraph at lines 448--448 []\T1/pcr/m/n/9 # This default is useful only in SDI mode: it will tile any F irefox window[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 450--450 []\T1/pcr/m/n/9 .arrangeWindowsDefaults <- list(c("R", "all"), pattern = c("", "Firefox"))[] Overfull \hbox (60.78088pt too wide) in paragraph at lines 467--467 [] \T1/pcr/m/n/10 prompts = getOption("askYesNo", gettext(c("Yes", "No ", "Cancel"))),[] [1864] [1865] Underfull \hbox (badness 1946) in paragraph at lines 624--628 \T1/ptm/m/n/10 28. [][]$\T1/pcr/m/n/10 https : / / journal . r-[]project . org / archive / 2011-[]2 / RJournal _ 2011-[]2 _ [1866] Overfull \hbox (0.78088pt too wide) in paragraph at lines 674--674 []\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 680--680 []\T1/pcr/m/n/10 aspell_package_R_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 681--681 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 682--682 []\T1/pcr/m/n/10 aspell_package_C_files(dir, ignore = character(), control = l ist(),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 683--683 [] \T1/pcr/m/n/10 program = NULL, dictionaries = charact er())[] Underfull \hbox (badness 10000) in paragraph at lines 717--723 []\T1/ptm/m/n/10 Functions \T1/pcr/m/n/10 aspell_package_Rd_files\T1/ptm/m/n/10 , \T1/pcr/m/n/10 aspell_package_vignettes\T1/ptm/m/n/10 , Underfull \hbox (badness 4416) in paragraph at lines 717--723 \T1/pcr/m/n/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/pcr/m/n/10 aspell_ package_C_files \T1/ptm/m/n/10 per-form spell check- [1867] Overfull \hbox (0.78088pt too wide) in paragraph at lines 786--786 [] \T1/pcr/m/n/10 ignore_repo_cache = FALSE, max_repo_cache _age,[] [1868] Underfull \hbox (badness 4505) in paragraph at lines 850--856 \T1/ptm/m/n/10 this value cor-re-sponds to [][]\T1/pcr/m/n/10 getOption[][][](" available_packages_filters") \T1/ptm/m/n/10 and to [1869] [1870] [1871] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1024--1024 []\T1/pcr/m/n/10 bibentry(bibtype, textVersion = NULL, header = NULL, footer = NULL, [1872] Underfull \hbox (badness 1748) in paragraph at lines 1089--1097 []\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/pcr/m/n/10 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1/ ptm/m/n/10 , in-di-cat- Underfull \hbox (badness 2961) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f or-mat- Underfull \hbox (badness 1661) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 as [][]\T1/pcr/m/n/10 getOption[][][]("citation.bibtex.max",1) \ T1/ptm/m/n/10 which is \T1/pcr/m/n/10 1 \T1/ptm/m/n/10 typ-i-cally. Underfull \hbox (badness 1817) in paragraph at lines 1089--1097 \T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f ault by Underfull \hbox (badness 10000) in paragraph at lines 1101--1103 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [1873] Underfull \hbox (badness 10000) in paragraph at lines 1209--1212 []\T1/ptm/m/n/10 The DOI ([][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Digital _ Object _ [1874] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1292--1292 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1790--1790 [] \T1/pcr/m/n/9 data = infert, family = b inomial())))[] Overfull \hbox (66.78088pt too wide) in paragraph at lines 1825--1825 []\T1/pcr/m/n/10 changedFiles(before, after, path = before$path, timestamp = b efore$timestamp,[] [1883] [1884] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1971--1971 []\T1/pcr/m/n/9 snapshot <- fileSnapshot(dir, timestamp = tempfile("timestamp" ), md5sum=TRUE)[] [1885] [1886] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2123--2123 []\T1/pcr/m/n/10 chooseBioCmirror(graphics = getOption("menu.graphics"), ind = NULL, [1887] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2175--2175 []\T1/pcr/m/n/10 chooseCRANmirror(graphics = getOption("menu.graphics"), ind = NULL, [1888] [1889] [1890] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2344--2344 [] \T1/pcr/m/n/9 warning("Recommended package \TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 mgcv\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is not installed properly")[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2367--2367 []\T1/pcr/m/n/10 citeNatbib(keys, bib, textual = FALSE, before = NULL, after = NULL,[] [1891] [1892] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2487--2487 [] \T1/pcr/m/n/9 author = as.person("Anthony C. Davison [aut], David V. Hi nkley [aut]"),[] [1893] Underfull \hbox (badness 1082) in paragraph at lines 2561--2565 [][][]\T1/pcr/m/n/10 citation[][][] \T1/ptm/m/n/10 for more in-for-ma-tion abou t cit-ing R and R pack-ages and `\T1/pcr/m/n/10 CITATION\T1/ptm/m/n/10 ' files; pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2566 ... the Clipboard in MS Windows}{clipboard} Underfull \hbox (badness 1163) in paragraph at lines 2597--2599 []\T1/ptm/m/n/10 The Win-dows clip-board of-fers data in a num-ber of for-mats: see e.g. [][]$\T1/pcr/m/n/10 https : / / docs . [1894] [1895] Underfull \hbox (badness 10000) in paragraph at lines 2685--2687 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1896] [1897] [1898] Underfull \hbox (badness 10000) in paragraph at lines 2902--2904 []\T1/ptm/m/n/10 character string, in-di-cat-ing which type of pack-ages: see [1899] [1900] [1901] [1902] Underfull \hbox (badness 1762) in paragraph at lines 3196--3199 []\T1/ptm/m/n/10 To just look in the `\T1/pcr/m/n/10 data\T1/ptm/m/n/10 ' di-re c-tory of the cur-rent work-ing di-rec-tory, set \T1/pcr/m/n/10 package = [1903] Overfull \hbox (25.98041pt too wide) in paragraph at lines 3283--3283 []\T1/pcr/m/n/9 data(USArrests, "VADeaths") # load the data sets \TS1/pcr/m /n/9 '\T1/pcr/m/n/9 USArrests\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 VADeaths\TS1/pcr/m/n/9 '[] [1904] Underfull \hbox (badness 2452) in paragraph at lines 3359--3362 []\T1/ptm/m/n/10 The data en-try win-dow re-sponds to X re-sources of class \T1 /pcr/m/n/10 R_dataentry\T1/ptm/m/n/10 . Re-sources [1905] [1906] [1907] [1908] [1909] [1910] Overfull \hbox (74.58035pt too wide) in paragraph at lines 3768--3768 [] \T1/pcr/m/n/9 DLL.version(file.path(R.home(), "library/stats/libs", .Platf orm$r_arch, "stats.dll"))[] [1911] [1912] Underfull \hbox (badness 10000) in paragraph at lines 3849--3853 []\T1/ptm/m/n/10 Support for method \T1/pcr/m/n/10 "libcurl" \T1/ptm/m/n/10 is op-tional on Win-dows: use Underfull \hbox (badness 1072) in paragraph at lines 3906--3914 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the \T1/pcr/m/n/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the [1913] Underfull \hbox (badness 1231) in paragraph at lines 3983--3995 []\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers via en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 3997--4002 []\T1/ptm/m/n/10 Much the same scheme is sup-ported by \T1/pcr/m/n/10 method = "libcurl"\T1/ptm/m/n/10 , in-clud-ing Underfull \hbox (badness 7595) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 no_proxy\T1/ptm/m/n/10 , \T1/pcr/m/n/10 http_proxy \T1/ptm/m/n/1 0 and \T1/pcr/m/n/10 ftp_proxy\T1/ptm/m/n/10 , and for the last two a con-tents of Underfull \hbox (badness 1331) in paragraph at lines 3997--4002 \T1/pcr/m/n/10 [user:password@]machine[:port] \T1/ptm/m/n/10 where the parts in brack-ets are op-tional. See [1914] [1915] Underfull \hbox (badness 4660) in paragraph at lines 4119--4122 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 10000) in paragraph at lines 4143--4145 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/pcr/m/n/10 down load.file[][][] \T1/ptm/m/n/10 and [1916] [1917] [1918] Underfull \hbox (badness 1565) in paragraph at lines 4328--4332 []\T1/ptm/m/n/10 Data frame columns are co-erced on in-put to \T1/ptm/m/it/10 c har-ac-ter \T1/ptm/m/n/10 un-less nu-meric (in the sense of [1919] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4411--4411 [] \T1/pcr/m/n/10 character.only = FALSE, give.lines = FALSE, local = F ALSE,[] [1920] Underfull \hbox (badness 1931) in paragraph at lines 4446--4453 []\T1/ptm/m/n/10 logical (or \T1/pcr/m/n/10 "default"\T1/ptm/m/n/10 ) in-di-cat -ing if [][]\T1/pcr/m/n/10 devAskNewPage[][][](ask = TRUE) [1921] [1922] [1923] [1924] [1925] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4770--4770 []\T1/pcr/m/n/9 # Set a breakpoint in both copies of that function, assuming o ne is in the[] [1926]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.for mat}) has been already used, duplicate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.format.1}) has been already used, dupl icate ignored \relax l.4841 ...mat Unordered and Ordered Lists}{format} [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] Underfull \hbox (badness 1622) in paragraph at lines 5360--5364 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5952--5952 [] \T1/pcr/m/n/9 ## -> nicely formatted pdf -- including math formula -- for h elp(dgamma):[] [1943] Underfull \hbox (badness 10000) in paragraph at lines 6036--6038 []\T1/ptm/m/n/10 The post-ing guide ([][]$\T1/pcr/m/n/10 https : / / www . r-[] project . org / posting-[]guide . html$[][]\T1/ptm/m/n/10 ), also [1944] Underfull \hbox (badness 1502) in paragraph at lines 6085--6090 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6085--6090 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [1945] [1946] [1947] Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 10000) in paragraph at lines 6258--6267 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 R.home("docs")/html/packages.html\T1/ptm/m/n/10 ', which can be re-made by [1948] Underfull \hbox (badness 2150) in paragraph at lines 6322--6325 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See Underfull \hbox (badness 5175) in paragraph at lines 6338--6341 []\T1/pcr/m/n/10 hsearch_db() \T1/ptm/m/n/10 builds and caches the help search database for sub-se-quent use by [1949] [1950] Underfull \hbox (badness 3118) in paragraph at lines 6460--6462 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [1951] [1952] Underfull \hbox (badness 5091) in paragraph at lines 6628--6630 []\T1/ptm/m/n/10 download method, see [][]\T1/pcr/m/n/10 download.file[][][]\T1 /ptm/m/n/10 . Un-used if a non-\T1/pcr/m/n/10 NULL Underfull \hbox (badness 5331) in paragraph at lines 6644--6650 []\T1/ptm/m/n/10 logical in-di-cat-ing whether to also in-stall unin-stalled pa ck-ages which Underfull \hbox (badness 1137) in paragraph at lines 6644--6650 \T1/ptm/m/n/10 these pack-ages de-pend on/link to/import/suggest (and so on re- cur-sively). Overfull \hbox (20.55087pt too wide) in paragraph at lines 6644--6650 \T1/pcr/m/n/10 c("Depends","Imports","LinkingTo","Suggests","Enhances")\T1/ptm/ m/n/10 . Overfull \hbox (30.30977pt too wide) in paragraph at lines 6658--6665 []\T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 means to use \T1/pcr/m/n/10 c("Depends","I mports","LinkingTo","Suggests") [1953] Underfull \hbox (badness 1270) in paragraph at lines 6673--6683 \T1/ptm/m/n/10 for the `\T1/pcr/m/n/10 --configure-args\T1/ptm/m/n/10 ' flag in the call to \T1/pcr/m/n/10 R CMD INSTALL\T1/ptm/m/n/10 . If Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 []\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to be Underfull \hbox (badness 10000) in paragraph at lines 6716--6719 \T1/ptm/m/n/10 passed to \T1/pcr/m/n/10 R CMD INSTALL \T1/ptm/m/n/10 for a sour ce pack-age in-stall. E.g., [1954] Underfull \hbox (badness 10000) in paragraph at lines 6778--6782 []\T1/ptm/m/n/10 Possible val-ues of \T1/pcr/m/n/10 type \T1/ptm/m/n/10 are (cu r-rently) \T1/pcr/m/n/10 "source"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "mac.binary"\T 1/ptm/m/n/10 , Underfull \hbox (badness 2376) in paragraph at lines 6792--6799 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/pcr/m/n/1 0 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 6792--6799 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1087) in paragraph at lines 6800--6803 []\T1/ptm/m/n/10 Using pack-ages with \T1/pcr/m/n/10 type = "source" \T1/ptm/m/ n/10 al-ways works pro-vided the pack-age con-tains no [1955] Underfull \hbox (badness 1314) in paragraph at lines 6879--6886 []\T1/pcr/m/n/10 install.packages \T1/ptm/m/n/10 needs to be able to com-pute a ll the de-pen-den-cies of \T1/pcr/m/n/10 pkgs \T1/ptm/m/n/10 from [1956] Underfull \hbox (badness 10000) in paragraph at lines 6936--6941 [][][]\T1/pcr/m/n/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 a vailable.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[][ ][]\T1/ptm/m/n/10 , Overfull \hbox (25.98041pt too wide) in paragraph at lines 6959--6959 [] \T1/pcr/m/n/9 configure.args = c(RNetCDF = "--with-netcdf-include=/usr/inc lude/udunits2"))[] [1957] Underfull \hbox (badness 5133) in paragraph at lines 6995--6999 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's Underfull \hbox (badness 1983) in paragraph at lines 7009--7012 []\T1/pcr/m/n/10 installed.packages \T1/ptm/m/n/10 scans the `\T1/pcr/m/n/10 DE SCRIPTION\T1/ptm/m/n/10 ' files of each pack-age found along Overfull \hbox (9.78043pt too wide) in paragraph at lines 7056--7056 []\T1/pcr/m/n/9 plic <- installed.packages(.Library, priority = "high", fields = "License")[] [1958] [1959] Underfull \hbox (badness 4132) in paragraph at lines 7176--7178 []\T1/ptm/m/n/10 The ac-tual link-ing com-mand is con-structed by the ver-sion of \T1/pcr/m/n/10 libtool \T1/ptm/m/n/10 in-stalled at [1960] [1961] [1962] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7343--7343 []\T1/pcr/m/n/9 ls.str(mode = "list") #- what are the structured objects I h ave defined?[] [1963] [1964] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7486--7486 []\T1/pcr/m/n/10 make.socket(host = "localhost", port, fail = TRUE, server = F ALSE) [1965] Underfull \hbox (badness 10000) in paragraph at lines 7526--7528 []\T1/ptm/m/n/10 Compiling in sup-port for sock-ets was op-tional prior to \T1/ phv/m/n/10 R \T1/ptm/m/n/10 3.3.0: see [1966] [1967] Underfull \hbox (badness 10000) in paragraph at lines 7711--7713 []\T1/ptm/m/n/10 a sym-bol or char-ac-ter string nam-ing a class: only used if Underfull \hbox (badness 10000) in paragraph at lines 7716--7718 []\T1/ptm/m/n/10 typically the re-sult of \T1/pcr/m/n/10 methods(..)\T1/ptm/m/n /10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of class [1968] [1969] [1970] [1971] Underfull \hbox (badness 1859) in paragraph at lines 7939--7942 []\T1/ptm/m/n/10 logical spec-i-fy-ing that the news should be opened in the br owser (by [1972] Underfull \hbox (badness 1655) in paragraph at lines 8032--8035 []\T1/ptm/m/n/10 A data frame in-her-it-ing from class \T1/pcr/m/n/10 "news_db" \T1/ptm/m/n/10 , with [][]\T1/pcr/m/n/10 attributes[][][] "package" \T1/ptm/m/n /10 (and Overfull \hbox (25.98041pt too wide) in paragraph at lines 8043--8043 []\T1/pcr/m/n/9 db3 <- news(Version == "3.0.1" & grepl("^BUG", Category) & gre pl("PR#", Text),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8047--8047 []\T1/pcr/m/n/9 ## News from a date range (\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 Matri x\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 is there in a regular R installation):[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8055--8055 []\T1/pcr/m/n/9 ## Which categories have been in use? % R-core maybe should st andardize a bit more[] [1973] [1974] Underfull \hbox (badness 1917) in paragraph at lines 8134--8136 []\T1/pcr/m/n/10 "B"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "KiB"\T1/ptm/m/n/10 , \T1/p cr/m/n/10 "MiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "GiB"\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 "TiB"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "PiB"\T1/ptm/m/n/10 , [1975] [1976] [1977] [1978] Overfull \hbox (66.78088pt too wide) in paragraph at lines 8406--8406 [] \T1/pcr/m/n/10 date.fields = c("Date", "Packaged", "Date/Publica tion", "Built"),[] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8407--8407 [] \T1/pcr/m/n/10 tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%D", "%m/ %d/%y"),[] Overfull \hbox (84.78088pt too wide) in paragraph at lines 8408--8408 [] \T1/pcr/m/n/10 desc = packageDescription(pkg, lib.loc=lib.loc, f ields=date.fields))[] Underfull \hbox (badness 10000) in paragraph at lines 8436--8438 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/pcr /m/n/10 character[][][] \T1/ptm/m/n/10 string as from [1979] Underfull \hbox (badness 10000) in paragraph at lines 8450--8452 []\T1/pcr/m/n/10 packageVersion() \T1/ptm/m/n/10 is a con-ve-nience short-cut, al-low-ing things like \T1/pcr/m/n/10 if Underfull \hbox (badness 1259) in paragraph at lines 8458--8463 []\T1/ptm/m/n/10 If a `\T1/pcr/m/n/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, Overfull \hbox (9.78043pt too wide) in paragraph at lines 8504--8504 [] \T1/pcr/m/n/9 identical(pu, packageDate("stats"))) # as "utils" an d "stats" are[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8505--8505 [] \T1/pcr/m/n/9 # both \TS1/pcr/m/n/9 '\T1/ pcr/m/n/9 base R\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 and "Built" at same time[] [1980] [1981] Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 []\T1/ptm/m/n/10 a data frame with columns as the \T1/ptm/m/it/10 ma-trix \T1/p tm/m/n/10 re-turned by Underfull \hbox (badness 10000) in paragraph at lines 8634--8639 [][]\T1/pcr/m/n/10 installed.packages[][][] \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev-els Underfull \hbox (badness 3635) in paragraph at lines 8634--8639 \T1/pcr/m/n/10 c("ok","upgrade","unavailable")\T1/ptm/m/n/10 . Only the newest ver-sion Underfull \hbox (badness 10000) in paragraph at lines 8641--8644 \T1/ptm/m/n/10 plus \T1/pcr/m/n/10 "Status"\T1/ptm/m/n/10 , a fac-tor with lev- els \T1/pcr/m/n/10 c("installed","not [1982] [1983] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8757--8757 [] \T1/pcr/m/n/10 include = c("given", "family", "email", "role", "comme nt"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 8758--8758 [] \T1/pcr/m/n/10 braces = list(given = "", family = "", email = c("<", ">"),[] [1984] [1985] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8929--8929 [] \T1/pcr/m/n/9 "S original, "),[] [1986] [1987] Underfull \hbox (badness 1789) in paragraph at lines 9060--9062 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [1988] [1989] [1990] [1991] [1992] [1993] [1994] [1995] Underfull \hbox (badness 5203) in paragraph at lines 9633--9636 []\T1/ptm/m/n/10 Valid com-ple-tions af-ter the \T1/pcr/m/n/10 $ \T1/ptm/m/n/10 ex-trac-tor are de-ter-mined by the generic func-tion [1996] [1997] [1998] Underfull \hbox (badness 1394) in paragraph at lines 9859--9866 \T1/pcr/m/n/10 = FALSE\T1/ptm/m/n/10 . Oth-er-wise, try-ing to com-plete \T1/pc r/m/n/10 foo@ba \T1/ptm/m/n/10 will eval-u-ate \T1/pcr/m/n/10 foo\T1/ptm/m/n/10 , try-ing to com-plete [1999] Overfull \hbox (30.78088pt too wide) in paragraph at lines 9883--9883 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", " no.loss"),[] [2000] [2001] Overfull \hbox (20.58041pt too wide) in paragraph at lines 10044--10044 []\T1/pcr/m/n/9 dd <- read.DIF(file.path(udir, "exDIF.dif"), header = TRUE, tr anspose = TRUE)[] [2002] [2003] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10225--10225 []\T1/pcr/m/n/9 read.fwf(ff, widths = list(c(1,0, 2,3), c(2,2,2))) #> 1 NA 23 456 98 76 54[] [2004] [2005] Overfull \hbox (42.78088pt too wide) in paragraph at lines 10311--10311 [] \T1/pcr/m/n/10 dec = ".", numerals = c("allow.loss", "warn.loss", "no.loss"),[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10314--10314 [] \T1/pcr/m/n/10 skip = 0, check.names = TRUE, fill = !blank.lines. skip,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 10319--10319 [] \T1/pcr/m/n/10 fileEncoding = "", encoding = "unknown", text, ski pNul = FALSE)[] [2006] Underfull \hbox (badness 2027) in paragraph at lines 10391--10394 []\T1/ptm/m/n/10 Using \T1/pcr/m/n/10 row.names = NULL \T1/ptm/m/n/10 forces ro w num-ber-ing. Miss-ing or \T1/pcr/m/n/10 NULL [2007] [2008] [2009] Overfull \hbox (12.78088pt too wide) in paragraph at lines 10664--10664 []\T1/pcr/m/n/10 readRegistry(key, hive = c("HLM", "HCR", "HCU", "HU", "HCC", "HPD"), Overfull \hbox (6.78088pt too wide) in paragraph at lines 10665--10665 [] \T1/pcr/m/n/10 maxdepth = 1, view = c("default", "32-bit", "64- bit"))[] [2010] Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/ptm/m/n/10 for \T1/pcr/m/n/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/pcr/m/ n/10 HKEY_CLASSES_ROOT\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 10672--10677 \T1/pcr/m/n/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 , \T1/pcr/m/n/10 HKEY_USERS\T1/p tm/m/n/10 , \T1/pcr/m/n/10 HKEY_CURRENT_CONFIG [2011] [2012] [2013] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10905--10905 [] \T1/pcr/m/n/10 ipar <- list(mean = c(0, 1), vcov = c bind(c(1, 1), c (1, 0))) [2014] [2015] [2016] [2017] Underfull \hbox (badness 10000) in paragraph at lines 11165--11169 \T1/pcr/m/n/10 en . wikipedia . org / w / index . php ? title = Roman _ numeral s & oldid = 78252134$[][]\T1/ptm/m/n/10 . [2018] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11183--11183 []\T1/pcr/m/n/9 as.roman(c(NA, 1:3, "", strrep("I", 1:6))) # + NA with a warni ng for "IIIIII"[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11188--11188 []\T1/pcr/m/n/9 ## simple consistency checks -- arithmetic when result is in {1,2,..,3899} :[] [2019] [2020] Overfull \hbox (0.78088pt too wide) in paragraph at lines 11372--11372 []\T1/pcr/m/n/10 Rprofmem(filename = "Rprofmem.out", append = FALSE, threshold = 0) [2021] [2022] Underfull \hbox (badness 1917) in paragraph at lines 11496--11499 []\T1/ptm/m/n/10 If `\T1/pcr/m/n/10 --default-packages\T1/ptm/m/n/10 ' is not u sed, then \T1/pcr/m/n/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment vari- Underfull \hbox (badness 4328) in paragraph at lines 11496--11499 \T1/ptm/m/n/10 able \T1/pcr/m/n/10 R_SCRIPT_DEFAULT_PACKAGES\T1/ptm/m/n/10 . If this is set, then it takes prece-dence over [2023] Overfull \hbox (106.98032pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 sessionInfo()\TS1/pcr/m/n/9 '[] [2024] Underfull \hbox (badness 10000) in paragraph at lines 11582--11584 []\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 Underfull \hbox (badness 6725) in paragraph at lines 11632--11641 \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 11632--11641 \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 11632--11641 \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 11632--11641 \T1/pcr/m/n/10 from \T1/ptm/m/n/10 or \T1/pcr/m/n/10 from:descending \T1/ptm/m/ n/10 for sender (when ap-pli-ca-ble), \T1/pcr/m/n/10 size \T1/ptm/m/n/10 or [2025] [2026] Underfull \hbox (badness 3646) in paragraph at lines 11758--11760 [][][]$\T1/pcr/m/n/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/p tm/m/n/10 , [][]$\T1/pcr/m/n/10 https : / / www . gnu . org / software / [2027] Overfull \hbox (30.78088pt too wide) in paragraph at lines 11796--11796 [] \T1/pcr/m/n/10 split = FALSE, quiet = FALSE, drop.evalFALSE = F ALSE, ...)[] [2028] [2029] [2030] Underfull \hbox (badness 10000) in paragraph at lines 11977--11981 []\T1/ptm/m/n/10 The de-fault for \T1/pcr/m/n/10 stylepath \T1/ptm/m/n/10 is no w taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12008--12014 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2031] [2032] Overfull \hbox (6.78088pt too wide) in paragraph at lines 12184--12184 [] \T1/pcr/m/n/10 units = "in", type = "quartz", bg = "transpa rent")[] Underfull \hbox (badness 1009) in paragraph at lines 12202--12214 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If [2033] Underfull \hbox (badness 2600) in paragraph at lines 12239--12241 []\T1/ptm/m/n/10 The file `\T1/pcr/m/n/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ures the R GUI (\T1/pcr/m/n/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows and [2034] Underfull \hbox (badness 1043) in paragraph at lines 12282--12287 []\T1/ptm/m/n/10 At the time of writ-ing `\T1/pcr/m/n/10 Rdevga\T1/ptm/m/n/10 ' con-fig-ured the map-ping of font num-bers to fonts, and [2035] [2036] [2037] [2038] Underfull \hbox (badness 1888) in paragraph at lines 12575--12578 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the plat-form \T1/phv/m/n/10 R \T1/ptm/m/n/10 was built un-der. Where Underfull \hbox (badness 10000) in paragraph at lines 12590--12593 []\T1/ptm/m/n/10 (not al-ways present): a named list of the re-sults of call-in g [2039] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12631--12631 []\T1/pcr/m/n/9 toLatex(sI, locale = FALSE) # shortest; possibly desirable at end of report[] Underfull \hbox (badness 2158) in paragraph at lines 12686--12689 []\T1/ptm/m/n/10 Repository `\T1/pcr/m/n/10 CRAN\T1/ptm/m/n/10 ' is treated spe -cially: the value is taken from the cur-rent set-ting of [2040] Overfull \hbox (0.78088pt too wide) in paragraph at lines 12734--12734 []\T1/pcr/m/n/10 setWindowTitle(suffix, title = paste(getIdentification(), suf fix)) [2041] [2042] Underfull \hbox (badness 2302) in paragraph at lines 12891--12893 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2043] [2044] Underfull \hbox (badness 3333) in paragraph at lines 12998--13000 []\T1/pcr/m/n/10 getSrcFilename \T1/ptm/m/n/10 and \T1/pcr/m/n/10 getSrcDirecto ry \T1/ptm/m/n/10 re-turn char-ac-ter vec-tors hold-ing the file- [2045] [2046] [2047] Overfull \hbox (42.78088pt too wide) in paragraph at lines 13163--13163 [] \T1/pcr/m/n/10 format(x, trim = TRUE, drop0trailing = TRUE, ...))[] Underfull \hbox (badness 2012) in paragraph at lines 13187--13192 []\T1/ptm/m/n/10 logical; if \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 (de-fault), [][ ]\T1/pcr/m/n/10 deparse[][][](control = ) \T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 13196--13199 []\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 13196--13199 [][]\T1/pcr/m/n/10 options[][][]("width")\T1/ptm/m/n/10 ; note that this has on ly a weak ef-fect, un-less [2048] Overfull \hbox (36.7804pt too wide) in paragraph at lines 13251--13251 []\T1/pcr/m/n/9 str(.Machine, digits.d = 20) # extra digits for identification of binary numbers[] [2049] Overfull \hbox (15.18042pt too wide) in paragraph at lines 13282--13282 []\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 13289--13289 []\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 13291--13291 []\T1/pcr/m/n/9 invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) # "1 is 1" here[] [2050] [2051] Underfull \hbox (badness 10000) in paragraph at lines 13459--13461 []\T1/ptm/m/n/10 Options other than \T1/pcr/m/n/10 memory = "none" \T1/ptm/m/n/ 10 ap-ply only to files pro-duced by [2052] [2053] [2054] Underfull \hbox (badness 6300) in paragraph at lines 13616--13623 []\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 13616--13623 \T1/ptm/m/n/10 turn, and se-lected if their \T1/pcr/m/n/10 extension \T1/ptm/m/ n/10 com-po-nent matches (as a reg-exp) the file Underfull \hbox (badness 4556) in paragraph at lines 13616--13623 \T1/ptm/m/n/10 name. Ob-jects \T1/pcr/m/n/10 SweaveSyntaxNoweb \T1/ptm/m/n/10 ( with \T1/pcr/m/n/10 extension = "[.][rsRS]nw$"\T1/ptm/m/n/10 ) and [2055] [2056] Underfull \hbox (badness 2020) in paragraph at lines 13785--13801 \T1/ptm/m/n/10 si-bly use-ful val-ues in-clude `\T1/pcr/m/n/10 -h\T1/ptm/m/n/10 ' (fol-low sym-bolic links, also `\T1/pcr/m/n/10 -L\T1/ptm/m/n/10 ' on some pl at-forms), Underfull \hbox (badness 1194) in paragraph at lines 13785--13801 \T1/ptm/m/n/10 `\T1/pcr/m/n/10 --acls\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclud e-backups\T1/ptm/m/n/10 ', `\T1/pcr/m/n/10 --exclude-vcs\T1/ptm/m/n/10 ' (and s im-i-lar) and on Win-dows [2057] [2058] Underfull \hbox (badness 5022) in paragraph at lines 13925--13929 []\T1/ptm/m/n/10 When ar-gu-ment \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 is set to th e com-mand \T1/pcr/m/n/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-abl e Underfull \hbox (badness 10000) in paragraph at lines 13932--13935 [][][]$\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 13932--13935 \T1/pcr/m/n/10 opengroup . org / onlinepubs / 9699919799 / utilities / pax . ht ml # tag _ 20 _ [2059] [2060] [2061] Overfull \hbox (18.78088pt too wide) in paragraph at lines 14096--14096 [] \T1/pcr/m/n/10 numerals = c("allow.loss", "warn.loss", "no.loss "), ...)[] [2062] [2063] [2064] [2065] [2066] [2067] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14536--14536 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 14542--14542 [] \T1/pcr/m/n/10 instPkgs = installed.packages(lib.loc = lib.loc, ...),[] Underfull \hbox (badness 4467) in paragraph at lines 14563--14565 []\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 14576--14580 \T1/ptm/m/n/10 able at the repos-i-to-ries, or \T1/pcr/m/n/10 NULL \T1/ptm/m/n/ 10 which makes an in-ter-nal call to Underfull \hbox (badness 1694) in paragraph at lines 14590--14594 []\T1/ptm/m/n/10 by de-fault all in-stalled pack-ages, [][]\T1/pcr/m/n/10 insta lled.packages[][][](lib.loc = Underfull \hbox (badness 10000) in paragraph at lines 14596--14601 []\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 14596--14601 \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 14596--14601 \T1/pcr/m/n/10 max_repo_cache_age \T1/ptm/m/n/10 and \T1/pcr/m/n/10 noCache \T1 /ptm/m/n/10 to [][]\T1/pcr/m/n/10 available.packages[][][] Underfull \hbox (badness 1052) in paragraph at lines 14602--14604 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See [2068] Underfull \hbox (badness 10000) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 available = NULL \T1/ptm/m/n/10 make a call to \T1/pcr/m/n/10 av ailable.packages(contriburl = Underfull \hbox (badness 1509) in paragraph at lines 14632--14637 \T1/pcr/m/n/10 contriburl,method = method) \T1/ptm/m/n/10 and hence by de-fault fil-ters on \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sion, OS type Underfull \hbox (badness 10000) in paragraph at lines 14653--14658 []\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 14661--14664 [][][]\T1/pcr/m/n/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 download.packages[] [][]\T1/ptm/m/n/10 , [2069] Overfull \hbox (9.78043pt too wide) in paragraph at lines 14715--14715 []\T1/pcr/m/n/9 ## Not run: url.show("http://www.stats.ox.ac.uk/pub/datasets/c sb/ch3a.txt") [2070] [2071] [2072] Underfull \hbox (badness 10000) in paragraph at lines 14917--14920 [][][]\T1/pcr/m/n/10 browseVignettes[][][] \T1/ptm/m/n/10 for an HTML-based vi- gnette browser; Underfull \hbox (badness 1253) in paragraph at lines 14917--14920 [][]\T1/pcr/m/n/10 RShowDoc[][][](,package = "") \T1/ptm/m/n/10 dis-plays a ``ren-dered'' vi-gnette (pdf or [2073] Overfull \hbox (42.18039pt too wide) in paragraph at lines 14933--14933 []\T1/pcr/m/n/9 ## Note that \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 package = *\TS1/pcr /m/n/9 ' \T1/pcr/m/n/9 is much faster in the case of many installed packages:[] [2074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 15000--15000 [] \T1/pcr/m/n/9 lm(weight ~ (Time + I(Time^2)) * Diet, d ata = DAT)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 15022--15022 [] \T1/pcr/m/n/9 nls(weight ~ SSlogis(Time, Asym, xmid, scal), data = DD)))[] [2075] [2076] Underfull \hbox (badness 1297) in paragraph at lines 15153--15155 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the ac-tion when that menu i s se-lected, or [2077] Underfull \hbox (badness 4036) in paragraph at lines 15200--15202 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 winMenuDel \T1/ptm/m/n/10 func-tion will de lete a menu and all of its items and sub-menus. [2078] [2079] Overfull \hbox (0.78088pt too wide) in paragraph at lines 15337--15337 []\T1/pcr/m/n/10 write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ", [2080] Underfull \hbox (badness 1715) in paragraph at lines 15389--15392 []\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 15434--15436 []\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec- tion e.g. \T1/pcr/m/n/10 file = [2081] [2082] [2083]) [2084] [2085] [2086] (./KernSmooth-pkg.tex Chapter 15. [2087] 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) [2088] [2089] [2090] [2091] [2092] 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, [2093] [2094] [2095] [2096]) (./MASS-pkg.tex Chapter 16. [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] [2106] [2107] 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))[] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117] [2118] [2119] [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] 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"),[] [2131] [2132] [2133] [2134] 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 [2135] [2136] [2137] 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 10000) 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 , [2138] [2139] 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 [2140] [2141] [2142] 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, ...)[] [2143] 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")[] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] 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 [2156] [2157] [2158] [2159] [2160] [2161] [2162] 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", ...)[] [2163] [2164] [2165] 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, [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175] [2176] [2177] [2178] [2179] 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) [2180] 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") [2181] [2182]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} [2183] 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 [2184] [2185] [2186] [2187] Underfull \vbox (badness 10000) has occurred while \output is active [2188] 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)))[] [2189] 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"))[] [2190] [2191] [2192] [2193] [2194] [2195] 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"))[] [2196] 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 ) = [2197] 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)[] [2198] [2199] 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 [2200] [2201] 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")[] [2202] 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"), ...)[] [2203] [2204] [2205] [2206] [2207] [2208] 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 [2209] [2210] 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 [2211] [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] 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, ...)[] [2231] Underfull \hbox (badness 2035) in paragraph at lines 9595--9597 []\T1/ptm/m/n/10 ``Fold your arms! Which is on top'' (Fac-tor, with lev-els \T1 /pcr/m/n/10 "R on L"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "L on R"\T1/ptm/m/n/10 , Underfull \hbox (badness 1158) in paragraph at lines 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), [2232] 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)[] [2233] [2234] [2235] [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] [2245]) (./Matrix-pkg.tex [2246] Chapter 17. Underfull \hbox (badness 10000) in paragraph at lines 41--44 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 41--44 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2247] Underfull \hbox (badness 1769) in paragraph at lines 95--98 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2248] Underfull \hbox (badness 2229) in paragraph at lines 159--162 []\T1/ptm/m/n/10 in gen-eral an ar-bi-trary num-ber of \T1/phv/m/n/10 R \T1/ptm /m/n/10 ob-jects; here, when the first is Underfull \hbox (badness 1147) in paragraph at lines 159--162 \T1/ptm/m/n/10 an \T1/pcr/m/n/10 "[][]abIndex[][][]" \T1/ptm/m/n/10 vec-tor, th ese ar-gu-ments will be con-cate-nated to a new [2249] 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 [2250] [2251] Overfull \hbox (42.78088pt too wide) in paragraph at lines 488--488 []\T1/pcr/m/n/10 bandSparse(n, m = n, k, diagonals, symmetric = FALSE, giveCsp arse = TRUE) 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 [2252] 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)],[] [2253] [2254] Overfull \hbox (52.98038pt too wide) in paragraph at lines 660--660 []\T1/pcr/m/n/9 ##\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 Fast version of Matrix :: .bd iag() -- for the case of *many* (k x k) matrices:[] 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)[] [2255] Underfull \hbox (badness 3189) in paragraph at lines 732--736 []\T1/ptm/m/n/10 The orig-i-nal LA-PACK source code, in-clud-ing doc-u-men-ta-t ion; [][]$\T1/pcr/m/n/10 http : / / www . netlib . [2256] [2257] [2258] 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"), ...)[] [2259] [2260]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.chol}) 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} [2261pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol,dsCMatrix.Rdash.method}) ha s been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' pdfTeX warning (ext4): destina tion with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.method}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.1163 ## S4 method for signature 'dsparseMatrix' ] Underfull \hbox (badness 2285) in paragraph at lines 1220--1225 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2262] 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[] [2263] 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 [2264] Underfull \hbox (badness 1609) in paragraph at lines 1435--1439 []\T1/ptm/m/n/10 Class def-i-ni-tions [][]\T1/pcr/m/n/10 CHMfactor[][][] \T1/pt m/m/n/10 and [][]\T1/pcr/m/n/10 dsCMatrix[][][] \T1/ptm/m/n/10 and func-tion [] []\T1/pcr/m/n/10 expand[][][]\T1/ptm/m/n/10 . Note the ex-tra [2265] 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)))[] [2266] Underfull \hbox (badness 10000) in paragraph at lines 1531--1538 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("Cholesky",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 5316) in paragraph at lines 1531--1538 \T1/pcr/m/n/10 new("BunchKaufman",...)\T1/ptm/m/n/10 , etc, or rather by calls of the form [][]\T1/pcr/m/n/10 chol[][][](pm) \T1/ptm/m/n/10 or 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 [2267]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} [2268] Underfull \hbox (badness 2922) in paragraph at lines 1710--1714 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be sparse, i.e., i n-her-it-ing from Underfull \hbox (badness 1728) in paragraph at lines 1710--1714 \T1/ptm/m/n/10 class [][]\T1/pcr/m/n/10 sparseVector[][][]\T1/ptm/m/n/10 . Only ap-pli-ca-ble when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is in-her-it-ing from a Underfull \hbox (badness 1237) in paragraph at lines 1721--1724 [][][]\T1/pcr/m/n/10 dimnames[][][](x) \T1/ptm/m/n/10 are only kept (as [][]\T1 /pcr/m/n/10 names[][][](v)\T1/ptm/m/n/10 ) when the re-sult-ing \T1/pcr/m/n/10 v \T1/ptm/m/n/10 is [][]\T1/pcr/m/n/10 numeric[][][]\T1/ptm/m/n/10 , since [2269] [2270] Underfull \hbox (badness 3547) in paragraph at lines 1875--1878 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2271] [2272] [2273] [2274] [2275] Underfull \hbox (badness 1484) in paragraph at lines 2234--2236 []\T1/ptm/m/n/10 Use [][]\T1/pcr/m/n/10 showMethods[][][](class = "denseMatrix" ,where = "package:Matrix") \T1/ptm/m/n/10 for an [2276] Underfull \hbox (badness 7379) in paragraph at lines 2330--2332 []\T1/pcr/m/n/10 signature(x = "dgCMatrix")\T1/ptm/m/n/10 : com-putes the LU de -com-po-si-tion of a square [2277] [2278] [2279] Underfull \hbox (badness 4846) in paragraph at lines 2605--2609 []\T1/ptm/m/n/10 Note that both \T1/pcr/m/n/10 new(.) \T1/ptm/m/n/10 and [][]\T 1/pcr/m/n/10 spMatrix[][][] \T1/ptm/m/n/10 con-struc-tors for \T1/pcr/m/n/10 "d gTMatrix" \T1/ptm/m/n/10 (and other Underfull \hbox (badness 2368) in paragraph at lines 2610--2614 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i n more than one pos-si-ble Underfull \hbox (badness 10000) in paragraph at lines 2617--2620 []\T1/ptm/m/n/10 Class [][]\T1/pcr/m/n/10 dgCMatrix[][][] \T1/ptm/m/n/10 or the su-per-classes [][]\T1/pcr/m/n/10 dsparseMatrix[][][] \T1/ptm/m/n/10 and [][]\ T1/pcr/m/n/10 TsparseMatrix[][][]\T1/ptm/m/n/10 ; [2280] Underfull \hbox (badness 2689) in paragraph at lines 2673--2675 []\T1/ptm/m/n/10 integer spec-i-fy-ing the di-men-sion of the (square) ma-trix. If miss-ing, Underfull \hbox (badness 10000) in paragraph at lines 2677--2682 []\T1/ptm/m/n/10 for \T1/pcr/m/n/10 .symDiagonal \T1/ptm/m/n/10 (\T1/pcr/m/n/10 .trDiagonal\T1/ptm/m/n/10 ), the re-sult-ing sparse Underfull \hbox (badness 3482) in paragraph at lines 2677--2682 [][]\T1/pcr/m/n/10 symmetricMatrix[][][] \T1/ptm/m/n/10 (or [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 ) will have slot \T1/pcr/m/n/10 uplo [2281] Underfull \hbox (badness 1097) in paragraph at lines 2700--2703 []\T1/pcr/m/n/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T1 /pcr/m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/pcr/m/n/10 ldiMatrix[][][ ] \T1/ptm/m/n/10 (with ``su-per-class'' Underfull \hbox (badness 1142) in paragraph at lines 2713--2718 [][]\T1/pcr/m/n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 (the re-sult-ing class de -pend-ing on \T1/pcr/m/n/10 shape \T1/ptm/m/n/10 and \T1/pcr/m/n/10 kind\T1/ptm /m/n/10 ) rep-re-sen-ta-tion of [2282] Underfull \hbox (badness 3646) in paragraph at lines 2951--2954 []\T1/ptm/m/n/10 the [][]\T1/pcr/m/n/10 dimnames[][][]\T1/ptm/m/n/10 , a [][]\T 1/pcr/m/n/10 list[][][]\T1/ptm/m/n/10 , see the [][]\T1/pcr/m/n/10 Matrix[][][] \T1/ptm/m/n/10 class de-scrip-tion. Typ-i-cally Underfull \hbox (badness 10000) in paragraph at lines 2983--2985 []\T1/pcr/m/n/10 signature(x = "nMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv -a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion Underfull \hbox (badness 6542) in paragraph at lines 2986--2990 []\T1/pcr/m/n/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these grou p meth-ods re-turn a Underfull \hbox (badness 5652) in paragraph at lines 2995--3001 []\T1/pcr/m/n/10 signature(e1 = "ddiMatrix",e2="denseMatrix")\T1/ptm/m/n/10 : t he re-sult is from class [2283] Underfull \hbox (badness 10000) in paragraph at lines 3002--3006 []\T1/pcr/m/n/10 (object = "diagonalMatrix")\T1/ptm/m/n/10 : Re-turns an ob-jec t of S3 class Underfull \hbox (badness 2318) in paragraph at lines 3012--3016 [][][]\T1/pcr/m/n/10 Diagonal[][][]() \T1/ptm/m/n/10 as con-struc-tor of these ma-tri-ces, and [][]\T1/pcr/m/n/10 isDiagonal[][][]\T1/ptm/m/n/10 . [][]\T1/pcr /m/n/10 ddiMatrix[][][] \T1/ptm/m/n/10 and [2284] [2285] Underfull \hbox (badness 10000) in paragraph at lines 3196--3198 []\T1/pcr/m/n/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : th is group con-tains Underfull \hbox (badness 10000) in paragraph at lines 3243--3245 [][][]\T1/pcr/m/n/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pref er-able to (and more ef-fi-cient than) [2286] Underfull \hbox (badness 2469) in paragraph at lines 3363--3366 []\T1/pcr/m/n/10 signature(x = "dpoMatrix")\T1/ptm/m/n/10 : Re-turns the [][]\T 1/pcr/m/n/10 determinant[][][] \T1/ptm/m/n/10 of \T1/pcr/m/n/10 x\T1/ptm/m/n/10 , via [2287] [2288] Underfull \hbox (badness 10000) in paragraph at lines 3528--3532 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsCMatrix",...) \T1/ptm/m/n/10 or Underfull \hbox (badness 3815) in paragraph at lines 3528--3532 \T1/pcr/m/n/10 new("dsTMatrix",...)\T1/ptm/m/n/10 , or au-to-mat-i-cally via e. g., \T1/pcr/m/n/10 as(*,"symmetricMatrix")\T1/ptm/m/n/10 , [2289] Underfull \hbox (badness 2285) in paragraph at lines 3578--3581 []\T1/pcr/m/n/10 signature(x = "dsCMatrix",pivot = "logical")\T1/ptm/m/n/10 : R e-turns (and stores) the [2290] [2291] Underfull \hbox (badness 10000) in paragraph at lines 3725--3730 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "dMatrix"\T1/ptm/m/n/10 , by class \T1/pc r/m/n/10 "dsparseMatrix"\T1/ptm/m/n/10 , class \T1/pcr/m/n/10 "sparseMatrix"\T1 /ptm/m/n/10 , by Underfull \hbox (badness 6961) in paragraph at lines 3725--3730 \T1/ptm/m/n/10 class \T1/pcr/m/n/10 "dsparseMatrix" \T1/ptm/m/n/10 or \T1/pcr/m /n/10 "RsparseMatrix"\T1/ptm/m/n/10 ; class \T1/pcr/m/n/10 "compMatrix" \T1/ptm /m/n/10 by class Underfull \hbox (badness 2608) in paragraph at lines 3737--3740 []\T1/pcr/m/n/10 signature(x = "dsRMatrix",uplo = "character")\T1/ptm/m/n/10 : if \T1/pcr/m/n/10 uplo == [2292] Underfull \hbox (badness 10000) in paragraph at lines 3813--3815 []\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/pcr/m/n/10 ne w("dsyMatrix",...) \T1/ptm/m/n/10 or [2293] [2294] [2295] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4023--4023 []\T1/pcr/m/n/9 U5 <- new("dtCMatrix", i= c(1L, 0:3), p=c(0L,0L,0:2, 5L), Dim = c(5L, 5L),[] Underfull \hbox (badness 3635) in paragraph at lines 4091--4095 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ddenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class [2296] Underfull \hbox (badness 10000) in paragraph at lines 4100--4103 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 4100--4103 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 4105--4109 []\T1/pcr/m/n/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/10 : the [2297] [2298] Underfull \hbox (badness 3158) in paragraph at lines 4288--4292 []\T1/pcr/m/n/10 signature(a = "dtrMatrix",b = "....")\T1/ptm/m/n/10 efficiente ly use a ``for-ward-solve'' or [2299] [2300] [2301] [2302] Overfull \hbox (85.38034pt too wide) in paragraph at lines 4527--4527 [] \T1/pcr/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/ Boeing/msc00726.tar.gz"))))[] Overfull \hbox (139.38028pt too wide) in paragraph at lines 4530--4530 [] \T1/pcr/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe ll-Boeing/counterx/jgl009.mtx.gz"))))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4534--4534 []\T1/pcr/m/n/9 ## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4537--4537 []\T1/pcr/m/n/9 file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s)[] Overfull \hbox (58.38037pt too wide) in paragraph at lines 4547--4547 []\T1/pcr/m/n/9 ## has columns (i, j, x) -> we can use via do.call() as argume nts to sparseMatrix():[] [2303] [2304] [2305] [2306] Underfull \hbox (badness 10000) in paragraph at lines 4849--4854 []\T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 compMatrix[][][]\T1/ptm/m/n/10 , an d the non-general vir-tual classes: [][]\T1/pcr/m/n/10 symmetricMatrix[][][]\T1 /ptm/m/n/10 , [2307] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4930--4930 []\T1/pcr/m/n/9 if(isTRUE(try(require(graph)))) { ## super careful .. for "che cking reasons" Overfull \hbox (20.58041pt too wide) in paragraph at lines 4932--4932 [] \T1/pcr/m/n/9 show(a1 <- sparseMatrix(i= c(1:4), j=c(2:4,1), x = 2, dimnames=dns))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4936--4936 [] \T1/pcr/m/n/9 show(a2 <- sparseMatrix(i= c(1:4,4), j=c(2:4,1:2), x = TRUE, dimnames=dns))[] [2308] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4943--4943 [] \T1/pcr/m/n/9 a. <- sparseMatrix(i= 4:1, j=1:4, dimnames=list(n4,n4), give C=FALSE) # no \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 x\TS1/pcr/m/n/9 '[] [2309] [2310] Underfull \hbox (badness 4120) in paragraph at lines 5087--5090 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ]\T1/pcr/m/n/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use Overfull \hbox (15.18042pt too wide) in paragraph at lines 5124--5124 []\T1/pcr/m/n/9 ## Using (xlim,ylim) has advantage : matrix dimension and (col /row) indices:[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5130--5130 [] \T1/pcr/m/n/9 I2 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, border.col=NA)[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5131--5131 [] \T1/pcr/m/n/9 I3 <- image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd =2, border.col=NA)[] Overfull \hbox (144.78027pt too wide) in paragraph at lines 5134--5134 []\T1/pcr/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5136--5136 []\T1/pcr/m/n/9 if(doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CH ECK_EXTRA")) ||[] [2311] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5143--5143 []\T1/pcr/m/n/9 image(USCounties, useRaster = TRUE) # should not suffer from a nti-aliasing[] Overfull \hbox (36.7804pt too wide) in paragraph at lines 5146--5146 [] \T1/pcr/m/n/9 ## and now look at the *.png image in a viewer you can easi ly zoom in and out[] [2312] Underfull \hbox (badness 1817) in paragraph at lines 5235--5244 []\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o r \T1/ptm/m/n/10 us-ing \T1/pcr/m/n/10 drop=FALSE\T1/ptm/m/n/10 ) stays within the Underfull \hbox (badness 10000) in paragraph at lines 5277--5279 []\T1/pcr/m/n/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 10000) in paragraph at lines 5279--5282 []\T1/pcr/m/n/10 signature(from = "integer",to = "indMatrix")\T1/ptm/m/n/10 : T his en-ables typ-i-cal Underfull \hbox (badness 1394) in paragraph at lines 5292--5295 []\T1/pcr/m/n/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : co -er-cion to a tra-di-tional [2313] Underfull \hbox (badness 4765) in paragraph at lines 5310--5313 []\T1/pcr/m/n/10 signature(X = "indMatrix",Y = "indMatrix")\T1/ptm/m/n/10 : re- turn the kro-necker [2314] Overfull \hbox (31.3804pt too wide) in paragraph at lines 5370--5370 [] \T1/pcr/m/n/9 if(getRversion() >= "3.2.0") identical(I12, rbind(I1 , I2)) else TRUE,[] [2315] [2316] [2317] Overfull \hbox (25.98041pt too wide) in paragraph at lines 5628--5628 []\T1/pcr/m/n/9 showMethods("isSymmetric", includeDefs=TRUE)# "ANY": base\TS1/ pcr/m/n/9 '\T1/pcr/m/n/9 s S3 generic; 6 more[] [2318] Underfull \hbox (badness 10000) in paragraph at lines 5709--5712 [][][]\T1/pcr/m/n/10 isSymmetric[][][]\T1/ptm/m/n/10 ; for-mal class (and sub-c lasses) \T1/pcr/m/n/10 "[][]triangularMatrix[][][]" \T1/ptm/m/n/10 and Overfull \hbox (9.78043pt too wide) in paragraph at lines 5720--5720 []\T1/pcr/m/n/9 isTriangular(as(M, "dgeMatrix")) # still triangular, even if n ot "formally"[] [2319] Underfull \hbox (badness 1622) in paragraph at lines 5757--5762 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 "[][]CsparseMatrix[][][]"\T1/ptm/m/n/10 , say \T1/pcr/m/n/10 R\T1/ptm/m/n/10 , the Khatri-Rao prod-uct of \T1/pcr/m/n/10 X \ T1/ptm/m/n/10 ($\OML/cmm/m/it/10 n \OMS/cmsy/m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ ptm/m/n/10 ) and \T1/pcr/m/n/10 Y \T1/ptm/m/n/10 ($\OML/cmm/m/it/10 m \OMS/cmsy /m/n/10 ^^B \OML/cmm/m/it/10 k$\T1/ptm/m/n/10 ), Underfull \hbox (badness 1418) in paragraph at lines 5757--5762 \T1/ptm/m/n/10 is of di-men-sion $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 n \OMS/cmsy /m/n/10 ^^A \OML/cmm/m/it/10 m\OT1/cmr/m/n/10 ) \OMS/cmsy/m/n/10 ^^B \OML/cmm/m /it/10 k$\T1/ptm/m/n/10 , where the j-th col-umn, \T1/pcr/m/n/10 R[,j] \T1/ptm/ m/n/10 is the kro-necker prod-uct [2320] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5818--5818 []\T1/pcr/m/n/9 stopifnot(all(K1 <- KhatriRao(nd, zm) == 0), identical(dim(K1) , c(12L, 4L)),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5819--5819 [] \T1/pcr/m/n/9 all(K2 <- KhatriRao(zm, nd) == 0), identical(dim(K2) , c(12L, 4L)))[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 5826--5826 [] \T1/pcr/m/n/9 identical(dimnames(KhatriRao(m, d0, make.dimnames=TRUE)), di mnames(Kmd)))[] [2321] Underfull \hbox (badness 1062) in paragraph at lines 5955--5958 []\T1/pcr/m/n/10 ldenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2322] Underfull \hbox (badness 6063) in paragraph at lines 5984--5987 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2323] Underfull \hbox (badness 2635) in paragraph at lines 6096--6101 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ldense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 6096--6101 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ldenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 6104--6107 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2324] Underfull \hbox (badness 10000) in paragraph at lines 6214--6224 \T1/pcr/m/n/10 lsTMatrix\T1/ptm/m/n/10 , and \T1/pcr/m/n/10 ltTMatrix\T1/ptm/m/ n/10 ) or in com-pressed column-oriented form (class Underfull \hbox (badness 1242) in paragraph at lines 6214--6224 [][]\T1/pcr/m/n/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/ 10 lgCMatrix\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lsCMatrix\T1/ptm/m/n/10 , and \T1/p cr/m/n/10 ltCMatrix\T1/ptm/m/n/10 ) or--\T1/ptm/m/it/10 rarely\T1/ptm/m/n/10 -- in [2325] Underfull \hbox (badness 3179) in paragraph at lines 6296--6299 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2326] Underfull \hbox (badness 10000) in paragraph at lines 6394--6397 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2327] Underfull \hbox (badness 10000) in paragraph at lines 6469--6472 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., Overfull \hbox (25.98041pt too wide) in paragraph at lines 6485--6485 []\T1/pcr/m/n/9 str(lutp <- as(lutr, "ltpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] [2328] Underfull \hbox (badness 2443) in paragraph at lines 6524--6530 []\T1/ptm/m/n/10 (when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is a \T1/pcr/m/n/10 "[][ ]sparseMatrix[][][]"\T1/ptm/m/n/10 ) log-i-cal spec-i-fy-ing if an er-ror (see Underfull \hbox (badness 1776) in paragraph at lines 6524--6530 [][]\T1/pcr/m/n/10 stop[][][]\T1/ptm/m/n/10 ) should be sig-nalled when \T1/pcr /m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar. When \T1/pcr/m/n/10 x \T1/ptm/m/n/10 is sin-gu-lar, Underfull \hbox (badness 1675) in paragraph at lines 6545--6548 []\T1/pcr/m/n/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth- ods for dif-fer-ent types of ma-tri-ces. Use [2329] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6615--6615 [] \T1/pcr/m/n/9 # q is a 0-based permutation o f the columns[] [2330] [2331] Underfull \hbox (badness 6268) in paragraph at lines 6751--6754 []\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math- e-mat-i-cally''), Underfull \hbox (badness 5036) in paragraph at lines 6775--6779 []\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1 /ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/pcr/m/n/10 matrix[][][]\T1/ptm/m/n/10 . How-ever, Underfull \hbox (badness 10000) in paragraph at lines 6775--6779 \T1/pcr/m/n/10 Matrix(0,nrow,ncol) \T1/ptm/m/n/10 di-rectly con-structs an ``em pty'' [][]sparse-Ma-trix[][][], as does [2332] [2333]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.det}) has been already used, duplicate ignored \relax l.6868 \aliasA{det}{Matrix-class}{det} Underfull \hbox (badness 10000) in paragraph at lines 6971--6974 Underfull \hbox (badness 10000) in paragraph at lines 6981--6983 []\T1/pcr/m/n/10 signature(from = "ANY",to = "Matrix")\T1/ptm/m/n/10 : This re- lies on a cor-rect [2334]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp cent.*.Rpcent.}) has been already used, duplicate ignored \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} Underfull \hbox (badness 1881) in paragraph at lines 7350--7356 \T1/ptm/m/n/10 ally im-ple-mented ef-fi-ciently with-out com-put-ing [][]\T1/pc r/m/n/10 t[][][](.)\T1/ptm/m/n/10 's un-nec-es-sar-ily. They also re-turn [2335] [2336pdfTeX warning (ext4): destination with the same identifier (name{R fn.crossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrossprod.Rdash.methods}) has been already used, duplicate ignored \AtBegShi@Output ...ipout \box \AtBeginShipoutBox \fi \fi l.7412 \end{Details} ] Underfull \hbox (badness 10000) in paragraph at lines 7423--7426 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : Ma- trix mul-ti-pli-ca-tion; Underfull \hbox (badness 1199) in paragraph at lines 7423--7426 \T1/ptm/m/n/10 ditto for sev-eral other sig-na-ture com-bi-na-tions, see \T1/pc r/m/n/10 showMethods("%*%",class = Underfull \hbox (badness 10000) in paragraph at lines 7426--7431 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na-tures (use Underfull \hbox (badness 1371) in paragraph at lines 7426--7431 \T1/pcr/m/n/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix mu l-ti-pli-ca-tion. Mul-ti-pli- Underfull \hbox (badness 1502) in paragraph at lines 7431--7435 []\T1/pcr/m/n/10 signature(x = "dgeMatrix",y = "dgeMatrix")\T1/ptm/m/n/10 : dit to for sev-eral other Underfull \hbox (badness 10000) in paragraph at lines 7431--7435 \T1/ptm/m/n/10 sig-na-tures, use \T1/pcr/m/n/10 showMethods("crossprod",class = "dgeMatrix")\T1/ptm/m/n/10 , ma-trix Underfull \hbox (badness 2837) in paragraph at lines 7441--7442 []\T1/pcr/m/n/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and oth er sig-na- [2337] [2338] Underfull \hbox (badness 1009) in paragraph at lines 7577--7579 []\T1/pcr/m/n/10 signature(a = "MatrixFactorization",b= .)\T1/ptm/m/n/10 : solv e $\OML/cmm/m/it/10 Ax \OT1/cmr/m/n/10 = \OML/cmm/m/it/10 b$ \T1/ptm/m/n/10 for $\OML/cmm/m/it/10 x$\T1/ptm/m/n/10 ; see Underfull \hbox (badness 1062) in paragraph at lines 7622--7625 []\T1/pcr/m/n/10 ndenseMatrix \T1/ptm/m/n/10 is the vir-tual class of all dense \T1/ptm/b/n/10 l\T1/ptm/m/n/10 ogical (S4) ma-tri-ces. It ex-tends both [2339] Underfull \hbox (badness 6063) in paragraph at lines 7656--7659 []\T1/pcr/m/n/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2340] Underfull \hbox (badness 10000) in paragraph at lines 7708--7710 []\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/pcr/m/n/10 X <-(X + t(X))/2 \T1/p tm/m/n/10 should be done, af-ter \T1/pcr/m/n/10 X [2341] [2342] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7847--7847 []\T1/pcr/m/n/9 stopifnot(all.equal(ncr, ncF))# norm type does not matter at a ll in this example[] Underfull \vbox (badness 10000) has occurred while \output is active [2343] Underfull \hbox (badness 2635) in paragraph at lines 7912--7917 []\T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/pcr/m/n/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/pcr/m/n/10 "ndense Matrix"\T1/ptm/m/n/10 . Underfull \hbox (badness 4229) in paragraph at lines 7912--7917 \T1/ptm/m/n/10 Class \T1/pcr/m/n/10 "denseMatrix"\T1/ptm/m/n/10 , by class \T1/ pcr/m/n/10 "ndenseMatrix"\T1/ptm/m/n/10 . Class \T1/pcr/m/n/10 "Matrix"\T1/ptm/ m/n/10 , by class Underfull \hbox (badness 10000) in paragraph at lines 7920--7923 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ); us e, e.g., [2344] Underfull \hbox (badness 3482) in paragraph at lines 7994--8000 []\T1/pcr/m/n/10 signature(from = "matrix",to = "nMatrix")\T1/ptm/m/n/10 : Note that these co-er-cions [2345] Underfull \hbox (badness 1867) in paragraph at lines 8114--8116 []\T1/ptm/m/n/10 fast sim- [2346]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.nor m}) has been already used, duplicate ignored \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} pdfTeX warning (ext4): destination wit h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor ed \relax l.8154 \HeaderA{norm}{Matrix Norms}{norm} [2347] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8241--8241 []\T1/pcr/m/n/9 A <- sparseMatrix(i, j, x = x) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8242--8242 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8243--8243 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Underfull \hbox (badness 2401) in paragraph at lines 8356--8366 []\T1/ptm/m/n/10 These can be stored in the ``triplet'' form ([][]\T1/pcr/m/n/1 0 TsparseMatrix[][][]\T1/ptm/m/n/10 , sub-classes \T1/pcr/m/n/10 ngTMatrix\T1/p tm/m/n/10 , [2348] Underfull \hbox (badness 3179) in paragraph at lines 8427--8430 []\T1/pcr/m/n/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [2349] Underfull \hbox (badness 10000) in paragraph at lines 8517--8520 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2350] Underfull \hbox (badness 10000) in paragraph at lines 8593--8596 []\T1/ptm/m/n/10 Currently, mainly [][]\T1/pcr/m/n/10 t[][][]() \T1/ptm/m/n/10 and co-er-cion meth-ods (for [][]\T1/pcr/m/n/10 as[][][](.)\T1/ptm/m/n/10 ; use , e.g., [2351] Overfull \hbox (25.98041pt too wide) in paragraph at lines 8609--8609 []\T1/pcr/m/n/9 str(nutp <- as(nutr, "ntpMatrix"))# packed matrix: only 10 = ( 4+1)*4/2 entries[] Overfull \vbox (41.60564pt too high) has occurred while \output is active [2352] Underfull \hbox (badness 10000) in paragraph at lines 8719--8721 []\T1/pcr/m/n/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 6493) in paragraph at lines 8721--8724 []\T1/pcr/m/n/10 signature(from = "integer",to = "pMatrix")\T1/ptm/m/n/10 : Thi s is en-ables typ-i-cal Underfull \hbox (badness 6428) in paragraph at lines 8727--8734 []\T1/pcr/m/n/10 signature(from = "pMatrix",to = "matrix")\T1/ptm/m/n/10 : co-e r-cion to a tra-di-tional [2353] [2354] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8820--8820 [] \T1/pcr/m/n/10 col.names, note.dropping.colnames = TRUE, uniD iag = TRUE,[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8823--8823 []\T1/pcr/m/n/10 printSpMatrix(x, digits = NULL, maxp = max(100L, getOption("m ax.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8825--8825 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 8829--8829 []\T1/pcr/m/n/10 printSpMatrix2(x, digits = NULL, maxp = max(100L, getOption(" max.print")),[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/10 zero.print = ".", col.names, note.dropping.coln ames = TRUE,[] Underfull \hbox (badness 3989) in paragraph at lines 8855--8865 []\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 8855--8865 \T1/ptm/m/n/10 be printed, pos-si-bly ab-bre-vi-ated. The de-fault is taken fro m [2355] [2356]pdfTeX warning (ext4): destination with the same identifier (name{ Rfn.qr}) has been already used, duplicate ignored \relax l.8956 \aliasA{qr}{qr-methods}{qr} [2357] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9029--9029 []\T1/pcr/m/n/9 stopifnot(identical(dimnames(X), dnX))# some versions changed X\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s dimnames![] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9040--9040 []\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 9044--9044 []\T1/pcr/m/n/9 doExtras <- interactive() || nzchar(Sys.getenv("R_MATRIX_CHECK _EXTRA")) ||[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9061--9061 []\T1/pcr/m/n/9 ##----- rank-deficient ("singular") case --------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9069--9069 []\T1/pcr/m/n/9 (X. <- drop0(Q. %*% R.[, qI], tol=tolE))## just = X, incl. cor rect colnames[] Underfull \vbox (badness 10000) has occurred while \output is active [2358] Underfull \hbox (badness 10000) in paragraph at lines 9122--9128 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of Underfull \hbox (badness 10000) in paragraph at lines 9139--9142 []\T1/ptm/m/n/10 is for back com-pat-i-bil-ity; for dense \T1/pcr/m/n/10 x\T1/p tm/m/n/10 , it cor-re-sponds to [2359] Overfull \hbox (85.38034pt too wide) in paragraph at lines 9211--9211 []\T1/pcr/m/n/9 ## The meaning of \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 tol\TS1/pcr/m/ n/9 ' \T1/pcr/m/n/9 for method="qrLINPACK" and *dense* x is not entirely "scale free"[] [2360] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9232--9232 []\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 9233--9233 []\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.9252 ... the Reciprocal Condition Number}{rcond} [2361] [2362] Overfull \hbox (20.58041pt too wide) in paragraph at lines 9365--9365 []\T1/pcr/m/n/9 rcond(x2 <- cbind(x1, 2:11))# practically 0, since x2 does not have full rank[] [2363] [2364] Underfull \hbox (badness 10000) in paragraph at lines 9550--9552 []\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 2351) in paragraph at lines 9556--9564 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1325) in paragraph at lines 9556--9564 \T1/ptm/m/n/10 in-dices, if not \T1/pcr/m/n/10 symmetric [][]sample.int[][][](n row*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/pcr/m/n/10 rand.x \T1/ptm/m/n/10 is not [2365] [2366] Underfull \hbox (badness 1558) in paragraph at lines 9701--9704 []\T1/ptm/m/n/10 numeric square Ma-trix (in-her-it-ing from class \T1/pcr/m/n/1 0 "Matrix"\T1/ptm/m/n/10 ) or tra-di-tional [2367] Overfull \hbox (52.98038pt too wide) in paragraph at lines 9763--9763 [] \T1/pcr/m/n/9 z[order(Mod(z), decreasing=TRUE)]}) , tolerance = 1e-13),[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 9767--9767 []\T1/pcr/m/n/9 ## For the faint of heart, we provide Schur() also for traditi onal matrices:[] [2368]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sol ve}) has been already used, duplicate ignored \relax l.9829 \aliasA{solve}{solve-methods}{solve} Overfull \hbox (54.78088pt too wide) in paragraph at lines 9926--9926 [] \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 9931--9931 [] \T1/pcr/m/n/10 solve(a, b, ...) ## *the* two-argument version, almost alwa ys preferred to[] [2369] Underfull \hbox (badness 1616) in paragraph at lines 9966--9978 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 solve \T1/ptm/m/n/10 meth-ods for a Underfull \hbox (badness 10000) in paragraph at lines 9983--9986 []\T1/ptm/m/n/10 (for all \T1/pcr/m/n/10 b\T1/ptm/m/n/10 ) work via Underfull \hbox (badness 10000) in paragraph at lines 9992--9999 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 10000) in paragraph at lines 10005--10015 []\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/pcr/m/n/10 ( Underfull \hbox (badness 4660) in paragraph at lines 10005--10015 \T1/pcr/m/n/10 sparse=FALSE,tol = .Machine$double.eps ) \T1/ptm/m/n/10 : Checks if \T1/pcr/m/n/10 a \T1/ptm/m/n/10 is sym-met-ric, [2370] Underfull \hbox (badness 6032) in paragraph at lines 10032--10036 []\T1/ptm/m/n/10 All these meth-ods first try Cholmod's Underfull \hbox (badness 10000) in paragraph at lines 10039--10041 []\T1/ptm/m/n/10 all end up call-ing LA-PACK rou-tines Underfull \hbox (badness 10000) in paragraph at lines 10062--10063 []\T1/ptm/m/n/10 works via Underfull \hbox (badness 10000) in paragraph at lines 10068--10070 []\T1/ptm/m/n/10 these meth-ods typ-i-cally use Underfull \hbox (badness 10000) in paragraph at lines 10072--10073 []\T1/ptm/m/n/10 all work via Underfull \hbox (badness 10000) in paragraph at lines 10080--10083 [][][]\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 10098--10098 []\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 10102--10102 [] \T1/pcr/m/n/9 ## Fails on 32-bit [Fedora 19, R 3.0.2] from Matrix 1.1-0 on [FIXME ??] only[] [2371] Underfull \hbox (badness 10000) in paragraph at lines 10123--10126 []\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 10151--10153 []\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 10159--10162 []\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 10159--10162 \T1/pcr/m/n/10 "[][]sparseMatrix[][][]"\T1/ptm/m/n/10 , spec-i-fy-ing the con-t rasts to be ap-plied to the Underfull \hbox (badness 10000) in paragraph at lines 10170--10174 []\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 10170--10174 \T1/pcr/m/n/10 sparse.model.matrix \T1/ptm/m/n/10 has been changed to \T1/pcr/m /n/10 FALSE\T1/ptm/m/n/10 , 2010-07, for [2372] Underfull \hbox (badness 6592) in paragraph at lines 10181--10183 []\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 Underfull \hbox (badness 1158) in paragraph at lines 10199--10205 []\T1/ptm/m/n/10 Note that [][]\T1/pcr/m/n/10 model.Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 from pack-age \T1/ptm/b/n/10 Ma-trix-Mod-els \T1/ptm/m/n/10 may be of- [2373] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10258--10258 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop= TRUE),"CsparseMatrix"), dim(M) == c(0, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10259--10259 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f30, drop=FALSE),"CsparseMatrix"), dim(M) == c(3, 0),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10260--10260 [] \T1/pcr/m/n/9 is(M <- fac2sparse(f12, drop= TRUE),"CsparseMatrix"), dim(M) == c(0,12),[] [2374] [2375] Overfull \hbox (0.78088pt too wide) in paragraph at lines 10444--10444 [] \T1/pcr/m/n/10 symmetric = FALSE, triangular = FALSE, index1 = TRUE,[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 10445--10445 [] \T1/pcr/m/n/10 giveCsparse = TRUE, check = TRUE, use.last.ij = FALSE)[] [2376] Underfull \hbox (badness 4621) in paragraph at lines 10485--10489 []\T1/ptm/m/n/10 logical in-di-cat-ing if the re-sult should be a [][]\T1/pcr/m /n/10 CsparseMatrix[][][] \T1/ptm/m/n/10 or a [2377] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10573--10573 []\T1/pcr/m/n/9 (A <- sparseMatrix(i, j, x = x)) ## 8 x 10 "dgCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10577--10577 []\T1/pcr/m/n/9 (sA <- sparseMatrix(i, j, x = x, symmetric = TRUE)) ## 10 x 10 "dsCMatrix"[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10578--10578 []\T1/pcr/m/n/9 (tA <- sparseMatrix(i, j, x = x, triangular= TRUE)) ## 10 x 10 "dtCMatrix"[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10583--10583 []\T1/pcr/m/n/9 (AA <- sparseMatrix(c(1,3:8), c(2,9,6:10), x = 7 * (1:7), dims = c(10,20)))[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 10586--10586 []\T1/pcr/m/n/9 ## i, j and x can be in an arbitrary order, as long as they ar e consistent[] [2378] Overfull \hbox (15.18042pt too wide) in paragraph at lines 10609--10609 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 10610--10610 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10636--10636 []\T1/pcr/m/n/9 ## pointers example in converting from other sparse matrix rep resentations.[] Overfull \hbox (47.58038pt too wide) in paragraph at lines 10638--10638 [] \T1/pcr/m/n/9 nzchar(dfil <- system.file("extdata", "rua_32_ax.rua", pack age = "SparseM"))) {[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10640--10640 [] \T1/pcr/m/n/9 XX <- sparseMatrix(j = X@ja, p = X@ia - 1L, x = X@ra, dims = X@dimension)[] [2379] Underfull \hbox (badness 10000) in paragraph at lines 10733--10741 []\T1/pcr/m/n/10 (object = "sparseMatrix")\T1/ptm/m/n/10 : Re-turns an ob-ject of S3 class [2380] Underfull \hbox (badness 10000) in paragraph at lines 10784--10788 [][][]\T1/pcr/m/n/10 sparseMatrix[][][]\T1/ptm/m/n/10 , and its ref-er-ences, s uch as [][]\T1/pcr/m/n/10 xtabs[][][](*,sparse=TRUE)\T1/ptm/m/n/10 , or pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.Q}) ha s been already used, duplicate ignored \relax l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q} [2381] [2382] Underfull \hbox (badness 10000) in paragraph at lines 10954--10956 []\T1/pcr/m/n/10 signature(a = "sparseQR",b = "ANY")\T1/ptm/m/n/10 : For \T1/pc r/m/n/10 solve(a,b)\T1/ptm/m/n/10 , sim-ply uses Overfull \hbox (58.38037pt too wide) in paragraph at lines 10982--10982 [] \T1/pcr/m/n/9 qc <- qr.coef (qrm, y); qc. <- qr.coef (qrm, y.) # 2nd fai led in Matrix <= 1.1-0[] Underfull \hbox (badness 5036) in paragraph at lines 11010--11012 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [2383] Underfull \hbox (badness 2970) in paragraph at lines 11143--11149 []\T1/ptm/m/n/10 Sparse Vec-tor Classes: The vir-tual mother class \T1/pcr/m/n/ 10 "sparseVector" \T1/ptm/m/n/10 has the five ac- Underfull \hbox (badness 3679) in paragraph at lines 11143--11149 \T1/ptm/m/n/10 tual daugh-ter classes \T1/pcr/m/n/10 "dsparseVector"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "isparseVector"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsparseVec tor"\T1/ptm/m/n/10 , [2384] Underfull \hbox (badness 10000) in paragraph at lines 11216--11219 []\T1/pcr/m/n/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/pcr/m /n/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list [2385] Underfull \hbox (badness 10000) in paragraph at lines 11234--11239 []\T1/pcr/m/n/10 (x = "nsparseVector")\T1/ptm/m/n/10 : re-turn [][]\T1/pcr/m/n/ 10 logical[][][] \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 11249--11251 [][][]\T1/pcr/m/n/10 sparseVector[][][]() \T1/ptm/m/n/10 for friendly con-struc -tion of sparse vec-tors (apart from [2386] [2387] Underfull \hbox (badness 2698) in paragraph at lines 11374--11380 [][][]\T1/pcr/m/n/10 Matrix[][][](*,sparse=TRUE) \T1/ptm/m/n/10 for the more us ual con-struc-tor of such ma-tri-ces. Then, [2388] Underfull \hbox (badness 10000) in paragraph at lines 11467--11469 []\T1/pcr/m/n/10 signature(from = "ddiMatrix",to = "symmetricMatrix")\T1/ptm/m/ n/10 : and many Underfull \hbox (badness 10000) in paragraph at lines 11485--11490 []\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/pcr/m/ n/10 Dimnames \T1/ptm/m/n/10 slot, so it can be Underfull \hbox (badness 2050) in paragraph at lines 11485--11490 \T1/pcr/m/n/10 list(NULL,)\T1/ptm/m/n/10 , e.g., for ef-fi-ciency. H ow-ever, [][]\T1/pcr/m/n/10 dimnames[][][]() \T1/ptm/m/n/10 and other Underfull \hbox (badness 2591) in paragraph at lines 11493--11498 \T1/ptm/m/n/10 Classes [][]\T1/pcr/m/n/10 triangularMatrix[][][]\T1/ptm/m/n/10 , and, e.g., [][]\T1/pcr/m/n/10 dsyMatrix[][][] \T1/ptm/m/n/10 for nu-meric \T1 /ptm/m/it/10 dense \T1/ptm/m/n/10 ma-tri-ces, or [2389] Underfull \hbox (badness 2057) in paragraph at lines 11565--11567 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., [2390] [2391] Underfull \hbox (badness 6641) in paragraph at lines 11651--11654 []\T1/ptm/m/n/10 Currently, [][]\T1/pcr/m/n/10 Schur[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 isSymmetric[][][] \T1/ptm/m/n/10 and \T1/pcr/m/n/10 as() \T1/ptm /m/n/10 (i.e. [][]\T1/pcr/m/n/10 coerce[][][]\T1/ptm/m/n/10 ) have meth-ods wit h Underfull \hbox (badness 5133) in paragraph at lines 11691--11695 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 "TsparseMatrix" \T1/ptm/m/n/10 class is the vir-tual class of all sparse ma-tri-ces coded in Underfull \hbox (badness 2818) in paragraph at lines 11691--11695 \T1/ptm/m/n/10 triplet form. Since it is a vir-tual class, no ob-jects may be c re-ated from it. See [2392] Underfull \hbox (badness 7649) in paragraph at lines 11798--11800 []\T1/ptm/m/n/10 a sparse ma-trix stored in triplet form, i.e., in-her-it-ing f rom class [2393] [2394] [2395] Underfull \hbox (badness 7362) in paragraph at lines 11999--12001 []\T1/ptm/m/n/10 any \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject, co-er-ca-ble to a sparse ma-trix (i.e., of sub-class of [2396] Overfull \hbox (15.18042pt too wide) in paragraph at lines 12037--12037 []\T1/pcr/m/n/9 ## pointer vectors can be used, and the (i,x) slots are sorted if necessary:[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 12038--12038 []\T1/pcr/m/n/9 m <- sparseMatrix(i = c(3,1, 3:2, 2:1), p= c(0:2, 4,4,6), x = 1:6, dimnames = dn)[] [2397] [2398] Underfull \hbox (badness 6910) in paragraph at lines 12288--12290 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [2399] [2400] [2401]) (./boot-pkg.tex [2402] Chapter 18. [2403] [2404] [2405] [2406] [2407] [2408] [2409] Overfull \hbox (12.78088pt too wide) in paragraph at lines 530--530 []\T1/pcr/m/n/10 boot(data, statistic, R, sim = "ordinary", stype = c("i", "f" , "w"), [2410] Underfull \hbox (badness 1325) in paragraph at lines 568--575 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sim-u-la-tion r e-quired. Pos-si-ble Underfull \hbox (badness 1275) in paragraph at lines 583--588 []\T1/ptm/m/n/10 An in-te-ger vec-tor or fac-tor spec-i-fy-ing the strata for m ulti-sample prob- [2411] [2412] [2413] Underfull \hbox (badness 1881) in paragraph at lines 824--826 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 6493) in paragraph at lines 851--855 [][][]\T1/pcr/m/n/10 boot.array[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.c i[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 censboot[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 empinf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 tilt.boot[][][]\T1/ptm/m/n/10 , [2414] Overfull \hbox (4.38043pt too wide) in paragraph at lines 885--885 []\T1/pcr/m/n/9 nuke.lm <- glm(log(cost) ~ date+log(cap)+ne+ct+log(cum.n)+pt, data = nuke)[] Underfull \vbox (badness 10000) has occurred while \output is active [2415] [2416] Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 []\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i n-ter- Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues Underfull \hbox (badness 10000) in paragraph at lines 1066--1070 \T1/pcr/m/n/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply \T1/pcr/m/n/10 "all" [2417] Underfull \hbox (badness 1496) in paragraph at lines 1082--1091 []\T1/ptm/m/n/10 If sup-plied, a value to be used as an es-ti-mate of the vari- ance of the Underfull \hbox (badness 2005) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 statis-tic for the nor-mal ap-prox-i-ma-tion and stu-den-tized i n-ter-vals. If it Underfull \hbox (badness 2343) in paragraph at lines 1082--1091 \T1/ptm/m/n/10 is not sup-plied and \T1/pcr/m/n/10 length(index) \T1/ptm/m/n/10 is 2 then \T1/pcr/m/n/10 var.t0 \T1/ptm/m/n/10 de-faults to Underfull \hbox (badness 2150) in paragraph at lines 1103--1109 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2418] [2419] [2420] [2421] Underfull \hbox (badness 1571) in paragraph at lines 1443--1445 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2422] [2423] [2424] [2425] [2426] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1735--1735 []\T1/pcr/m/n/10 censboot(data, statistic, R, F.surv, G.surv, strata = matrix( 1,n,2), [2427] [2428] [2429] Underfull \vbox (badness 10000) has occurred while \output is active [2430] Overfull \hbox (31.3804pt too wide) in paragraph at lines 2010--2010 []\T1/pcr/m/n/9 mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),[] [2431] Underfull \hbox (badness 6268) in paragraph at lines 2081--2083 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2432] [2433] [2434] Underfull \hbox (badness 1565) in paragraph at lines 2335--2340 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2435] Underfull \hbox (badness 4595) in paragraph at lines 2360--2365 \T1/ptm/m/n/10 are passed un-changed ev-ery time \T1/pcr/m/n/10 boot.out$statis tic \T1/ptm/m/n/10 is called. Underfull \hbox (badness 1881) in paragraph at lines 2429--2431 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. Underfull \hbox (badness 2057) in paragraph at lines 2437--2438 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 empinf[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 k3.linear[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 saddle.distn[][] []\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.spline[][][]\T1/ptm/m/n/10 , [2436] [2437] Underfull \hbox (badness 1077) in paragraph at lines 2533--2537 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/pcr/m/n /10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/pcr/m/n/10 n \T1/ptm/m/n/10 is the sam-ple Underfull \hbox (badness 1112) in paragraph at lines 2533--2537 \T1/ptm/m/n/10 size, if \T1/pcr/m/n/10 unbiased \T1/ptm/m/n/10 is \T1/pcr/m/n/1 0 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/pcr/m/n/10 1/n \T1/ptm/m/n/10 is used. This is mul-ti-plied by [2438] [2439] [2440] [2441] [2442] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2892--2892 []\T1/pcr/m/n/10 EEF.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25, Overfull \hbox (18.78088pt too wide) in paragraph at lines 2894--2894 []\T1/pcr/m/n/10 EL.profile(y, tmin = min(y) + 0.1, tmax = max(y) - 0.1, n.t = 25,[] [2443] [2444] [2445] Underfull \hbox (badness 3861) in paragraph at lines 3102--3105 [][][]\T1/pcr/m/n/10 boot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.array[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 boot.ci[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 jack.after.boot[][][ ]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 linear.approx[][][]\T1/ptm/m/n/10 , [2446] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3155--3155 []\T1/pcr/m/n/10 envelope(boot.out = NULL, mat = NULL, level = 0.95, index = 1 :ncol(mat)) [2447] [2448] [2449] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3375--3375 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling [2450] [2451] [2452] [2453] [2454] [2455] [2456] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3835--3835 [] \T1/pcr/m/n/10 t = boot.out$t[, index], w = NULL, def = TRUE, q = NULL)[] [2457] [2458] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3974--3974 []\T1/pcr/m/n/9 grav.p <- imp.prob(grav.tilt.boot, w = grav.w, index = 3, t0 = grav.z0[3])[] [2459] [2460] [2461] Underfull \hbox (badness 10000) in paragraph at lines 4187--4189 []\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault is [2462] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4256--4256 []\T1/pcr/m/n/9 # To draw the jackknife-after-bootstrap plot for the head siz e data as in [2463] [2464] Underfull \hbox (badness 10000) in paragraph at lines 4359--4361 []\T1/ptm/m/n/10 The in-dex of the vari-able of in-ter-est within the out-put o f Underfull \hbox (badness 1430) in paragraph at lines 4368--4372 \T1/ptm/m/n/10 If \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is sup-plied but nei-ther \T 1/pcr/m/n/10 t \T1/ptm/m/n/10 nor \T1/pcr/m/n/10 L \T1/ptm/m/n/10 are sup-plied then \T1/pcr/m/n/10 t0 \T1/ptm/m/n/10 is set to [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] Underfull \hbox (badness 3000) in paragraph at lines 4956--4959 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2474] [2475] [2476] [2477] Underfull \hbox (badness 2293) in paragraph at lines 5235--5238 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5235--5238 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2478] Overfull \hbox (20.58041pt too wide) in paragraph at lines 5314--5314 []\T1/pcr/m/n/9 grav.boot <- boot(grav1, grav.fun, R = 499, stype = "w", strat a = grav1[, 2])[] [2479] [2480] [2481] [2482] [2483] [2484] [2485] [2486] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5863--5863 []\T1/pcr/m/n/9 city.sp1$spa[1] <- jacobian(city, 1.25, city.sp1$zeta.hat) * c ity.sp1$spa[1][] [2487] Underfull \hbox (badness 1127) in paragraph at lines 5985--6003 \T1/ptm/m/n/10 etc. un-til a point is found with a cdf ap-prox-i-ma-tion less t han \T1/pcr/m/n/10 min(alpha)/10\T1/ptm/m/n/10 , then [2488] Underfull \hbox (badness 2837) in paragraph at lines 6018--6021 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/pcr/m/n/10 "sad dle.distn"\T1/ptm/m/n/10 . See the help file for [2489] [2490] [2491] [2492] Overfull \hbox (15.18042pt too wide) in paragraph at lines 6303--6303 []\T1/pcr/m/n/9 # This example is taken from Exercise 7.5 of Gill, Murray and Wright (1991). [2493] [2494] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6492--6492 []\T1/pcr/m/n/9 # Example 9.8 of Davison and Hinkley (1997) requires tilting t he resampling Overfull \hbox (20.58041pt too wide) in paragraph at lines 6494--6494 []\T1/pcr/m/n/9 # value of the test statistic 1.84. In the book exponential t ilting was used[] [2495] [2496] [2497] Underfull \hbox (badness 1596) in paragraph at lines 6739--6743 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2498] [2499] Overfull \hbox (20.58041pt too wide) in paragraph at lines 6899--6899 [] \T1/pcr/m/n/9 stype = "i", sim = "balanced", alpha = c(0.05, 0.95),[] [2500] [2501] [2502] [2503] [2504] [2505] [2506] [2507]) (./class-pkg.tex [2508] Chapter 19. [2509] [2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517] [2518] [2519] [2520] [2521] [2522] [2523] [2524]) (./cluster-pkg.tex Chapter 20. [2525] Underfull \hbox (badness 1655) in paragraph at lines 133--142 []\T1/ptm/b/n/10 Care \T1/ptm/m/n/10 and ex-per-tise is prob-a-bly needed when us-ing \T1/pcr/m/n/10 method = "flexible" \T1/ptm/m/n/10 par-tic-u-larly Underfull \hbox (badness 2073) in paragraph at lines 133--142 \T1/ptm/m/n/10 for the case when \T1/pcr/m/n/10 par.method \T1/ptm/m/n/10 is sp ec-i-fied of longer length than one. Since \T1/ptm/b/n/10 clus- Underfull \hbox (badness 1635) in paragraph at lines 133--142 \T1/ptm/b/n/10 ter \T1/ptm/m/n/10 ver-sion 2.0, choices lead-ing to in-valid \T 1/pcr/m/n/10 merge \T1/ptm/m/n/10 struc-tures now sig-nal an er-ror (from Underfull \hbox (badness 2134) in paragraph at lines 133--142 \T1/ptm/m/n/10 the C code al-ready). The \T1/ptm/m/it/10 weighted av-er-age \T1 /ptm/m/n/10 (\T1/pcr/m/n/10 method="weighted"\T1/ptm/m/n/10 ) is the same as [2526] [2527] Overfull \hbox (42.18039pt too wide) in paragraph at lines 252--252 [] \T1/pcr/m/n/9 all.equal(a.wgt [iC], agnes(d.vr, method="flexible", par.met hod = 0.5)[iC]) ,[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 253--253 [] \T1/pcr/m/n/9 all.equal(a.sing[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, -.5))[iC]),[] Overfull \hbox (63.78036pt too wide) in paragraph at lines 254--254 [] \T1/pcr/m/n/9 all.equal(a.comp[iC], agnes(d.vr, method="flex", par.method= c(.5,.5,0, +.5))[iC]))[] [2528] [2529] Underfull \vbox (badness 10000) has occurred while \output is active [2530] [2531] Overfull \hbox (18.78088pt too wide) in paragraph at lines 518--518 [] \T1/pcr/m/n/10 col = c(2, 0), border = 0, axes = TRUE, frame.plot = axes,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 522--522 [] \T1/pcr/m/n/10 yaxRight = fromLeft, y.mar = 2.4 + max.strlen/2.5, ...)[] [2532] [2533] Overfull \hbox (66.78088pt too wide) in paragraph at lines 637--637 [] \T1/pcr/m/n/10 keep.data = medoids.x, rngR = FALSE, pamLike = FALSE, c orrect.d = TRUE)[] [2534] Underfull \hbox (badness 3078) in paragraph at lines 688--691 []\T1/ptm/m/n/10 Setting this to \T1/pcr/m/n/10 FALSE \T1/ptm/m/n/10 saves mem- ory (and hence time), but dis-ables [2535] [2536] Underfull \hbox (badness 2941) in paragraph at lines 779--782 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 clara.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , Overfull \hbox (9.78043pt too wide) in paragraph at lines 817--817 []\T1/pcr/m/n/9 ## those that are not always in same cluster (5 out of 3000 fo r this seed):[] [2537] Underfull \hbox (badness 10000) in paragraph at lines 864--866 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2538] Overfull \hbox (24.78088pt too wide) in paragraph at lines 929--929 [] \T1/pcr/m/n/10 arrowArgs = list(col="red3", length=1/16, angle=90, code =3), ...)[] [2539] Underfull \hbox (badness 4872) in paragraph at lines 975--977 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 989--993 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2540] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1103--1103 [] \T1/pcr/m/n/9 sapply(mets, function(M) maxSE(fk, sk, method = M, SE. factor = SEf)))[] [2541] Overfull \hbox (42.18039pt too wide) in paragraph at lines 1120--1120 []\T1/pcr/m/n/9 ## You can manually set it before running this : doExtras < - TRUE # or FALSE[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1158--1158 []\T1/pcr/m/n/9 plot(gsP.Z, main = "clusGap() ==> k = 1 clust er is optimal")[] [2542] Underfull \hbox (badness 4144) in paragraph at lines 1190--1194 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 nor a \T1/pcr/m/n/10 data \T1/ptm/m/n/10 com-po-nent, e.g., for [2543] Overfull \hbox (60.78088pt too wide) in paragraph at lines 1266--1266 [] \T1/pcr/m/n/10 col.clus = if(color) c(2, 4, 6, 3) else 5, cex = 1, cex.txt = cex,[] Overfull \hbox (72.78088pt too wide) in paragraph at lines 1272--1272 [] \T1/pcr/m/n/10 round(100 * var.dec, digits = 2), "% of the poin t variability."),[] [2544] [2545] Underfull \hbox (badness 10000) in paragraph at lines 1411--1416 []\T1/pcr/m/n/10 clusplot \T1/ptm/m/n/10 uses func-tion calls [][]\T1/pcr/m/n/1 0 princomp[][][](*,cor = (ncol(x) > 2)) \T1/ptm/m/n/10 or Underfull \hbox (badness 10000) in paragraph at lines 1459--1462 [2546] Underfull \hbox (badness 10000) in paragraph at lines 1476--1480 [][][]\T1/pcr/m/n/10 princomp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cmdscale [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 daisy[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 identify[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cov.mve[][][]\T1/ptm/m/n/10 , Overfull \hbox (31.3804pt too wide) in paragraph at lines 1500--1500 []\T1/pcr/m/n/9 clusplot(pamv, col.p = votes.clus, labels = 4)# color points a nd label ellipses[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1510--1510 [] \T1/pcr/m/n/9 clusplot(votes.diss, votes.clus, diss = TRUE, labels = 5)# i dent. only points[] [2547] Underfull \hbox (badness 5741) in paragraph at lines 1550--1553 []\T1/pcr/m/n/10 coefHier() \T1/ptm/m/n/10 di-rectly in-ter-faces to the un-der -ly-ing C code, and ``proves'' that \T1/ptm/m/it/10 only [2548] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1616--1616 [] \T1/pcr/m/n/10 warnBin = warnType, warnAsym = warnType, warnConst = wa rnType,[] [2549] Underfull \hbox (badness 1540) in paragraph at lines 1733--1741 \T1/ptm/m/n/10 In other words, $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 is a weigh ted mean of $\OML/cmm/m/it/10 d[]$ \T1/ptm/m/n/10 with weights $\OML/cmm/m/it/1 0 w[]^^N[]$\T1/ptm/m/n/10 , where $\OML/cmm/m/it/10 w[]$\T1/pcr/m/n/10 = [2550] [2551] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1824--1824 []\T1/pcr/m/n/9 summary(dfl2 <- daisy(flower, type = list(asymm = c(1, 3), ord ratio = 7)))[] Overfull \hbox (42.78088pt too wide) in paragraph at lines 1843--1843 []\T1/pcr/m/n/10 diana(x, diss = inherits(x, "dist"), metric = "euclidean", st and = FALSE, [2552] [2553] [2554] [2555] Underfull \hbox (badness 10000) in paragraph at lines 2162--2165 [2556] Underfull \hbox (badness 3179) in paragraph at lines 2176--2182 [][][]\T1/pcr/m/n/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the [ ][]\T1/pcr/m/n/10 predict[][][] \T1/ptm/m/n/10 method for \T1/pcr/m/n/10 ellips oid \T1/ptm/m/n/10 ob-jects. [2557] [2558] Underfull \hbox (badness 10000) in paragraph at lines 2334--2337 [][][]\T1/pcr/m/n/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-ence s; [][]\T1/pcr/m/n/10 fanny.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par tition.object[][][]\T1/ptm/m/n/10 , [2559] Underfull \hbox (badness 1292) in paragraph at lines 2402--2405 []\T1/ptm/m/n/10 named vec-tor with \T1/pcr/m/n/10 iterations\T1/ptm/m/n/10 , t he num-ber of it-er-a-tions needed and Underfull \hbox (badness 6675) in paragraph at lines 2411--2413 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see Underfull \hbox (badness 10000) in paragraph at lines 2434--2437 [][][]\T1/pcr/m/n/10 fanny[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.fanny [][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 dissimilarity.object[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [2560] [2561] [2562] [2563] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2650--2650 []\T1/pcr/m/n/9 ## One place to see if/how error messages are *translated* (to \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 de\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 / \TS1/pcr/m/n/ 9 '\T1/pcr/m/n/9 pl\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ):[] [2564] [2565] [2566] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2919--2919 []\T1/pcr/m/n/9 ## no _build_ *and* no _swap_ phase: just cluster all obs. aro und (1, 16):[] [2567] [2568] Overfull \hbox (20.58041pt too wide) in paragraph at lines 3022--3022 []\T1/pcr/m/n/9 axis(1, k.best, paste("best",k.best,sep="\n"), col = "red", co l.axis = "red")[] [2569] [2570] [2571] Overfull \hbox (78.78088pt too wide) in paragraph at lines 3218--3218 [] \T1/pcr/m/n/10 sub = paste("Agglomerative Coefficient = ",round(x $ac, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3219--3219 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2572] Underfull \hbox (badness 10000) in paragraph at lines 3286--3289 []\T1/ptm/m/n/10 For the den-dro-gram, more flex-i-bil-ity than via \T1/pcr/m/n /10 pltree() \T1/ptm/m/n/10 is pro-vided by \T1/pcr/m/n/10 dg [2573] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3336--3336 [] \T1/pcr/m/n/10 sub = paste("Divisive Coefficient = ", round(x$dc, digits = 2)),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 3337--3337 [] \T1/pcr/m/n/10 adj = 0, nmax.lab = 35, max.strlen = 5, xax.pretty = TRUE, ...)[] [2574] [2575] [2576] Underfull \hbox (badness 10000) in paragraph at lines 3522--3525 []\T1/ptm/m/n/10 when \T1/pcr/m/n/10 x \T1/ptm/m/n/10 does not have a \T1/pcr/m /n/10 diss \T1/ptm/m/n/10 com-po-nent as for [2577] Underfull \hbox (badness 10000) in paragraph at lines 3585--3590 [][][]\T1/pcr/m/n/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clusplot.default[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pam[][][]\T1/ptm/m/n/10 , [2578] Underfull \hbox (badness 3884) in paragraph at lines 3647--3652 \T1/ptm/m/n/10 dis-patches to [][]\T1/pcr/m/n/10 plot.hclust[][][](..)\T1/ptm/m /n/10 . If more flex-i-ble plots are needed, con-sider \T1/pcr/m/n/10 xx Underfull \hbox (badness 6268) in paragraph at lines 3659--3662 [][][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.objec t[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 diana[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 diana.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 hclust[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 par[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.agnes[][][]\T1/ptm/m/n/10 , [2579] [2580] [2581] Underfull \hbox (badness 10000) in paragraph at lines 3844--3847 [][][]\T1/pcr/m/n/10 summary.agnes[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 agnes[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 agnes.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3875--3878 [][][]\T1/pcr/m/n/10 summary.clara[][][] \T1/ptm/m/n/10 pro-duc-ing more out-pu t; [][]\T1/pcr/m/n/10 clara[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 clara.obje ct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print[][][]\T1/ptm/m/n/10 , [2582] Overfull \hbox (36.78088pt too wide) in paragraph at lines 3928--3928 [] \T1/pcr/m/n/10 digits = getOption("digits"), justify = "none", right = TRUE, ...)[] Underfull \hbox (badness 2035) in paragraph at lines 3939--3941 []\T1/ptm/m/n/10 a \T1/pcr/m/n/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T1 /pcr/m/n/10 summary.dissimilarity \T1/ptm/m/n/10 one for [2583] [2584] [2585] [2586] Overfull \hbox (54.78088pt too wide) in paragraph at lines 4132--4132 [] \T1/pcr/m/n/10 main = NULL, sub = NULL, xlab = expression("Silhouette w idth "* s[i]),[] Overfull \hbox (48.78088pt too wide) in paragraph at lines 4134--4134 [] \T1/pcr/m/n/10 cex.names = par("cex.axis"), do.n.k = TRUE, do.clus.stat = TRUE, ...)[] [2587] [2588] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4272--4272 []\T1/pcr/m/n/9 plot(si, col = c("red", "green", "blue", "purple"))# with clus ter-wise coloring[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4281--4281 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4283--4283 [] \T1/pcr/m/n/9 outer = TRUE, font = par("font.main"), cex = par("cex.ma in")); frame()[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 4286--4286 []\T1/pcr/m/n/9 c6 <- c("tomato", "forest green", "dark blue", "purple2", "gol denrod4", "gray20")[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4288--4288 [] \T1/pcr/m/n/9 plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 4295--4295 []\T1/pcr/m/n/9 str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # ro wnames == indices[] [2589] [2590] [2591] [2592] [2593] [2594] Underfull \hbox (badness 10000) in paragraph at lines 4668--4674 []\T1/ptm/m/n/10 Our ver-sion of the \T1/pcr/m/n/10 xclara \T1/ptm/m/n/10 is sl ightly more rounded than the one from Underfull \hbox (badness 10000) in paragraph at lines 4684--4686 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/pcr/m/n/10 xclara.dat\T1/ptm/m/n/10 ' in side [2595] Overfull \hbox (52.98038pt too wide) in paragraph at lines 4697--4697 []\T1/pcr/m/n/9 ## Visualization: Assuming groups are defined as {1:1000}, {10 01:2000}, {2001:3000} Overfull \hbox (9.78043pt too wide) in paragraph at lines 4699--4699 []\T1/pcr/m/n/9 p.ID <- c(78, 1411, 2535) ## PAM\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 s medoid indices == pam(xclara, 3)$id.med[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4709--4709 [] \T1/pcr/m/n/9 ## We see 3 + 2 + 2 = 7 clear "outlier"s or "wrong group" o bservations:[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4713--4713 [] \T1/pcr/m/n/9 ## Apart from these, what are the robust ranges of indices? - - Robust range:[] [2596]) (./codetools-pkg.tex Chapter 21. Overfull \hbox (24.78088pt too wide) in paragraph at lines 16--16 [] \T1/pcr/m/n/10 suppressParamUnused = !all, suppressFundefMismatch = FALSE,[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 17--17 [] \T1/pcr/m/n/10 suppressLocalUnused = FALSE, suppressNoLocalFun = !all,[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 18--18 [] \T1/pcr/m/n/10 skipWith = FALSE, suppressUndefined = dfltSuppress Undefined,[] [2597] Underfull \hbox (badness 10000) in paragraph at lines 65--70 []\T1/pcr/m/n/10 checkUsageEnv \T1/ptm/m/n/10 and \T1/pcr/m/n/10 checkUsagePack age \T1/ptm/m/n/10 are con-ve-nience func-tions that ap-ply [2598] Overfull \hbox (48.78088pt too wide) in paragraph at lines 119--119 []\T1/pcr/m/n/10 makeUsageCollector(fun, ..., name, enterLocal, enterGlobal, e nterInternal,[] [2599] [2600] [2601]) (./foreign-pkg.tex [2602] Chapter 22. [2603] Underfull \hbox (badness 1231) in paragraph at lines 67--70 []\T1/ptm/m/n/10 a char-ac-ter string with the name of the ARFF file to read fr om, or a Underfull \hbox (badness 6708) in paragraph at lines 78--81 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2604] [2605] Underfull \hbox (badness 3601) in paragraph at lines 235--243 []\T1/ptm/m/n/10 A data frame with at-tributes. These will in-clude \T1/pcr/m/n /10 "datalabel"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "time.stamp"\T1/ptm/m/n/10 , [2606] 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, [2607] [2608] [2609] Overfull \hbox (48.78088pt too wide) in paragraph at lines 462--462 [] \T1/pcr/m/n/10 trim_values = TRUE, reencode = NA, use.missings = t o.data.frame,[] [2610] Overfull \hbox (30.78088pt too wide) in paragraph at lines 463--463 [] \T1/pcr/m/n/10 sub = ".", add.undeclared.levels = c("sort", "appen d", "no"),[] 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/10 , 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 [2611] Underfull \hbox (badness 10000) in paragraph at lines 551--559 []\T1/ptm/m/n/10 URL [][]$\T1/pcr/m/n/10 http : / / msdn . microsoft . com / en -[]us / library / ms776446(VS . 85 ) .aspx$[][] Underfull \hbox (badness 7613) in paragraph at lines 569--575 []\T1/ptm/m/n/10 There may be at-tributes \T1/pcr/m/n/10 "label.table" \T1/ptm/ m/n/10 and \T1/pcr/m/n/10 "variable.labels"\T1/ptm/m/n/10 . At-tribute [2612] Overfull \hbox (20.58041pt too wide) in paragraph at lines 624--624 []\T1/pcr/m/n/9 ### hence may need some special treatment with appropriate arg ument settings.[] 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,[] [2613] 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="")[] [2614] [2615] Underfull \hbox (badness 10000) in paragraph at lines 813--814 Overfull \hbox (4.38043pt too wide) in paragraph at lines 823--823 []\T1/pcr/m/n/9 iris.s <- read.systat(system.file("files/Iris.syd", package="f oreign")[1])[] [2616] [2617] Overfull \hbox (24.78088pt too wide) in paragraph at lines 899--899 [] \T1/pcr/m/n/10 data.restore(file, print = FALSE, verbose = FALSE, env = .G lobalEnv) [2618] 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 [][]$\T1/pcr/m/n/10 http : / / www . cs . waikato . ac . nz / ~ml / weka / arff . [2619] [2620] Underfull \hbox (badness 10000) in paragraph at lines 1073--1074 [][][]$\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"))[] [2621] [2622] Underfull \hbox (badness 10000) in paragraph at lines 1267--1273 []\T1/ptm/m/n/10 The work for this func-tion is done by \T1/pcr/m/n/10 foreign: ::writeForeignStata\T1/ptm/m/n/10 , [2623] Underfull \hbox (badness 2088) in paragraph at lines 1293--1296 []\T1/ptm/m/n/10 For \T1/pcr/m/n/10 package="SPSS"\T1/ptm/m/n/10 , as a side ef -fect, the dec-i-mal in-di-ca-tor is al-ways set by \T1/pcr/m/n/10 SET [2624]) (./lattice-pkg.tex Chapter 23. [2625] [2626] [2627] 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"),[] [2628] 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"),[] [2629] [2630] [2631] [2632] Underfull \hbox (badness 1221) in paragraph at lines 650--658 []\T1/ptm/m/n/10 A log-i-cal, or a list con-tain-ing com-po-nents to be used as ar-gu-ments to [2633] [2634] [2635] [2636] 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. [2637] Underfull \hbox (badness 1661) in paragraph at lines 1099--1105 []\T1/pcr/m/n/10 x \T1/ptm/m/n/10 and \T1/pcr/m/n/10 y \T1/ptm/m/n/10 should be num-bers be-tween 0 and 1, giv-ing co-or-di-nates [2638] [2639] Underfull \hbox (badness 1097) in paragraph at lines 1225--1227 []\T1/ptm/m/n/10 Logical flag, whether leg-end should have a 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 [2640] [2641] [2642] Underfull \hbox (badness 1540) in paragraph at lines 1479--1485 []\T1/ptm/m/n/10 A list con-tain-ing pos-si-ble ar-gu-ments to [][]\T1/pcr/m/n/ 10 plot.trellis[][][]\T1/ptm/m/n/10 , [2643] Underfull \hbox (badness 10000) in paragraph at lines 1566--1583 [][]\T1/pcr/m/n/10 panel.dotplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel .stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 panel.superpose[][][]\T1/pt m/m/n/10 , [][]\T1/pcr/m/n/10 panel.loess[][][]\T1/ptm/m/n/10 , [2644] Underfull \vbox (badness 10000) has occurred while \output is active [2645] Overfull \hbox (36.7804pt too wide) in paragraph at lines 1671--1671 [] \T1/pcr/m/n/9 text = list(lab = as.character(unique(Orchar dSprays$rowpos))),[] Underfull \hbox (badness 2012) in paragraph at lines 1725--1727 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/pcr/m/n/10 xyplot[][] []\T1/ptm/m/n/10 , which may pass them on to [2646] Underfull \hbox (badness 6808) in paragraph at lines 1755--1759 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to Underfull \hbox (badness 10000) in paragraph at lines 1772--1775 []\T1/ptm/m/n/10 style set-tings be-yond the stan-dard \T1/pcr/m/n/10 col\T1/pt m/m/n/10 , \T1/pcr/m/n/10 lty\T1/ptm/m/n/10 , \T1/pcr/m/n/10 lwd\T1/ptm/m/n/10 , etc; see Underfull \hbox (badness 10000) in paragraph at lines 1825--1827 []\T1/ptm/m/n/10 Gabor Grothendieck, Achim Zeileis, Deep-ayan Sarkar and Fe-lix An-drews [2647] [2648] [2649] [2650] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2071--2071 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.densitypl ot"),[] [2651] Underfull \hbox (badness 10000) in paragraph at lines 2141--2144 []\T1/ptm/m/n/10 When \T1/pcr/m/n/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, t he value of Underfull \hbox (badness 1320) in paragraph at lines 2141--2144 \T1/pcr/m/n/10 lattice.getOption("histogram.breaks") \T1/ptm/m/n/10 is first ch ecked. If [2652] [2653] [2654] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2345--2345 [] \T1/pcr/m/n/10 drop.unused.levels = lattice.getOption("drop.unused.le vels"),[] Overfull \hbox (30.78088pt too wide) in paragraph at lines 2349--2349 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.default .qqmath"),[] [2655] [2656] [2657] [2658] [2659] Overfull \hbox (60.78088pt too wide) in paragraph at lines 2689--2689 [] \T1/pcr/m/n/10 panel = if (useRaster) lattice.getOption("panel.lev elplot.raster")[] Overfull \hbox (0.78088pt too wide) in paragraph at lines 2721--2721 [] \T1/pcr/m/n/10 lattice.getOption("prepanel.default.contourpl ot"),[] [2660] [2661] Underfull \hbox (badness 2913) in paragraph at lines 2791--2796 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 2791--2796 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as 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 [2662] Underfull \hbox (badness 1609) in paragraph at lines 2935--2941 []\T1/ptm/m/n/10 A log-i-cal flag in-di-cat-ing whether raster rep-re-sen-ta-ti ons should be used, Underfull \hbox (badness 2772) in paragraph at lines 2935--2941 \T1/ptm/m/n/10 both for the false color im-age and the color key (if present). Ef- 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 [2663] [2664] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3060--3060 [] \T1/pcr/m/n/10 xlim = if (is.factor(x)) levels(x) else range(x, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3061--3061 [] \T1/pcr/m/n/10 ylim = if (is.factor(y)) levels(y) else range(y, finite = TRUE),[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 3062--3062 [] \T1/pcr/m/n/10 zlim = if (is.factor(z)) levels(z) else range(z, finite = TRUE),[] 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"),[] [2665] Underfull \hbox (badness 2913) in paragraph at lines 3143--3150 []\T1/ptm/m/n/10 Optional vec-tors of val-ues that de-fine the grid when \T1/pc r/m/n/10 x \T1/ptm/m/n/10 is a ma-trix. Underfull \hbox (badness 3058) in paragraph at lines 3143--3150 \T1/pcr/m/n/10 row.values \T1/ptm/m/n/10 and \T1/pcr/m/n/10 column.values \T1/p tm/m/n/10 must have the same lengths as [2666] [2667] [2668] [2669]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.parallel}) has been already used, duplicate ignored \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"),[] [2670] Overfull \hbox (54.78088pt too wide) in paragraph at lines 3496--3496 [] \T1/pcr/m/n/10 default.prepanel = lattice.getOption("prepanel.defau lt.parallel"),[] [2671] [2672] [2673] [2674] [2675] Overfull \hbox (18.78088pt too wide) in paragraph at lines 3832--3832 []\T1/pcr/m/n/10 oneway(formula, data, location=mean, spread=function(x) sqrt( var(x))) [2676] Underfull \hbox (badness 2277) in paragraph at lines 3922--3926 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings by 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 [2677] [2678] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4052--4052 []\T1/pcr/m/n/10 trellis.par.set(name, value, ..., theme, warn = TRUE, strict = FALSE) 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 [2679] Underfull \hbox (badness 5161) in paragraph at lines 4170--4174 []\T1/ptm/m/n/10 The ac-tual list of the com-po-nents in \T1/pcr/m/n/10 trellis .settings \T1/ptm/m/n/10 has not been fi-nal-ized, Underfull \hbox (badness 4913) in paragraph at lines 4170--4174 \T1/ptm/m/n/10 so I'm not at-tempt-ing to list them here. The cur-rent value ca n be ob-tained by [2680] [2681] Underfull \hbox (badness 1067) in paragraph at lines 4284--4294 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/pcr/m/n/10 col \T1/ptm/m/n/10 i s used for com-po-nents \T1/pcr/m/n/10 "plot.symbol"\T1/ptm/m/n/10 , 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 [2682] [2683] [2684] [2685] [2686] [2687] Overfull \hbox (4.38043pt too wide) in paragraph at lines 4716--4716 []\T1/pcr/m/n/9 p12 <- densityplot( ~ height | voice.part, data = singer, xlab = "Height")[] [2688] [2689] Underfull \hbox (badness 10000) in paragraph at lines 4903--4906 []\T1/ptm/m/n/10 An ob-ject of class \T1/pcr/m/n/10 trellis\T1/ptm/m/n/10 , by de-fault plot-ted by \T1/pcr/m/n/10 print.trellis\T1/ptm/m/n/10 . [2690] [2691] 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 [2692] [2693] [2694] [2695] [2696] [2697] Underfull \hbox (badness 3646) in paragraph at lines 5367--5370 [][][]\T1/pcr/m/n/10 Lattice[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 draw.key[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 trellis.par.get[][][]\T1/ptm/m/n/10 , and [][]\T1/pcr/m/n/10 xyplot[][][]\T1/ptm/m/n/10 , specif-i-cally the en-try f or 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],[] [2698] 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 [2699] 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 [2700] 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,[] [2701] 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 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 [2702] [2703] Underfull \hbox (badness 2538) in paragraph at lines 5846--5850 \T1/ptm/m/n/10 For \T1/pcr/m/n/10 trellis.focus\T1/ptm/m/n/10 , the de-fault is \T1/pcr/m/n/10 TRUE \T1/ptm/m/n/10 in in-ter-ac-tive mode, and 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 [2704] [2705] Underfull \hbox (badness 10000) in paragraph at lines 6010--6014 [][][]\T1/pcr/m/n/10 identify[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Lattice[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 print.trellis[][][]\T1/ptm/m/n/10 , [] []\T1/pcr/m/n/10 trellis.currentLayout[][][]\T1/ptm/m/n/10 , [2706] [2707] Underfull \hbox (badness 4242) in paragraph at lines 6157--6162 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- [2708] [2709] Underfull \hbox (badness 3601) in paragraph at lines 6273--6278 []\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/pcr/m/n/10 x \T1/ptm/m/n/1 0 for ev-ery level of \T1/pcr/m/n/10 y \T1/ptm/m/n/10 (or the other way round 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 [2710] 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,[] [2711] [2712] Underfull \hbox (badness 1888) in paragraph at lines 6492--6499 \T1/pcr/m/n/10 at \T1/ptm/m/n/10 can be a nu-meric vec-tor, \T1/pcr/m/n/10 col. regions \T1/ptm/m/n/10 a vec-tor of col-ors, and [2713] 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 [2714] [2715] [2716] [2717] [2718] [2719] Underfull \hbox (badness 1320) in paragraph at lines 6955--6962 []\T1/pcr/m/n/10 panel.levelplot.raster \T1/ptm/m/n/10 is an al-ter-na-tive pan el func-tion that uses the raster draw- 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 [2720] Overfull \hbox (0.78088pt too wide) in paragraph at lines 7025--7025 [] \T1/pcr/m/n/10 varname = NULL, limits, at = NULL, labels = NULL,[] [2721] 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 [2722] Underfull \hbox (badness 10000) in paragraph at lines 7160--7163 \T1/ptm/m/n/10 and \T1/pcr/m/n/10 diag.panel \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.pairs\T1/ptm/m/n/10 . Cur-rently ig-nored by [2723] [2724] Underfull \hbox (badness 2012) in paragraph at lines 7326--7329 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2725] 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))[] [2726] [2727] Underfull \hbox (badness 2644) in paragraph at lines 7513--7517 \T1/ptm/m/n/10 ig-nores these. For types "r" and "smooth", these are passed on to Underfull \hbox (badness 2772) in paragraph at lines 7526--7529 []\T1/ptm/m/n/10 Most gen-er-ally, \T1/pcr/m/n/10 grid \T1/ptm/m/n/10 can be a list of ar-gu-ments to be sup-plied to [2728] Overfull \hbox (25.98041pt too wide) in paragraph at lines 7596--7596 [] \T1/pcr/m/n/9 ylab = list(c("horizontal=TRUE", "horizontal=FALSE"), y = c(1/6, 4/6)),[] 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),[] [2729] 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)[] [2730] [2731] [2732] 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")[] [2733] Underfull \hbox (badness 1436) in paragraph at lines 7912--7918 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2734] [2735] [2736] [2737] [2738] [2739] [2740] [2741] Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/pcr/m/n/10 panel.superpo se Underfull \hbox (badness 10000) in paragraph at lines 8470--8473 \T1/ptm/m/n/10 from \T1/pcr/m/n/10 panel.superpose.2\T1/ptm/m/n/10 , and to \T1 /pcr/m/n/10 panel.groups \T1/ptm/m/n/10 from [2742] [2743] Overfull \hbox (24.78088pt too wide) in paragraph at lines 8645--8645 []\T1/pcr/m/n/10 prepanel.default.bwplot(x, y, horizontal, nlevels, origin, st ack, ...)[] 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, ...)[] [2744] Underfull \hbox (badness 3118) in paragraph at lines 8677--8680 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/pcr/m/n/10 type \T1 /ptm/m/n/10 has a dif-fer-ent mean-ing in [2745] Underfull \hbox (badness 1515) in paragraph at lines 8753--8757 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2746] Underfull \hbox (badness 6316) in paragraph at lines 8859--8864 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in [2747] [2748] Overfull \hbox (47.58038pt too wide) in paragraph at lines 8966--8966 [] \T1/pcr/m/n/9 ans$bottom$labels$labels <- parse(text = ans$b ottom$labels$labels)[] [2749] [2750] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9105--9105 []\T1/pcr/m/n/9 xyplot(sunspot.year ~ time(sunspot.year) | equal.count(time(su nspot.year)),[] [2751] Overfull \hbox (42.94879pt too wide) in paragraph at lines 9164--9168 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/pcr /m/n/10 left,right,left.name,right.name,condition Overfull \hbox (50.63074pt too wide) in paragraph at lines 9164--9168 \T1/ptm/m/n/10 for 2-D, and \T1/pcr/m/n/10 left,right.x,right.y,left.name,right .x.name,right.y.name,condition [2752] [2753] [2754] [2755] [2756] [2757] [2758] Underfull \hbox (badness 7238) in paragraph at lines 9622--9626 []\T1/ptm/m/n/10 Factor with lev-els \T1/pcr/m/n/10 "Svansota"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 462"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Manchuria"\T1/ptm/m/n/ 10 , \T1/pcr/m/n/10 "No. 475"\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9622--9626 \T1/pcr/m/n/10 "Velvet"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Peatland"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Glabron"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "No. 457"\T1/ptm/m/n /10 , \T1/pcr/m/n/10 "Wisconsin No. 38"\T1/ptm/m/n/10 , [2759] [2760] [2761]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma}) has been already used, duplicate ignored \relax l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma} [2762] [2763] [2764] Underfull \hbox (badness 10000) in paragraph at lines 10015--10020 \T1/pcr/m/n/10 diseases\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Diabetes\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Flu and pneumonia\T1/ptm/m/n/10 , \T1/pcr/m/n/10 Heart disease\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 Lower 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),[] [2765] [2766]) (./mgcv-pkg.tex Chapter 24. [2767] [2768] 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,[] [2769] 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. [2770] [2771] [2772] [2773] Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][][]\T1/pcr/m/n/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 mgc v-package[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gamObject[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smoo th.terms[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 365--372 [][]\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 365--372 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2774] Overfull \hbox (4.38043pt too wide) in paragraph at lines 408--408 []\T1/pcr/m/n/9 system.time(b2 <- bam(y ~ s(x0,bs=bs,k=k)+s(x1,bs=bs,k=k)+s(x2 ,bs=bs,k=k)+[] [2775] [2776] [2777] Underfull \hbox (badness 2922) in paragraph at lines 607--608 []\T1/ptm/m/n/10 The link func-tion: one of \T1/pcr/m/n/10 "logit"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "probit"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "cloglog" \T1/ptm/m/ n/10 and [2778] [2779] [2780] Underfull \hbox (badness 1158) in paragraph at lines 753--755 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [2781] Underfull \hbox (badness 1259) in paragraph at lines 816--817 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [2782] Underfull \vbox (badness 10000) has occurred while \output is active [2783] [2784] [2785] [2786] [2787] Overfull \hbox (4.38043pt too wide) in paragraph at lines 1164--1164 []\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 1165--1165 []\T1/pcr/m/n/9 lines(b$family$data$tr,exp(-b$family$data$h - 2*b$family$data$ q^.5),col=2)[] [2788] Overfull \hbox (47.58038pt too wide) in paragraph at lines 1171--1171 []\T1/pcr/m/n/9 bs <- gam(cbind(time,strata)~s(age,by=sex)+sex+s(nodes)+perfor +rx+obstruct+adhere,[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 1178--1178 []\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 1180--1180 []\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 1182--1182 [] \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 1213--1213 []\T1/pcr/m/n/9 b <- gam(t~s(x0)+s(x1)+s(x2,k=15)+s(x3),family=cox.ph,weights= d,data=surv)[] Underfull \vbox (badness 10000) has occurred while \output is active [2789] [2790] Overfull \hbox (9.78043pt too wide) in paragraph at lines 1274--1274 [] \T1/pcr/m/n/9 if (inter) prg <- txtProgressBar(min = 0, max = length(sid), initial = 0,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 1285--1285 [] \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 1319--1319 []\T1/pcr/m/n/9 pd <- data.frame(lapply(X=di,FUN=app,t=di$day,to=te)) ## inter polate to te[] Underfull \vbox (badness 10000) has occurred while \output is active [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] Overfull \hbox (30.78088pt too wide) in paragraph at lines 1822--1822 []\T1/pcr/m/n/10 fixDependence(X1,X2,tol=.Machine$double.eps^.5,rank.def=0,str ict=FALSE) [2800] [2801] [2802] [2803] [2804] [2805] Underfull \hbox (badness 1052) in paragraph at lines 2197--2205 \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 2214--2214 []\T1/pcr/m/n/10 gam(formula,family=gaussian(),data=list(),weights=NULL,subset =NULL,[] Underfull \hbox (badness 1728) in paragraph at lines 2226--2229 []\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 2239--2243 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2806] Underfull \hbox (badness 1043) in paragraph at lines 2265--2270 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [2807] [2808] Underfull \hbox (badness 1043) in paragraph at lines 2428--2434 \T1/ptm/m/n/10 eral lin-ear func-tion-als of smooths, via the sum-ma-tion con-v en-tion mech-a-nism de-scribed in [2809] [2810] Underfull \hbox (badness 10000) in paragraph at lines 2564--2570 [][][]\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 2564--2570 [][]\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 2564--2570 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.sid e[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.selection[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gam.control[][][] [][]gam.check[][][]\T1/ptm/m/n/10 , [2811] Underfull \vbox (badness 10000) has occurred while \output is active [2812] Underfull \vbox (badness 10000) has occurred while \output is active [2813] Underfull \vbox (badness 10000) has occurred while \output is active [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] Overfull \hbox (6.78088pt too wide) in paragraph at lines 3220--3220 [] \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 3223--3223 [] \T1/pcr/m/n/10 printWarn=TRUE,scoreType="REML",null.coef=rep(0,ncol (x)),[] [2822] [2823] [2824] [2825] [2826] [2827] Underfull \hbox (badness 5189) in paragraph at lines 3584--3588 []\T1/ptm/m/n/10 Random ef-fects can be added to \T1/pcr/m/n/10 gam \T1/ptm/m/n /10 mod-els us-ing \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see [2828] [2829] Overfull \hbox (9.78043pt too wide) in paragraph at lines 3701--3701 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \vbox (badness 10000) has occurred while \output is active [2830] [2831] [2832] Underfull \hbox (badness 1184) in paragraph at lines 3870--3874 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [2833] [2834] [2835] [2836] [2837] [2838] [2839] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4316--4316 [] \T1/pcr/m/n/9 mod <- gam(y~s(a,bs="re")+s(b,bs="re")+s(a,b,bs="re")+s(x0,i d=1)+s(x1,id=1)+[] [2840] [2841] [2842] Overfull \hbox (18.78088pt too wide) in paragraph at lines 4466--4466 []\T1/pcr/m/n/10 gamlss.gH(X, jj, l1, l2, i2, l3 = 0, i3 = 0, l4 = 0, i4 = 0, d1b = 0, [2843] Overfull \hbox (12.78088pt too wide) in paragraph at lines 4560--4560 []\T1/pcr/m/n/10 niterPQL=20,verbosePQL=TRUE,method="ML",drop.unused.levels=TR UE,...)[] [2844] Underfull \hbox (badness 1142) in paragraph at lines 4591--4595 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2845] Underfull \hbox (badness 10000) in paragraph at lines 4660--4669 []\T1/ptm/m/n/10 In the event of \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 con-ver-genc e fail-ures, con-sider mod-i-fy-ing [2846] [2847] Underfull \hbox (badness 5970) in paragraph at lines 4777--4783 [][][]\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 4777--4783 [][]\T1/pcr/m/n/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 negbin[ ][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 vis.gam[][][]\T1/ptm/m/n/10 ,[][]\T1/p cr/m/n/10 pdTens[][][]\T1/ptm/m/n/10 , \T1/pcr/m/n/10 gamm4 \T1/ptm/m/n/10 ( [] []$\T1/pcr/m/n/10 https : / / cran . r-[]project . [2848] Underfull \vbox (badness 10000) has occurred while \output is active [2849] [2850] [2851] Underfull \hbox (badness 1577) in paragraph at lines 5057--5060 []\T1/ptm/m/n/10 If `outer' it-er-a-tion has been used to fit the model (see [] []\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 ar-gu-ment Underfull \hbox (badness 2181) in paragraph at lines 5064--5065 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [2852] [2853] [2854] [2855] [2856] [2857] [2858] Underfull \hbox (badness 6708) in paragraph at lines 5453--5454 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/pcr/m/n/10 gam(..., fit=FALSE) \T1/ptm/m/n/10 or [2859] Overfull \hbox (58.38037pt too wide) in paragraph at lines 5502--5502 [] \T1/pcr/m/n/9 ## example using a scale location model for the motorcycle d ata. A simple plotting[] [2860] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5527--5527 [] \T1/pcr/m/n/9 } else lines(xg,predict(din,xg)$y,col=lcol[j],lwd=lwd[j] ,lty=lty[j])[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5556--5556 [] \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 [2861] Overfull \hbox (4.38043pt too wide) in paragraph at lines 5609--5609 [] \T1/pcr/m/n/9 (1+exp(-10*(x[201:300]-.5)))-0.9933071) + z*(1-z)*5 + r norm(100)*.4[] [2862] [2863] [2864] [2865] [2866] [2867] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5933--5933 []\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 5935--5935 []\T1/pcr/m/n/10 control=gam.control(),centred=TRUE,sp.prior = "gamma",diagona lize=FALSE)[] Underfull \hbox (badness 1142) in paragraph at lines 5956--5960 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [2868] [2869] [2870] [2871] [2872] [2873] Overfull \hbox (24.78088pt too wide) in paragraph at lines 6219--6219 []\T1/pcr/m/n/10 ldetS(Sl, rho, fixed, np, root = FALSE, repara = TRUE, nt = 1 ,deriv=2) Overfull \hbox (72.78088pt too wide) in paragraph at lines 6273--6273 []\T1/pcr/m/n/10 ldTweedie(y,mu=y,p=1.5,phi=1,rho=NA,theta=NA,a=1.001,b=1.999, all.derivs=FALSE) [2874] [2875] [2876] [2877] Underfull \vbox (badness 10000) has occurred while \output is active [2878] Underfull \vbox (badness 10000) has occurred while \output is active [2879] [2880] [2881] Overfull \hbox (52.98038pt too wide) in paragraph at lines 6702--6702 []\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 6729--6729 [] \T1/pcr/m/n/10 .Machine$double.eps^0.5),extra.rss=0,n.score=length(y), nthreads=1)[] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] Underfull \hbox (badness 1242) in paragraph at lines 7272--7273 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and [2891] [2892] Overfull \hbox (20.58041pt too wide) in paragraph at lines 7359--7359 []\T1/pcr/m/n/9 ## Alternative, better scaling example, using the discrete opt ion with bam...[] [2893] [2894] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7422--7422 []\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 7441--7441 [] \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 [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] Underfull \vbox (badness 10000) has occurred while \output is active [2913] [2914] Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/pcr/m/n/10 Dim.p dIndot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 corMatrix.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 logDet.pdIdnot\ T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdConstruct.pdIdnot\T1/ptm/m/n/10 , Underfull \hbox (badness 3118) in paragraph at lines 8661--8664 \T1/pcr/m/n/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 pdMatrix.pdIdnot \T1/ptm/m/n/10 , \T1/pcr/m/n/10 solve.pdIdnot\T1/ptm/m/n/10 , \T1/pcr/m/n/10 su mmary.pdIdnot\T1/ptm/m/n/10 . [2915] Underfull \hbox (badness 10000) in paragraph at lines 8717--8720 []\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 8717--8720 \T1/pcr/m/n/10 pdMatrix.pdTens\T1/ptm/m/n/10 , \T1/pcr/m/n/10 coef.pdTens \T1/p tm/m/n/10 and \T1/pcr/m/n/10 summary.pdTens\T1/ptm/m/n/10 ) would not nor-mally be [2916] [2917] [2918] Overfull \hbox (18.78088pt too wide) in paragraph at lines 8937--8937 []\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 8938--8938 [] \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 8941--8941 [] \T1/pcr/m/n/10 trans=I,seWithMean=FALSE,unconditional=FALSE,by.resi ds=FALSE,[] [2919] [2920] [2921] Underfull \hbox (badness 1629) in paragraph at lines 9099--9104 \T1/ptm/m/n/10 just won't let you do it. In this case, the quick-est op-tion is some-times to clone the [2922] [2923] [2924] [2925] Overfull \hbox (18.78088pt too wide) in paragraph at lines 9310--9310 [] \T1/pcr/m/n/10 na.action=na.pass,cluster=NULL,discrete=TRUE,n.thread s=1,...)[] [2926] [2927] Overfull \hbox (6.78088pt too wide) in paragraph at lines 9474--9474 [] \T1/pcr/m/n/10 na.action=na.pass,unconditional=FALSE,iterms.type=NUL L,...)[] [2928] [2929] [2930] [2931] Underfull \vbox (badness 10000) has occurred while \output is active [2932] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9742--9742 [] \T1/pcr/m/n/9 Xi[,(i-1)*9+1:9+1] <- Xp[,(i-1)*9+1:9+1] ## Xi%*%coef(b) = s mooth deriv i[] [2933] Underfull \hbox (badness 1205) in paragraph at lines 9780--9782 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 9780--9782 \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 9786--9791 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2934] Underfull \hbox (badness 1205) in paragraph at lines 9870--9872 []\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 9870--9872 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [2935] Underfull \hbox (badness 10000) in paragraph at lines 9939--9942 []\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 9939--9942 [][]\T1/pcr/m/n/10 smooth.construct.so.smooth.spec[][][]\T1/ptm/m/n/10 , al-tho ugh el-e-ments \T1/pcr/m/n/10 X \T1/ptm/m/n/10 and \T1/pcr/m/n/10 S \T1/ptm/m/n /10 are not needed, [2936] [2937] Underfull \hbox (badness 1253) in paragraph at lines 10069--10071 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [2938] [2939] [2940] [2941] Underfull \hbox (badness 1946) in paragraph at lines 10247--10254 []\T1/ptm/m/n/10 The sec-ond method rep-re-sents the con-ven-tional ran-dom ef- fects in a GAM in the same Underfull \hbox (badness 2221) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 way that the smooths are rep-re-sented --- as pe-nal-ized re-gre s-sion terms. This method Underfull \hbox (badness 2042) in paragraph at lines 10247--10254 \T1/ptm/m/n/10 can be used with [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 by mak-ing use of \T1/pcr/m/n/10 s(...,bs="re") \T1/ptm/m/n/10 terms in a model: s ee Underfull \hbox (badness 2846) in paragraph at lines 10255--10258 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/pcr/m/n/1 0 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n /10 can be used: Underfull \hbox (badness 5862) in paragraph at lines 10255--10258 \T1/ptm/m/n/10 see [][]\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 . If smoot h-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [2942] Overfull \hbox (9.78043pt too wide) in paragraph at lines 10321--10321 []\T1/pcr/m/n/9 rm1 <- gam(y ~ s(fac,bs="re")+s(x0)+s(x1)+s(x2)+s(x3),data=dat ,method="ML")[] Underfull \hbox (badness 10000) in paragraph at lines 10350--10353 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/pcr/m/n/10 "deviance"\T1/ptm/m/n/10 , [2943] [2944] [2945] [2946] [2947] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10637--10637 []\T1/pcr/m/n/10 s(..., k=-1,fx=FALSE,bs="tp",m=NA,by=NA,xt=NULL,id=NULL,sp=NU LL,pc=NULL) [2948] [2949] [2950] [2951] [2952] [2953] Underfull \hbox (badness 3861) in paragraph at lines 10978--10981 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if Overfull \hbox (36.78088pt too wide) in paragraph at lines 10985--10985 []\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 10998--11002 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2954] Underfull \hbox (badness 10000) in paragraph at lines 11038--11042 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 inverse==TRUE \T1/ptm/m/n/10 and \T1/pcr/m/n /10 both.sides==FALSE \T1/ptm/m/n/10 then the re- [2955] [2956] [2957] Overfull \hbox (20.58041pt too wide) in paragraph at lines 11179--11179 [] \T1/pcr/m/n/9 range(er$values-um$values[ind]);range(abs(er$vectors)-abs(um$ vectors[,ind]))[] Underfull \hbox (badness 1975) in paragraph at lines 11190--11195 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [2958] Underfull \hbox (badness 1803) in paragraph at lines 11267--11271 \T1/ptm/m/n/10 The last en-try will be the \T1/pcr/m/n/10 by \T1/ptm/m/n/10 var i-able, if \T1/pcr/m/n/10 object$by \T1/ptm/m/n/10 is not \T1/pcr/m/n/10 "NA"\T 1/ptm/m/n/10 . Underfull \hbox (badness 1502) in paragraph at lines 11279--11291 \T1/pcr/m/n/10 cs.smooth.spec \T1/ptm/m/n/10 (cu-bic re-gres-sion splines with shrinkage-to-zero); \T1/pcr/m/n/10 cc.smooth.spec Underfull \hbox (badness 2401) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 method is used if there is no more spe-cific method avail-able. Plot meth-ods can be Underfull \hbox (badness 2970) in paragraph at lines 11296--11300 \T1/ptm/m/n/10 added for spe-cific smooth classes, see source code for \T1/pcr/ m/n/10 mgcv:::plot.sos.smooth\T1/ptm/m/n/10 , [2959] [2960] [2961] Underfull \vbox (badness 10000) has occurred while \output is active [2962] Underfull \hbox (badness 6876) in paragraph at lines 11491--11497 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one or two vari-ables, spec-i-fied via terms like Underfull \hbox (badness 10000) in paragraph at lines 11532--11533 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2963] [2964] Underfull \hbox (badness 10000) in paragraph at lines 11649--11650 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2965] [2966] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11703--11703 [] \T1/pcr/m/n/9 b <- gam(y~s(x0,bs=bs,m=c(4,2))+s(x1,bs=bs)+s(x2,k=15,bs=bs, m=c(4,3,0))+[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11715--11715 [] \T1/pcr/m/n/9 ## now a model with first order penalty evaluated over (-.5, 1.5) (black)[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11727--11727 [] \T1/pcr/m/n/9 ## penalty defined on (-.5,1.5) gives plausible predictions and intervals[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 11732--11732 [] \T1/pcr/m/n/9 ## penalty defined on whole real line gives constant width i ntervals away[] [2967] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11738--11738 [] \T1/pcr/m/n/9 ## penalty defined only over the data interval (0,1) gives w ild and wide[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 11739--11739 [] \T1/pcr/m/n/9 ## extrapolation since penalty has been \TS1/pcr/m/n/9 `\T1/ pcr/m/n/9 turned off\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 outside data range:[] [2968] Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a Underfull \hbox (badness 10000) in paragraph at lines 11808--11810 \T1/ptm/m/n/10 term \T1/pcr/m/n/10 s(...,bs="cr",...)\T1/ptm/m/n/10 , \T1/pcr/m /n/10 s(...,bs="cs",...) \T1/ptm/m/n/10 or [2969] [2970] Underfull \hbox (badness 10000) in paragraph at lines 11936--11937 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2971] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12017--12017 []\T1/pcr/m/n/9 b <- gam(y~s(x,z,bs="ds",m=c(1,.5),k=50),data=data) ## first deriv penalty[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12018--12018 []\T1/pcr/m/n/9 b1 <- gam(y~s(x,z,bs="ds",m=c(2,.5),k=50),data=data) ## modifi ed 2nd deriv[] [2972] [2973] [2974] Underfull \hbox (badness 10000) in paragraph at lines 12168--12169 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2975] [2976] [2977] [2978] Overfull \hbox (9.78043pt too wide) in paragraph at lines 12407--12407 []\T1/pcr/m/n/9 b <- gam(crime ~ s(district,bs="mrf",k=20,xt=xt),data=columb,m ethod="REML")[] [2979] Underfull \hbox (badness 10000) in paragraph at lines 12468--12470 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2980] [2981] Underfull \vbox (badness 10000) has occurred while \output is active [2982] Underfull \hbox (badness 10000) in paragraph at lines 12627--12630 []\T1/ptm/m/n/10 For the \T1/pcr/m/n/10 smooth.construct \T1/ptm/m/n/10 method a smooth spec-i-fi-ca-tion ob- Underfull \hbox (badness 3312) in paragraph at lines 12627--12630 \T1/ptm/m/n/10 ject, usu-ally gen-er-ated by a term \T1/pcr/m/n/10 s(x,...,bs=" re",)\T1/ptm/m/n/10 . For the Underfull \hbox (badness 7099) in paragraph at lines 12627--12630 \T1/pcr/m/n/10 predict.Matrix \T1/ptm/m/n/10 method an ob-ject of class \T1/pcr /m/n/10 "random.effect" [2983] Overfull \hbox (4.38043pt too wide) in paragraph at lines 12709--12709 []\T1/pcr/m/n/9 b <- c(rnorm(nb/2)*2,rnorm(nb/2)*.5) ## random effect now with 2 variances[] [2984] Underfull \hbox (badness 10000) in paragraph at lines 12754--12760 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 7832) in paragraph at lines 12754--12760 \T1/pcr/m/n/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T1 /pcr/m/n/10 gam \T1/ptm/m/n/10 for- [2985] [2986] [2987] Underfull \vbox (badness 10000) has occurred while \output is active [2988] Overfull \hbox (36.7804pt too wide) in paragraph at lines 12968--12968 []\T1/pcr/m/n/9 ## notice NULL element in \TS1/pcr/m/n/9 '\T1/pcr/m/n/9 xt\TS1 /pcr/m/n/9 ' \T1/pcr/m/n/9 list - to indicate no xt object for "cr" basis...[] Underfull \vbox (badness 10000) has occurred while \output is active [2989] Underfull \hbox (badness 10000) in paragraph at lines 13071--13079 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths on the sphere, via terms like [2990] Underfull \hbox (badness 10000) in paragraph at lines 13097--13098 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2991] [2992] [2993] [2994] Underfull \hbox (badness 3396) in paragraph at lines 13358--13361 [][][]\T1/pcr/m/n/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any num-ber of vari-ables, spec-i-fied via terms like [2995] Underfull \hbox (badness 10000) in paragraph at lines 13403--13405 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [2996] [2997] [2998] [2999] Underfull \hbox (badness 10000) in paragraph at lines 13627--13630 []\T1/pcr/m/n/10 bs="fs" \T1/ptm/m/n/10 Smooth fac-tor in-ter-ac-tions are of-t en pro- Underfull \hbox (badness 3068) in paragraph at lines 13627--13630 \T1/ptm/m/n/10 duced us-ing \T1/pcr/m/n/10 by \T1/ptm/m/n/10 vari-ables (see [] []\T1/pcr/m/n/10 gam.models[][][]\T1/ptm/m/n/10 ), but a spe-cial smoother clas s (see [3000] Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][][]\T1/pcr/m/n/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 te[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr /m/n/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cubic.regression .spline[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 p.spline[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 soap[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 13660--13664 [][]\T1/pcr/m/n/10 user.defined.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [3001] [3002] [3003] [3004] [3005] Underfull \hbox (badness 2158) in paragraph at lines 13950--13950 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3006] Overfull \hbox (48.78088pt too wide) in paragraph at lines 14029--14029 []\T1/pcr/m/n/10 spasm.sp(object,sp,w=rep(1,object$nobs),get.trH=TRUE,block=0, centre=FALSE)[] [3007] [3008] Overfull \hbox (12.78088pt too wide) in paragraph at lines 14163--14163 [] \T1/pcr/m/n/10 signif.stars = getOption("show.signif.stars "),...)[] [3009] [3010] Underfull \hbox (badness 4846) in paragraph at lines 14294--14297 []\T1/ptm/m/n/10 The es-ti-mated co-vari-ance ma-trix of the pa-ram-e-ters (or es-ti-ma-tors if [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018] [3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026] [3027] [3028] [3029] [3030] Overfull \hbox (24.78088pt too wide) in paragraph at lines 15483--15483 []\T1/pcr/m/n/10 vcov(object, freq = FALSE, dispersion = NULL,unconditional=FA LSE, ...)[] [3031] [3032] [3033] [3034] [3035] Overfull \hbox (20.58041pt too wide) in paragraph at lines 15777--15777 []\T1/pcr/m/n/9 ## 1. If the zero inflation rate becomes decoupled from the li near predictor,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 15778--15778 []\T1/pcr/m/n/9 ## it is possible for the linear predictor to be almost unboun ded in regions[] Overfull \hbox (25.98041pt too wide) in paragraph at lines 15790--15790 []\T1/pcr/m/n/9 ## 3. Refit fixing the theta parameters at their estimated val ues, to check we[] [3036] [3037] [3038]) (./nlme-pkg.tex Chapter 25. [3039] Underfull \hbox (badness 1009) in paragraph at lines 84--93 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3040] Underfull \hbox (badness 1009) in paragraph at lines 174--183 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3041] [3042] [3043] [3044] [3045] Overfull \hbox (4.38043pt too wide) in paragraph at lines 454--454 [] \T1/pcr/m/n/9 lme(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3046] [3047] Overfull \hbox (20.58041pt too wide) in paragraph at lines 595--595 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 251-254 --------------------------- ---------------[] Overfull \hbox (9.78043pt too wide) in paragraph at lines 611--611 []\T1/pcr/m/n/9 # Compare an "lme" object with a "gls" object (test would be n on-sensical!)[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 614--614 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 222-225 --------------------------- ---------------[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 621--621 []\T1/pcr/m/n/9 ## Pinheiro and Bates, pp. 352-365 --------------------------- ---------------[] [3048] [3049] [3050] [3051] [3052] [3053] [3054] [3055] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1085--1085 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxil lary fissure"),[] [3056] Underfull \hbox (badness 5446) in paragraph at lines 1147--1149 []\T1/ptm/m/n/10 `\T1/pcr/m/n/10 http://stat.gamma.rug.nl/snijders/multilevel.h tm\T1/ptm/m/n/10 ', the first edi-tion of [3057] [3058] [3059] [3060] [3061] [3062] [3063] Underfull \hbox (badness 10000) in paragraph at lines 1630--1633 [][][]\T1/pcr/m/n/10 lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 fixed.effe cts.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 ranef.lmList[][][]\T1/ptm/m /n/10 , [][]\T1/pcr/m/n/10 plot.ranef.lmList[][][]\T1/ptm/m/n/10 , [3064] Underfull \hbox (badness 3780) in paragraph at lines 1647--1649 []\T1/ptm/m/n/10 This method func-tion ex-tracts the co-ef-fi-cients as-so-ci-a ted with each com-po-nent of the [3065] [3066] [3067] [3068] [3069] Underfull \hbox (badness 2042) in paragraph at lines 1994--2000 \T1/ptm/m/n/10 is in-ner to the \T1/pcr/m/n/10 displayLevel \T1/ptm/m/n/10 grou p-ing fac-tor. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3070] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2056--2056 []\T1/pcr/m/n/9 collapse(Pixel, collapse = 1) # same as collapse(Pixel, colla pse = "Dog")[] [3071] Underfull \hbox (badness 1132) in paragraph at lines 2145--2147 []\T1/ptm/m/n/10 fitted model ob-jects, from which pre-dic-tions can be ex-trac ted us-ing the [3072] [3073] Underfull \hbox (badness 4168) in paragraph at lines 2256--2262 [][][]\T1/pcr/m/n/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corARMA[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T 1/pcr/m/n/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize .corStruct[][][]\T1/ptm/m/n/10 , [3074] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2281--2281 [] \T1/pcr/m/n/9 gls(rate ~(pressure + I(pressure^2) + I(pressure^3) + I(pres sure^4))*QB,[] [3075] [3076] [3077] [3078] [3079] [3080] [3081] [3082] Underfull \hbox (badness 10000) in paragraph at lines 2844--2848 [][][]\T1/pcr/m/n/10 corFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corMatr ix.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 recalc.corStruct[][][]\T1 /ptm/m/n/10 , [3083] [3084] [3085] [3086] [3087] [3088] [3089] [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 6493) in paragraph at lines 3580--3588 [][][]\T1/pcr/m/n/10 corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corGaus[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 corSpher[][][]\T1/ptm /m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [3095] [3096] [3097] [3098] [3099] [3100] [3101] [3102] [3103] [3104] [3105] [3106] [3107] [3108] [3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] Underfull \hbox (badness 10000) in paragraph at lines 5160--5164 [][][]\T1/pcr/m/n/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [3119] [3120] [3121] [3122] [3123] [3124] [3125] Underfull \hbox (badness 10000) in paragraph at lines 5592--5595 [][][]\T1/pcr/m/n/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 getGroups.gls[][] []\T1/ptm/m/n/10 , [3126] [3127] [3128] [3129] [3130] [3131] [3132] [3133] [3134] Underfull \hbox (badness 2799) in paragraph at lines 6098--6104 \T1/ptm/m/n/10 covariance ma-trix, ei-ther \T1/pcr/m/n/10 "random.effects" \T1/ ptm/m/n/10 for the random-effects [3135] Underfull \hbox (badness 7133) in paragraph at lines 6159--6163 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3136] Underfull \hbox (badness 2057) in paragraph at lines 6243--6254 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsCon trol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 glsObject[][][]\T1/ptm/m/n/10 , [ ][]\T1/pcr/m/n/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.gls[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.gls[][][]\T1/ptm/m/n/10 , [3137] Underfull \hbox (badness 10000) in paragraph at lines 6307--6309 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 6339--6339 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3138] [3139] [3140] [3141] Underfull \hbox (badness 7133) in paragraph at lines 6557--6561 []\T1/ptm/m/n/10 an op-tional data frame con-tain-ing the vari-ables named in \ T1/pcr/m/n/10 model\T1/ptm/m/n/10 , [3142] Underfull \hbox (badness 10000) in paragraph at lines 6656--6662 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsCo ntrol[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsObject[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gnlsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict .gnls[][][]\T1/ptm/m/n/10 , Overfull \hbox (54.78088pt too wide) in paragraph at lines 6683--6683 []\T1/pcr/m/n/10 gnlsControl(maxIter = 50, nlsMaxIter = 7, msMaxIter = 50, min Scale = 0.001, [3143] Underfull \hbox (badness 10000) in paragraph at lines 6721--6723 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3144] Overfull \hbox (9.78043pt too wide) in paragraph at lines 6751--6751 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3145] [3146] [3147] Underfull \hbox (badness 10000) in paragraph at lines 6994--7001 [][][]\T1/pcr/m/n/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gapply[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nffGroupedData[][][ ]\T1/ptm/m/n/10 , [3148] Overfull \hbox (15.18042pt too wide) in paragraph at lines 7012--7012 [] \T1/pcr/m/n/9 y = "Distance from pituitary to pterygomaxilla ry fissure" ),[] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7017--7017 []\T1/pcr/m/n/9 fm1 <- lme( Orth.new ) # fixed and groups formulae extracted from object[] Underfull \hbox (badness 2875) in paragraph at lines 7039--7041 []\T1/ptm/m/n/10 an ob-ject to be sum-ma-rized - usu-ally a \T1/pcr/m/n/10 grou pedData \T1/ptm/m/n/10 ob-ject or a [3149] [3150] [3151] Underfull \hbox (badness 10000) in paragraph at lines 7254--7259 [][][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.gl sStruct[][][]\T1/ptm/m/n/10 , [3152] [3153] [3154] Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 []\T1/ptm/m/n/10 an op-tional list with con-trol pa-ram-e-ters for the ini-tial -iza- Underfull \hbox (badness 10000) in paragraph at lines 7406--7414 \T1/ptm/m/n/10 tion and op-ti-miza-tion al-go-rithms used in \T1/pcr/m/n/10 lme \T1/ptm/m/n/10 . De-faults to Underfull \hbox (badness 4036) in paragraph at lines 7406--7414 \T1/pcr/m/n/10 list(niterEM=20,gradHess=TRUE)\T1/ptm/m/n/10 , im-ply-ing that 2 0 EM it-er-a- Underfull \hbox (badness 3118) in paragraph at lines 7429--7432 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.re Struct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.corStruct[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 Initialize.varFunc[][][]\T1/ptm/m/n/10 , [3155] [3156] [3157] Underfull \hbox (badness 3354) in paragraph at lines 7644--7646 []\T1/ptm/m/n/10 linear model co-ef-fi-cients, only present when \T1/pcr/m/n/10 which \T1/ptm/m/n/10 is not equal to [3158] [3159] [3160] [3161] [3162] [3163] [3164] [3165] Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][][]\T1/pcr/m/n/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.lm List[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme.groupedData[][][]\T1/ptm/m/n/ 10 , [][]\T1/pcr/m/n/10 lmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme Object[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 8156--8173 [][]\T1/pcr/m/n/10 lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lmList[][ ][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/ pcr/m/n/10 plot.lme[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 predict.lme[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 qqnorm.lme[][][]\T1/ptm/m/n/10 , Overfull \hbox (12.78088pt too wide) in paragraph at lines 8199--8199 [] \T1/pcr/m/n/10 subset, method, na.action, control, contrasts, keep.data = TRUE)[] Underfull \hbox (badness 1642) in paragraph at lines 8208--8230 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a one-sided for-mula o f the form [3166] [3167] [3168] [3169] [3170] Overfull \hbox (36.78088pt too wide) in paragraph at lines 8473--8473 []\T1/pcr/m/n/10 lmeControl(maxIter = 50, msMaxIter = 50, tolerance = 1e-6, ni terEM = 25, Underfull \hbox (badness 10000) in paragraph at lines 8521--8523 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3171] Overfull \hbox (9.78043pt too wide) in paragraph at lines 8565--8565 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sigma}) h as been already used, duplicate ignored \relax l.8572 \aliasA{sigma}{lmeObject}{sigma} [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] Underfull \hbox (badness 10000) in paragraph at lines 9324--9331 [][][]\T1/pcr/m/n/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/pcr/m/n/10 gls[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/p cr/m/n/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 logLik.lmeS truct[][][]\T1/ptm/m/n/10 , Overfull \hbox (4.38043pt too wide) in paragraph at lines 9335--9335 []\T1/pcr/m/n/9 fm1 <- lme(distance ~ Sex * age, Orthodont, random = ~ age, me thod = "ML") [3184] Underfull \hbox (badness 6300) in paragraph at lines 9417--9420 []\T1/ptm/m/n/10 an op-tional log-i-cal value in-di-cat-ing whether all \T1/pcr /m/n/10 lm \T1/ptm/m/n/10 com-po-nents of [3185] [3186] [3187] [3188]pdfTeX warning (ext4): destination with the same ide ntifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl icate ignored \relax l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3189] Underfull \hbox (badness 10000) in paragraph at lines 9706--9709 []\T1/ptm/m/n/10 a ma-trix, or list of ma-tri-ces, with the same di-men-sions a s Underfull \hbox (badness 3108) in paragraph at lines 9750--9753 []\T1/ptm/m/n/10 a ma-trix with the new val-ues to be as-signed to the positive -definite Underfull \hbox (badness 2521) in paragraph at lines 9750--9753 \T1/ptm/m/n/10 ma-trix rep-re-sented by \T1/pcr/m/n/10 object\T1/ptm/m/n/10 . M ust have the same di-men-sions as [3190] [3191] [3192] [3193] [3194] [3195] [3196] [3197] Underfull \hbox (badness 7291) in paragraph at lines 10214--10216 []\T1/ptm/m/n/10 On the left side of an as-sign-ment, sets the \T1/pcr/m/n/10 D imnames \T1/ptm/m/n/10 at-tribute of \T1/pcr/m/n/10 object \T1/ptm/m/n/10 to [3198] [3199] [3200] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10430--10430 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights, [3201] Underfull \hbox (badness 1596) in paragraph at lines 10459--10485 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3202] [3203] [3204] Overfull \hbox (18.78088pt too wide) in paragraph at lines 10635--10635 []\T1/pcr/m/n/10 nlme(model, data, fixed, random, groups, start, correlation, weights,[] [3205] [3206] Overfull \hbox (36.78088pt too wide) in paragraph at lines 10786--10786 [] \T1/pcr/m/n/10 opt = c("nlminb", "nlm"), natural = TRUE, sigma = NULL, ...)[] Underfull \hbox (badness 2213) in paragraph at lines 10797--10802 []\T1/ptm/m/n/10 maximum num-ber of it-er-a-tions for [][]\T1/pcr/m/n/10 nlminb [][][] \T1/ptm/m/n/10 (\T1/pcr/m/n/10 iter.max\T1/ptm/m/n/10 ) or the [][]\T1/p cr/m/n/10 nlm[][][] [3207] Underfull \hbox (badness 8075) in paragraph at lines 10819--10823 []\T1/ptm/m/n/10 a log-i-cal value passed as the \T1/pcr/m/n/10 trace \T1/ptm/m /n/10 to [][]\T1/pcr/m/n/10 nlminb[][][](..,control= Underfull \hbox (badness 10000) in paragraph at lines 10838--10840 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is Overfull \hbox (9.78043pt too wide) in paragraph at lines 10874--10874 []\T1/pcr/m/n/9 # request that information on the evolution of the ms iteratio ns be printed[] [3208] [3209] [3210] [3211] Overfull \hbox (96.18033pt too wide) in paragraph at lines 11130--11130 []\T1/pcr/m/n/9 cfm1 <- confint(fm1) # via profiling each % FIXME: only *one* message instead of one *each*[] [3212] [3213] [3214] [3215] [3216] [3217] Overfull \hbox (25.98041pt too wide) in paragraph at lines 11519--11519 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3218] [3219] [3220] [3221] [3222] [3223] Underfull \hbox (badness 6268) in paragraph at lines 11906--11916 [][][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdIdent[][][]\T 1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/1 0 pdMatrix[][][]\T1/ptm/m/n/10 , [3224] [3225] [3226] [3227] Underfull \hbox (badness 10000) in paragraph at lines 12167--12173 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 c oef.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdBlocked[][][]\T1/ptm/m/n/1 0 , [][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCon struct[][][]\T1/ptm/m/n/10 , [3228] [3229] [3230] [3231] [3232] Underfull \hbox (badness 6876) in paragraph at lines 12489--12491 []\T1/ptm/m/n/10 If \T1/pcr/m/n/10 value \T1/ptm/m/n/10 is an \T1/ptm/m/it/10 i ni-tial-ized \T1/pcr/m/n/10 pdMat \T1/ptm/m/n/10 ob-ject, \T1/pcr/m/n/10 object \T1/ptm/m/n/10 will be con-structed from [3233] [3234] Underfull \hbox (badness 2452) in paragraph at lines 12645--12652 [][][]\T1/pcr/m/n/10 pdClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdCompS ymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdDiag[][][]\T1/ptm/m/n/10 , [][]\ T1/pcr/m/n/10 pdIdent[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdNatural[][][]\ T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdSymm[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n /10 reStruct[][][]\T1/ptm/m/n/10 , [3235] Underfull \hbox (badness 10000) in paragraph at lines 12710--12716 [][][]\T1/pcr/m/n/10 as.matrix.pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 p dClasses[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdFactor[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMatrix.re Struct[][][]\T1/ptm/m/n/10 , [3236] [3237] [3238] [3239] [3240] [3241] [3242] [3243] [3244] Overfull \hbox (25.98041pt too wide) in paragraph at lines 13299--13299 []\T1/pcr/m/n/9 example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodo nt)), .. lme(*)) [3245] [3246] [3247] [3248] [3249] Overfull \hbox (9.78043pt too wide) in paragraph at lines 13664--13664 []\T1/pcr/m/n/9 plot(fm1, resid(., type = "pool") ~ fitted(.) | Sex, abline = 0, id = 0.05)[] [3250] Underfull \hbox (badness 10000) in paragraph at lines 13691--13694 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nffGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a [3251] Underfull \hbox (badness 1838) in paragraph at lines 13734--13741 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/pcr/m/n/ 10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/pcr/m/n/10 inner Underfull \hbox (badness 3713) in paragraph at lines 13734--13741 \T1/ptm/m/n/10 or \T1/pcr/m/n/10 innerGroups \T1/ptm/m/n/10 are non-\T1/pcr/m/n /10 NULL\T1/ptm/m/n/10 , a leg-end for the dif-fer-ent \T1/pcr/m/n/10 inner Overfull \hbox (12.78088pt too wide) in paragraph at lines 13791--13791 []\T1/pcr/m/n/10 plot(x, outer, inner, innerGroups, xlab, ylab, strip, aspect, panel,[] [3252] Underfull \hbox (badness 10000) in paragraph at lines 13798--13801 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nfnGroupedD ata\T1/ptm/m/n/10 , rep-re-sent-ing a Underfull \hbox (badness 2469) in paragraph at lines 13798--13801 \T1/pcr/m/n/10 groupedData \T1/ptm/m/n/10 ob-ject with a nu-meric pri-mary co-v ari-ate and a sin-gle Underfull \hbox (badness 4582) in paragraph at lines 13826--13829 []\T1/ptm/m/n/10 optional char-ac-ter strings with the la-bels for the plot. De -fault is Underfull \hbox (badness 10000) in paragraph at lines 13826--13829 \T1/ptm/m/n/10 the cor-re-spond-ing el-e-ments of \T1/pcr/m/n/10 attr(object,"l abels") \T1/ptm/m/n/10 and [3253] Underfull \hbox (badness 10000) in paragraph at lines 13906--13909 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 nmGroupedDa ta\T1/ptm/m/n/10 , rep-re-sent-ing a [3254] Underfull \hbox (badness 1472) in paragraph at lines 13931--13938 \T1/ptm/m/n/10 ciate points within each panel of the Trel-lis plot. If equal to \T1/pcr/m/n/10 TRUE\T1/ptm/m/n/10 , [3255] Underfull \hbox (badness 10000) in paragraph at lines 14000--14002 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 colla pse.groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 plot.nfnGroupedData[][ ][]\T1/ptm/m/n/10 , [3256] [3257] [3258] [3259] Underfull \hbox (badness 1215) in paragraph at lines 14280--14282 []\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis. De-faults to [3260] [3261] [3262] [3263] Overfull \hbox (20.58041pt too wide) in paragraph at lines 14524--14524 []\T1/pcr/m/n/9 newOrth <- data.frame(Sex = c("Male","Male","Female","Female", "Male","Male"),[] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272]pdfTeX warning (e xt4): destination with the same identifier (name{Rfn.random.effects}) has been already used, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destin ation with the same identifier (name{Rfn.random.effects.1}) has been already us ed, duplicate ignored \relax l.15177 ...Extract Random Effects}{random.effects} [3273] [3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] Underfull \hbox (badness 1009) in paragraph at lines 15834--15843 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3283] [3284] [3285] Overfull \hbox (66.78088pt too wide) in paragraph at lines 15981--15981 [] \T1/pcr/m/n/10 type = c("response", "pearson", "normalized"), asLi st = FALSE, ...)[] [3286] [3287] [3288] [3289] [3290] Underfull \hbox (badness 10000) in paragraph at lines 16316--16322 [][][]\T1/pcr/m/n/10 groupedData[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 lme[] [][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 pdMat[][][]\T1/ptm/m/n/10 , [][]\T1/pcr /m/n/10 solve.reStruct[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 summary.reStruc t[][][]\T1/ptm/m/n/10 , [3291] Overfull \hbox (18.78088pt too wide) in paragraph at lines 16347--16347 [] \T1/pcr/m/n/10 method = c("REML", "ML"), niterEM = c(40, 200), useG en, ...)[] [3292] [3293] [3294] [3295] [3296] [3297] [3298] Underfull \hbox (badness 1728) in paragraph at lines 16836--16839 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1867) in paragraph at lines 17171--17180 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Blocked" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdBlocked\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 "Compound Symmetry" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdCompSymm \T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Diagonal" \T1/ptm/m/n/10 for Underfull \hbox (badness 5563) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdDiag\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Multiple of an Identity" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Gener al Underfull \hbox (badness 10000) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 Positive-Definite,Natural Parametrization" \T1/ptm/m/n/10 for Underfull \hbox (badness 7397) in paragraph at lines 17171--17180 \T1/pcr/m/n/10 pdNatural\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "General Positive-Defin ite" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 pdSymm\T1/ptm/m/n/10 , and [3304] Underfull \hbox (badness 1521) in paragraph at lines 17235--17243 \T1/ptm/m/n/10 fault de-pends on the method func-tion: \T1/pcr/m/n/10 "Combinat ion of variance Underfull \hbox (badness 10000) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varExp\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Different standard deviat ions per stratum" \T1/ptm/m/n/10 for Underfull \hbox (badness 1694) in paragraph at lines 17235--17243 \T1/pcr/m/n/10 varIdent\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "Power of variance covar iate" \T1/ptm/m/n/10 for \T1/pcr/m/n/10 varPower\T1/ptm/m/n/10 , and [3305] [3306] [3307] [3308] Underfull \hbox (badness 10000) in paragraph at lines 17482--17489 [][][]\T1/pcr/m/n/10 varComb[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varConstP ower[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varExp[][][]\T1/ptm/m/n/10 , [][] \T1/pcr/m/n/10 varFixed[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varIdent[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 varPower[][][]\T1/ptm/m/n/10 , [3309] [3310] [3311] [3312] [3313] [3314] [3315] Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corLin[][] []\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18017--18027 [][]\T1/pcr/m/n/10 Variogram.corRatio[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corSphe r[][][]\T1/ptm/m/n/10 , [3316] Underfull \hbox (badness 3579) in paragraph at lines 18055--18060 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3317] Underfull \hbox (badness 3579) in paragraph at lines 18119--18124 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3318] Underfull \hbox (badness 3579) in paragraph at lines 18182--18187 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3319] Underfull \hbox (badness 1577) in paragraph at lines 18243--18245 []\T1/ptm/m/n/10 an ob-ject in-her-it-ing from class \T1/pcr/m/n/10 "[][]corRat io[][][]"\T1/ptm/m/n/10 , rep-re-sent-ing an Ra-tio-nal Underfull \hbox (badness 3579) in paragraph at lines 18245--18250 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3320] Underfull \hbox (badness 3579) in paragraph at lines 18308--18313 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][][]\T1/pcr/m/n/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variog ram[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.default[][][]\T1/ptm/m/n /10 , [][]\T1/pcr/m/n/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18341--18350 [][]\T1/pcr/m/n/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 V ariogram.corLin[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Variogram.corRatio[][] []\T1/ptm/m/n/10 , [3321] Underfull \hbox (badness 3579) in paragraph at lines 18380--18385 \T1/ptm/m/n/10 is to be cal-cu-lated. De-faults to \T1/pcr/m/n/10 NULL\T1/ptm/m /n/10 , in which case a se-quence [3322] [3323] Underfull \hbox (badness 1009) in paragraph at lines 18526--18535 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3324] [3325] Underfull \hbox (badness 1009) in paragraph at lines 18658--18667 \T1/pcr/m/n/10 "response"\T1/ptm/m/n/10 , the "raw" resid-u-als (ob-served - fi t-ted) are used; else, if [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334]) (./nnet-pkg.tex Chapter 26. pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \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} [3335] Overfull \hbox (12.78088pt too wide) in paragraph at lines 70--70 [] \T1/pcr/m/n/10 contrasts = NULL, Hess = FALSE, summ = 0, censored = FALSE,[] [3336] [3337] [3338] Overfull \hbox (15.18042pt too wide) in paragraph at lines 369--369 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3339] Overfull \hbox (4.38043pt too wide) in paragraph at lines 426--426 []\T1/pcr/m/n/9 targets <- matrix(c(rep(c(1,0,0),50), rep(c(0,1,0),50), rep(c( 0,0,1),50)),[] Overfull \hbox (31.3804pt too wide) in paragraph at lines 429--429 []\T1/pcr/m/n/9 ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, decay =5e-4, maxit=200)[] [3340] [3341] Overfull \hbox (15.18042pt too wide) in paragraph at lines 509--509 []\T1/pcr/m/n/9 ir.nn2 <- nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,[] [3342]) (./rpart-pkg.tex Chapter 27. [3343] [3344] [3345] [3346] Overfull \hbox (36.78088pt too wide) in paragraph at lines 324--324 []\T1/pcr/m/n/10 labels(object, digits = 4, minlength = 1L, pretty, collapse = TRUE, ...)[] [3347] [3348] [3349] [3350] Underfull \hbox (badness 1442) in paragraph at lines 591--597 []\T1/ptm/m/n/10 if \T1/pcr/m/n/10 FALSE\T1/ptm/m/n/10 , the leaf nodes will be at the hor-i-zon-tal plot co-or-di-nates of [3351] [3352] Overfull \hbox (0.78088pt too wide) in paragraph at lines 728--728 [] \T1/pcr/m/n/10 filename = paste(deparse(substitute(tree)), ".ps", sep = ""),[] [3353] [3354] Overfull \hbox (25.98041pt too wide) in paragraph at lines 904--904 []\T1/pcr/m/n/9 predict(fit, type = "matrix") # level number, class frequencie s, probabilities[] [3355] Overfull \hbox (48.78088pt too wide) in paragraph at lines 923--923 []\T1/pcr/m/n/10 print(x, minlength = 0, spaces = 2, cp, digits = getOption("d igits"), ...)[] [3356] [3357] [3358] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1165--1165 []\T1/pcr/m/n/10 rpart(formula, data, weights, subset, na.action = na.rpart, m ethod, Overfull \hbox (12.78088pt too wide) in paragraph at lines 1166--1166 [] \T1/pcr/m/n/10 model = FALSE, x = FALSE, y = TRUE, parms, control, cos t, ...)[] [3359] Underfull \hbox (badness 2846) in paragraph at lines 1228--1230 []\T1/ptm/m/n/10 a list of op-tions that con-trol de-tails of the \T1/pcr/m/n/1 0 rpart \T1/ptm/m/n/10 al-go-rithm. See [3360] Overfull \hbox (20.58041pt too wide) in paragraph at lines 1272--1272 []\T1/pcr/m/n/9 par(mfrow = c(1,2), xpd = NA) # otherwise on some devices the text is clipped[] Overfull \hbox (24.78088pt too wide) in paragraph at lines 1288--1288 []\T1/pcr/m/n/10 rpart.control(minsplit = 20, minbucket = round(minsplit/3), c p = 0.01, Overfull \hbox (60.78088pt too wide) in paragraph at lines 1289--1289 [] \T1/pcr/m/n/10 maxcompete = 4, maxsurrogate = 5, usesurrogate = 2, xval = 10,[] [3361] [3362] [3363] [3364] [3365] [3366] Underfull \hbox (badness 1565) in paragraph at lines 1745--1748 []\T1/ptm/m/n/10 the ploidy sta-tus of the tu-mor, from flow cy-tom-e-try. Val- ues are `\T1/pcr/m/n/10 diploid\T1/ptm/m/n/10 ', [3367] [3368] Overfull \hbox (12.78088pt too wide) in paragraph at lines 1839--1839 [] \T1/pcr/m/n/10 pretty = NULL, digits = getOption("digits") - 3, use.n = FALSE,[] [3369] [3370] [3371]) (./spatial-pkg.tex [3372] Chapter 28. [3373] [3374] [3375] [3376] [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3379] [3380] [3381] [3382] [3383] [3384] [3385] [3386] [3387] [3388] [3389] [3390] [3391]) (./survival-pkg.tex [3392] Chapter 29. [3393] [3394] 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.[] [3395] [3396]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} [3397] [3398] 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)[] [3399] 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)[] [3400] [3401] Underfull \vbox (badness 10000) has occurred while \output is active [3402] 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"),[] [3403] [3404] Overfull \hbox (9.78043pt too wide) in paragraph at lines 805--805 [] \T1/pcr/m/n/9 subcoh = ~subcohort, id=~seqno, stratum=~instit, cohort.siz e=stratsizes,[] [3405] [3406] [3407] Underfull \hbox (badness 1097) in paragraph at lines 975--977 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. Overfull \hbox (4.38043pt too wide) in paragraph at lines 995--995 []\T1/pcr/m/n/9 ppois(4, 10.24153) #chance of seeing 4 or fewer events wit h large rate[] [3408] [3409] Overfull \hbox (31.3804pt too wide) in paragraph at lines 1110--1110 []\T1/pcr/m/n/9 ## Not run: clogit(case ~ spontaneous + induced + strata(strat um), data=infert) [3410]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col on}) has been already used, duplicate ignored \relax l.1178 ...erapy for Stage B/C colon cancer}{colon} [3411] 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"),[] [3412] [3413] Overfull \hbox (36.78088pt too wide) in paragraph at lines 1425--1425 [] \T1/pcr/m/n/10 timewt = c("n", "S", "S/G", "n/G", "n/G2", "I"), cluster, in fluence =0,[] [3414] [3415] [3416] [3417] [3418] Underfull \hbox (badness 1337) in paragraph at lines 1799--1803 [][][]\T1/pcr/m/n/10 coxph.object[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 coxp h.control[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 cluster[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 strata[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 Surv[][][] \T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m /n/10 pspline[][][]\T1/ptm/m/n/10 , [3419] Overfull \hbox (6.78088pt too wide) in paragraph at lines 1854--1854 []\T1/pcr/m/n/10 iter.max = 20, toler.inf = sqrt(eps), outer.max = 10, timefix =TRUE)[] [3420] [3421] [3422] [3423] [3424] [3425] [3426] Overfull \hbox (4.38043pt too wide) in paragraph at lines 2324--2324 [] \T1/pcr/m/n/9 [1] "extreme" "logistic" "gaussian" "weibull" " exponential"[] Overfull \hbox (6.78088pt too wide) in paragraph at lines 2351--2351 []\T1/pcr/m/n/10 finegray(formula, data, weights, subset, na.action= na.pass, etype, [3427] [3428] [3429] Overfull \hbox (12.78088pt too wide) in paragraph at lines 2574--2574 []\T1/pcr/m/n/10 frailty.t(x, sparse = (nclass > 5), theta, df, eps = 1e-05, t df = 5,[] [3430] [3431] [3432] [3433] Overfull \hbox (15.18042pt too wide) in paragraph at lines 2858--2858 []\T1/pcr/m/n/9 kfit <- coxph(Surv(time, status)~ age + sex + disease + frailt y(id), kidney) [3434] Overfull \hbox (36.7804pt too wide) in paragraph at lines 2894--2894 [] \T1/pcr/m/n/9 factor(c(0, 1, 2,1,0,2), 0:2, c("censored", "progre ssion", "death")))[] Underfull \hbox (badness 1389) in paragraph at lines 2908--2910 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3435] Underfull \hbox (badness 1048) in paragraph at lines 2963--2965 []\T1/ptm/m/n/10 this pa-ram-e-ter is no longer nec-es-sary and is ig-nored. Se e the note in [3436] Overfull \hbox (36.7804pt too wide) in paragraph at lines 3037--3037 [] \T1/pcr/m/n/9 rmap=list(sex=sex, age=age*365.35, year=as.Da te(\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 1979/01/01\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3437] [3438] Underfull \vbox (badness 10000) has occurred while \output is active [3439] Underfull \vbox (badness 10000) has occurred while \output is active [3440] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3294--3294 []\T1/pcr/m/n/9 # surprise) but their rates of conversion to PCM are essential ly the same.[] [3441] [3442] [3443] [3444] [3445] Overfull \hbox (4.38043pt too wide) in paragraph at lines 3560--3560 [] \T1/pcr/m/n/9 entry.dt = as.Date(paste("2011", 1:10, "5" , sep=\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 -\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )))[] [3446] Underfull \vbox (badness 10000) has occurred while \output is active [3447] [3448] [3449] [3450] [3451] [3452] Overfull \hbox (0.78088pt too wide) in paragraph at lines 3977--3977 [] \T1/pcr/m/n/10 pch=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, ysca le=1,[] [3453] [3454] Overfull \hbox (24.78088pt too wide) in paragraph at lines 4165--4165 []\T1/pcr/m/n/10 se.fit=FALSE, na.action=na.pass, terms=names(object$assign), collapse,[] [3455] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4291--4291 []\T1/pcr/m/n/9 mresid <- (lung$status-1) - predict(fit, type=\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 expected\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 ) #Martingale resid[] [3456] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4299--4299 [] \T1/pcr/m/n/9 predict(fit, reference="sample") + sum(coef(fit) * fit$means , na.rm=TRUE)[] [3457] Overfull \hbox (25.98041pt too wide) in paragraph at lines 4385--4385 []\T1/pcr/m/n/9 pct <- 1:98/100 # The 100th percentile of predicted survival is at +infinity[] [3458] [3459] Underfull \hbox (badness 1852) in paragraph at lines 4533--4535 []\T1/ptm/m/n/10 an ob-ject of class \T1/pcr/m/n/10 "summary.survfit"\T1/ptm/m/ n/10 , which is the re-sult of the [3460] [3461] Overfull \hbox (0.78088pt too wide) in paragraph at lines 4668--4668 []\T1/pcr/m/n/10 pspline(x, df=4, theta, nterm=2.5 * df, degree=3, eps=0.1, me thod, Overfull \hbox (36.78088pt too wide) in paragraph at lines 4669--4669 [] \T1/pcr/m/n/10 Boundary.knots=range(x), intercept=FALSE, penalty=TRUE, co mbine, ...)[] [3462] [3463] [3464] Overfull \hbox (30.78088pt too wide) in paragraph at lines 4833--4833 [] \T1/pcr/m/n/10 py <- pyears(futime ~ rx, rmap=list(age=age, sex=sex, year= entry.dt),[] [3465] Overfull \hbox (9.78043pt too wide) in paragraph at lines 4935--4935 []\T1/pcr/m/n/9 pfit <- pyears(Surv(ptime/365.25, pstat) ~ temp.yr + temp.age + sex, mgus,[] Overfull \hbox (15.18042pt too wide) in paragraph at lines 4956--4956 []\T1/pcr/m/n/9 fit1 <- pyears(Surv(stop/365.25, event) ~ cut(age + 48, c(0,50 ,60,70,100)) +[] Overfull \hbox (20.58041pt too wide) in paragraph at lines 4958--4958 []\T1/pcr/m/n/9 fit2 <- pyears(Surv(stop/365.25, event) ~ tcut(age + 48, c(0,5 0,60,70,100)) +[] [3466] [3467] [3468] [3469] [3470] Underfull \vbox (badness 2126) has occurred while \output is active [3471] [3472] [3473] Overfull \hbox (6.78088pt too wide) in paragraph at lines 5548--5548 []\T1/pcr/m/n/10 residuals(object, type=c("response", "deviance","dfbeta","dfb etas",[] Underfull \hbox (badness 1043) in paragraph at lines 5560--5563 \T1/pcr/m/n/10 "dfbetas"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "working"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "ldcase"\T1/ptm/m/n/10 , \T1/pcr/m/n/10 "lsresp"\T1/ptm/m/n/1 0 , \T1/pcr/m/n/10 "ldshape"\T1/ptm/m/n/10 , and [3474] [3475] [3476] [3477] [3478] Overfull \hbox (15.18042pt too wide) in paragraph at lines 5860--5860 []\T1/pcr/m/n/9 lfit1 <- survreg(Surv(time, status) ~ age + ridge(ph.ecog, the ta=5), cancer)[] Overfull \hbox (42.18039pt too wide) in paragraph at lines 5861--5861 []\T1/pcr/m/n/9 lfit2 <- survreg(Surv(time, status) ~ sex + ridge(age, ph.ecog , theta=1), cancer)[] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.5866 ...ata from a soldering experiment}{solder} [3479] [3480] Overfull \hbox (24.78088pt too wide) in paragraph at lines 5972--5972 []\T1/pcr/m/n/10 statefig(layout, connect, margin = 0.03, box = TRUE, cex = 1, col = 1, [3481] [3482] [3483] [3484] [3485] Overfull \hbox (42.78088pt too wide) in paragraph at lines 6333--6333 []\T1/pcr/m/n/10 event = TRUE, pyears = TRUE, expected = TRUE, rate = FALSE, r r =expected,[] Overfull \hbox (36.78088pt too wide) in paragraph at lines 6334--6334 []\T1/pcr/m/n/10 ci.r = FALSE, ci.rr = FALSE, totals=FALSE, legend = TRUE, vli ne = FALSE,[] [3486] [3487] [3488] [3489] Overfull \hbox (54.78088pt too wide) in paragraph at lines 6626--6626 [] \T1/pcr/m/n/10 type=c(\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 right\TS1/pcr/m/n/ 10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 left\TS1/pcr/m/n/10 '\T1/p cr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval\TS1/pcr/m/n/10 '\T1/pcr/m/ n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 counting\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \TS1/pcr/m/n/10 '\T1/pcr/m/n/10 interval2\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 , \T S1/pcr/m/n/10 '\T1/pcr/m/n/10 mstate\TS1/pcr/m/n/10 '\T1/pcr/m/n/10 ),[] [3490] [3491] [3492] Underfull \hbox (badness 1253) in paragraph at lines 6915--6918 []\T1/ptm/m/n/10 The \T1/pcr/m/n/10 median\T1/ptm/m/n/10 , \T1/pcr/m/n/10 quant ile \T1/ptm/m/n/10 and \T1/pcr/m/n/10 plot \T1/ptm/m/n/10 meth-ods first con-st ruct a sur-vival curve us-ing [3493] [3494] Underfull \hbox (badness 10000) in paragraph at lines 7041--7050 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the form Underfull \hbox (badness 3758) in paragraph at lines 7041--7050 \T1/pcr/m/n/10 Surv(time,status) ~ predictors\T1/ptm/m/n/10 . For a one-sample test, the [3495] Overfull \hbox (36.7804pt too wide) in paragraph at lines 7137--7137 [] \T1/pcr/m/n/9 rmap= list(age=(accept.dt - birth.dt), sex=1 , year=accept.dt),[] [3496] Overfull \hbox (24.78088pt too wide) in paragraph at lines 7155--7155 [] \T1/pcr/m/n/10 method=c("ederer", "hakulinen", "conditional", "indiv idual.h",[] Underfull \hbox (badness 1038) in paragraph at lines 7197--7203 \T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d icted sur-vival [3497] Overfull \hbox (48.78088pt too wide) in paragraph at lines 7249--7249 [] \T1/pcr/m/n/10 rmap = list(year=entry.dt, age=(birth.d t-entry.dt)),[] [3498] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7335--7335 []\T1/pcr/m/n/9 summary(fit1, times=1:10*182.5, scale=365) #expected survival by 1/2 years[] [3499] [3500] [3501] Underfull \hbox (badness 10000) in paragraph at lines 7560--7565 [][][]\T1/pcr/m/n/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 s urvfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/pcr/m/n/10 survfit.object[][][]\T1/p tm/m/n/10 , [][]\T1/pcr/m/n/10 print.survfit[][][]\T1/ptm/m/n/10 , [3502] Overfull \hbox (30.78088pt too wide) in paragraph at lines 7581--7581 [] \T1/pcr/m/n/10 conf.type=c("log","log-log","plain","none", "logit", "arcsin"),[] [3503] [3504] Overfull \hbox (4.38043pt too wide) in paragraph at lines 7798--7798 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3505] [3506] [3507] Underfull \hbox (badness 3058) in paragraph at lines 7969--7974 []\T1/ptm/m/n/10 an older ar-gu-ment that com-bined \T1/pcr/m/n/10 stype \T1/pt m/m/n/10 and \T1/pcr/m/n/10 ctype\T1/ptm/m/n/10 , now de- Underfull \hbox (badness 7759) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 pri-cated. Le-gal val-ues were "kaplan-meier" which is equiv-a- Underfull \hbox (badness 2913) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 lent to \T1/pcr/m/n/10 stype=1,ctype=1\T1/ptm/m/n/10 , "fleming- harrington" which is equiv- Underfull \hbox (badness 4353) in paragraph at lines 7969--7974 \T1/ptm/m/n/10 a-lent to \T1/pcr/m/n/10 stype=2,ctype=1\T1/ptm/m/n/10 , and "fh 2" which is equiv-a-lent to [3508] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8087--8087 []\T1/pcr/m/n/9 # There are no interval censored subjects, only left-censored (status=3),[] [3509] [3510] [3511] [3512] Overfull \hbox (30.78088pt too wide) in paragraph at lines 8381--8381 []\T1/pcr/m/n/10 survfitcoxph.fit(y, x, wt, x2, risk, newrisk, strata, se.fit, survtype, [3513] Underfull \hbox (badness 1354) in paragraph at lines 8422--8426 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3514] [3515] Underfull \hbox (badness 2035) in paragraph at lines 8597--8604 \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 8597--8604 \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 8597--8604 \T1/pcr/m/n/10 "logistic"\T1/ptm/m/n/10 ,\T1/pcr/m/n/10 "lognormal" \T1/ptm/m/n /10 and \T1/pcr/m/n/10 "loglogistic"\T1/ptm/m/n/10 . Oth-er-wise, it is [3516] Overfull \hbox (20.58041pt too wide) in paragraph at lines 8673--8673 []\T1/pcr/m/n/9 # There are multiple ways to parameterize a Weibull distributi on. The survreg[] [3517] [3518] [3519] Overfull \hbox (31.3804pt too wide) in paragraph at lines 8830--8830 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3520] [3521] Overfull \hbox (4.38043pt too wide) in paragraph at lines 8962--8962 [] \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 8965--8965 [] \T1/pcr/m/n/9 deviance= function(...) stop(\TS1/pcr/m/n/9 ' \T1/pcr/m/n/9 deviance residuals not defined\TS1/pcr/m/n/9 '\T1/pcr/m/n/9 )[] [3522] [3523] [3524] [3525] Overfull \hbox (9.78043pt too wide) in paragraph at lines 9267--9267 []\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 9268--9268 []\T1/pcr/m/n/9 # 106 that agreed to be followed off protocol, the second data set has data[] [3526] Overfull \hbox (4.38043pt too wide) in paragraph at lines 9274--9274 [] \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 9276--9276 []\T1/pcr/m/n/9 fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bil i), data=pbc2)[] [3527] [3528] [3529] [3530] [3531] [3532] [3533] Overfull \hbox (12.78088pt too wide) in paragraph at lines 9727--9727 []\T1/pcr/m/n/10 levels, test = c("global", "trend", "pairwise"), predict = "l inear",[] [3534] [3535] [3536]) (./fullrefman.ind [3537] [3538] [3539] [3540] [3541] [3542] [3543] [3544] [3545] [3546] [3547] [3548] [3549] [3550] [3551] [3552] [3553] [3554] [3555] [3556] [3557] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2205--2207 []| \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 2207--2209 []| \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 2209--2211 []| \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 2211--2213 []| \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 2213--2215 []| \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 2215--2217 []| \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 2217--2219 []| \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 2219--2221 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2221--2223 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2223--2225 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2225--2227 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2227--2229 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2229--2231 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2231--2233 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3558] [3559] [3560] [3561] [3562] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2771--2773 []| \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 2773--2775 []| \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 2775--2777 []| \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 2777--2779 []| \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 2779--2781 []| \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 2781--2783 []| \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 2783--2785 []| \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 2785--2787 []| \T1/pcr/m/n/10 smooth.construct.ps.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2787--2789 []| \T1/pcr/m/n/10 smooth.construct.re.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2789--2791 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (25.3567pt too wide) in paragraph at lines 2791--2793 []| \T1/pcr/m/n/10 smooth.construct.sos.smooth.spec\T1/ptm/m/n/10 , [3563] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2793--2795 []| \T1/pcr/m/n/10 smooth.construct.t2.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (43.3567pt too wide) in paragraph at lines 2795--2797 []| \T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (19.3567pt too wide) in paragraph at lines 2797--2799 []| \T1/pcr/m/n/10 smooth.construct.tp.smooth.spec\T1/ptm/m/n/10 , [3564] Overfull \hbox (19.3567pt too wide) in paragraph at lines 2934--2936 []| \T1/pcr/m/n/10 smooth.construct.so.smooth.spec\T1/ptm/m/n/10 , [3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572] Overfull \hbox (62.8567pt too wide) in paragraph at lines 3939--3941 []\T1/pcr/m/n/10 [,CsparseMatrix,index,index,logical-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 3941--3943 []\T1/pcr/m/n/10 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13729--13731 []\T1/pcr/m/n/10 kronecker,ANY,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13731--13733 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13733--13735 []\T1/pcr/m/n/10 kronecker,dgTMatrix,dtTMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 13735--13737 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,ANY-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13737--13739 []\T1/pcr/m/n/10 kronecker,diagonalMatrix,Matrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13739--13741 []\T1/pcr/m/n/10 kronecker,dsparseMatrix,dsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13741--13743 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dgTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13743--13745 []\T1/pcr/m/n/10 kronecker,dtTMatrix,dtTMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 13745--13747 []\T1/pcr/m/n/10 kronecker,indMatrix,indMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 13749--13751 []\T1/pcr/m/n/10 kronecker,Matrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 13751--13753 []\T1/pcr/m/n/10 kronecker,sparseMatrix,ANY-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13753--13755 []\T1/pcr/m/n/10 kronecker,sparseMatrix,TsparseMatrix-method Overfull \hbox (68.8567pt too wide) in paragraph at lines 13755--13757 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,sparseMatrix-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 13757--13759 []\T1/pcr/m/n/10 kronecker,TsparseMatrix,TsparseMatrix-method [3633] [3634] [3635] [3636] Overfull \hbox (50.8567pt too wide) in paragraph at lines 14533--14535 []\T1/pcr/m/n/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 14539--14541 []\T1/pcr/m/n/10 Logic,dMatrix,sparseVector-method 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wide) in paragraph at lines 14605--14607 []\T1/pcr/m/n/10 Logic,sparseVector,sparseVector-method Overfull \hbox (74.8567pt too wide) in paragraph at lines 14607--14609 []\T1/pcr/m/n/10 Logic,triangularMatrix,diagonalMatrix-method [3637] [3638] [3639] [3640] [3641] Overfull \hbox (52.01662pt too wide) in paragraph at lines 15599--15601 \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 , [3642] [3643] Overfull \hbox (8.8567pt too wide) in paragraph at lines 16156--16158 []\T1/pcr/m/n/10 nonstandardGenericWithTrace-class Overfull \hbox (14.8567pt too wide) in paragraph at lines 16175--16177 []\T1/pcr/m/n/10 norm,ddenseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 16177--16179 []\T1/pcr/m/n/10 norm,ddenseMatrix,missing-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16183--16185 []\T1/pcr/m/n/10 norm,diagonalMatrix,character-method [3644] Overfull \hbox (14.8567pt too wide) in paragraph at 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in paragraph at lines 16575--16577 []\T1/pcr/m/n/10 Ops,nonStructure,nonStructure-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16579--16581 []\T1/pcr/m/n/10 Ops,nsparseMatrix,dsparseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16581--16583 []\T1/pcr/m/n/10 Ops,nsparseMatrix,lsparseMatrix-method [3647] Overfull \hbox (32.8567pt too wide) in paragraph at lines 16583--16585 []\T1/pcr/m/n/10 Ops,nsparseMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16603--16605 []\T1/pcr/m/n/10 Ops,sparseMatrix,ddiMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 16605--16607 []\T1/pcr/m/n/10 Ops,sparseMatrix,diagonalMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 16607--16609 []\T1/pcr/m/n/10 Ops,sparseMatrix,ldiMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 16609--16611 []\T1/pcr/m/n/10 Ops,sparseMatrix,nsparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16613--16615 []\T1/pcr/m/n/10 Ops,sparseMatrix,sparseMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16617--16619 []\T1/pcr/m/n/10 Ops,sparseVector,atomicVector-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 16621--16623 []\T1/pcr/m/n/10 Ops,sparseVector,sparseVector-method [3648] Overfull \hbox (46.01662pt too wide) in paragraph at lines 16824--16826 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (77.3567pt too wide) in paragraph at lines 16850--16852 []\T1/pcr/m/n/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [3649] [3650] [3651] [3652] [3653] Overfull \hbox (46.01662pt too wide) in paragraph at lines 18124--18126 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18127--18129 \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 , [3654] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18129--18131 \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 18131--18133 \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 18133--18135 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 18135--18137 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18137--18139 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18139--18141 \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 18141--18143 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18143--18145 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 Predict.matrix.soap.film\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , Overfull \hbox (52.01662pt too wide) in paragraph at lines 18147--18149 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (4.01662pt too wide) in paragraph at lines 18149--18151 \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 18151--18153 \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 18153--18155 \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 18155--18157 \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 18157--18159 \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 , [3655] [3656] Overfull \hbox (4.01662pt too wide) in paragraph at lines 18507--18509 \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 18579--18581 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 getDLLRegisteredRoutines\T1/ptm/m/it/10 )\T1/p tm/m/n/10 , [3657] [3658] [3659] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19043--19045 []\T1/pcr/m/n/10 qr.coef,sparseQR,ddenseMatrix-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19052--19054 []\T1/pcr/m/n/10 qr.fitted,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19054--19056 []\T1/pcr/m/n/10 qr.fitted,sparseQR,Matrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19056--19058 []\T1/pcr/m/n/10 qr.fitted,sparseQR,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19058--19060 []\T1/pcr/m/n/10 qr.fitted,sparseQR,numeric-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19070--19072 []\T1/pcr/m/n/10 qr.qty,sparseQR,ddenseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19080--19082 []\T1/pcr/m/n/10 qr.qy,sparseQR,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19095--19097 []\T1/pcr/m/n/10 qr.resid,sparseQR,ddenseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19101--19103 []\T1/pcr/m/n/10 qr.resid,sparseQR,numeric-method [3660] Overfull \hbox (62.8567pt too wide) in paragraph at lines 19217--19219 []\T1/pcr/m/n/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [3661] Overfull \hbox (26.8567pt too wide) in paragraph at lines 19424--19426 []\T1/pcr/m/n/10 rbind2,atomicVector,ddiMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19426--19428 []\T1/pcr/m/n/10 rbind2,atomicVector,ldiMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19428--19430 []\T1/pcr/m/n/10 rbind2,atomicVector,Matrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19430--19432 []\T1/pcr/m/n/10 rbind2,ddiMatrix,atomicVector-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 19434--19436 []\T1/pcr/m/n/10 rbind2,denseMatrix,denseMatrix-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19436--19438 []\T1/pcr/m/n/10 rbind2,denseMatrix,matrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19438--19440 []\T1/pcr/m/n/10 rbind2,denseMatrix,numeric-method Overfull \hbox (38.8567pt too wide) in paragraph at lines 19440--19442 []\T1/pcr/m/n/10 rbind2,denseMatrix,sparseMatrix-method Overfull \hbox (56.8567pt too wide) in paragraph at lines 19442--19444 []\T1/pcr/m/n/10 rbind2,diagonalMatrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19444--19446 []\T1/pcr/m/n/10 rbind2,indMatrix,indMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 19446--19448 []\T1/pcr/m/n/10 rbind2,ldiMatrix,atomicVector-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19452--19454 []\T1/pcr/m/n/10 rbind2,Matrix,atomicVector-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19456--19458 []\T1/pcr/m/n/10 rbind2,matrix,denseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19466--19468 []\T1/pcr/m/n/10 rbind2,matrix,sparseMatrix-method Overfull \hbox (8.8567pt too wide) in paragraph at lines 19470--19472 []\T1/pcr/m/n/10 rbind2,numeric,denseMatrix-method Overfull \hbox (14.8567pt too wide) in paragraph at lines 19472--19474 []\T1/pcr/m/n/10 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[]\T1/pcr/m/n/10 rcond,denseMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19517--19519 []\T1/pcr/m/n/10 rcond,dgeMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19521--19523 []\T1/pcr/m/n/10 rcond,dpoMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19525--19527 []\T1/pcr/m/n/10 rcond,dppMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19529--19531 []\T1/pcr/m/n/10 rcond,dspMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19533--19535 []\T1/pcr/m/n/10 rcond,dsyMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19537--19539 []\T1/pcr/m/n/10 rcond,dtpMatrix,character-method Overfull \hbox (2.8567pt too wide) in paragraph at lines 19541--19543 []\T1/pcr/m/n/10 rcond,dtrMatrix,character-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 19545--19547 []\T1/pcr/m/n/10 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wide) in paragraph at lines 21196--21198 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (23.3567pt too wide) in paragraph at lines 21199--21203 []\T1/pcr/m/n/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 21204--21206 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (46.01662pt too wide) in paragraph at lines 21252--21254 \T1/ptm/m/it/10 (\T1/pcr/m/sl/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (20.8567pt too wide) in paragraph at lines 21285--21287 []\T1/pcr/m/n/10 solve,CHMfactor,ddenseMatrix-method Overfull \hbox (32.8567pt too wide) in paragraph at lines 21287--21289 []\T1/pcr/m/n/10 solve,CHMfactor,diagonalMatrix-method Overfull \hbox (26.8567pt too wide) in paragraph at lines 21289--21291 []\T1/pcr/m/n/10 solve,CHMfactor,dsparseMatrix-method 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but does not e xist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.chron} has been referenced but does not exist, replaced by a fixed one {/usr/share/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on fullrefman.pdf (3744 pages, 10279426 bytes). Transcript written on fullrefman.log. make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/doc/manual' + exit 0 Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.27385 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + /bin/chmod -Rf u+rwX -- /usr/src/tmp/R-base-buildroot + : + /bin/rm -rf -- /usr/src/tmp/R-base-buildroot + PATH=/usr/libexec/rpm-build:/usr/src/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games + cd R-3.6.1 + make 'INSTALL=/usr/libexec/rpm-build/install -p' install DESTDIR=/usr/src/tmp/R-base-buildroot install-pdf install-info make: Entering directory '/usr/src/RPM/BUILD/R-3.6.1' mkdir -p -- /usr/src/tmp/R-base-buildroot/usr/lib64/R make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/m4' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/m4' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tools' make[1]: Nothing to be done for 'install'. make[1]: Leaving directory 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'./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/cluster/libs/cluster.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/class/libs/class.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/MASS/libs/MASS.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/foreign/libs/foreign.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/rpart/libs/rpart.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/lattice/libs/lattice.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/spatial/libs/spatial.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/nnet/libs/nnet.so' changed from 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'./usr/lib64/R/library/utils/libs/utils.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/library/tools/libs/tools.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/R_de.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/R_X11.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/lapack.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) mode of './usr/lib64/R/modules/internet.so' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--) Verifying and fixing files in /usr/src/tmp/R-base-buildroot (binconfig,pkgconfig,libtool,desktop,gnuconfig) /usr/lib64/pkgconfig/libR.pc: Libs: '-Wl,--export-dynamic -fopenmp -L/usr/local/lib64 -L${rlibdir} -lR' --> '-Wl,--export-dynamic -fopenmp -L${rlibdir} -lR' Checking contents of files in /usr/src/tmp/R-base-buildroot/ (default) Compressing files in /usr/src/tmp/R-base-buildroot (auto) Verifying info files in /usr/src/tmp/R-base-buildroot/usr/share/info (normal) Adjusting library links in /usr/src/tmp/R-base-buildroot ./usr/lib64: libR.so -> libR.so ./usr/lib64/R/lib: Verifying ELF objects in /usr/src/tmp/R-base-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal) Hardlinking identical .pyc and .pyo files Executing(%check): /bin/sh -e /usr/src/tmp/rpm-tmp.4146 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.6.1 + export TZ= + TZ= + make check make: Entering directory '/usr/src/RPM/BUILD/R-3.6.1' make[1]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests/Examples' Testing examples for package 'base' Testing examples for package 'tools' comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK Testing examples for package 'utils' Testing examples for package 'grDevices' comparing 'grDevices-Ex.Rout' to 'grDevices-Ex.Rout.save' ... OK Testing examples for package 'graphics' comparing 'graphics-Ex.Rout' to 'graphics-Ex.Rout.save' ... OK Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... OK Testing examples for package 'datasets' comparing 'datasets-Ex.Rout' to 'datasets-Ex.Rout.save' ... OK Testing examples for package 'methods' Testing examples for package 'grid' comparing 'grid-Ex.Rout' to 'grid-Ex.Rout.save' ... OK Testing examples for package 'splines' comparing 'splines-Ex.Rout' to 'splines-Ex.Rout.save' ... OK Testing examples for package 'stats4' comparing 'stats4-Ex.Rout' to 'stats4-Ex.Rout.save' ... OK Testing examples for package 'tcltk' Testing examples for package 'compiler' Testing examples for package 'parallel' make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests/Examples' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running strict specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ... OK running code in 'simple-true.R' ... OK comparing 'simple-true.Rout' to './simple-true.Rout.save' ... OK running code in 'arith-true.R' ... OK comparing 'arith-true.Rout' to './arith-true.Rout.save' ... OK running code in 'arith.R' ... OK comparing 'arith.Rout' to './arith.Rout.save' ... OK running code in 'lm-tests.R' ... OK comparing 'lm-tests.Rout' to './lm-tests.Rout.save' ... OK running code in 'ok-errors.R' ... OK comparing 'ok-errors.Rout' to './ok-errors.Rout.save' ... OK running code in 'method-dispatch.R' ... OK comparing 'method-dispatch.Rout' to './method-dispatch.Rout.save' ... OK running code in 'any-all.R' ... OK comparing 'any-all.Rout' to './any-all.Rout.save' ... OK running code in 'd-p-q-r-tests.R' ... OK comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running sloppy specific tests make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'complex.R' ... OK comparing 'complex.Rout' to './complex.Rout.save' ... OK running code in 'eval-etc-2.R' ... OK comparing 'eval-etc-2.Rout' to './eval-etc-2.Rout.save' ... OK running code in 'print-tests.R' ... OK comparing 'print-tests.Rout' to './print-tests.Rout.save' ... OK running code in 'lapack.R' ... OK comparing 'lapack.Rout' to './lapack.Rout.save' ... OK running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK running code in 'datetime.R' ... OK comparing 'datetime.Rout' to './datetime.Rout.save' ...33c33 < [1] "2040-07-01 12:00:00 GMT" --- > [1] "2040-07-01 12:00:00 BST" 44c44 < [1] "2040-07-01 12:00:00 EST" --- > [1] "2040-07-01 12:00:00 EDT" OK running code in 'iec60559.R' ... OK comparing 'iec60559.Rout' to './iec60559.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' checking Sys.timezone ... make[4]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'timezone.R' ...make[4]: *** [Makefile.common:106: timezone.Rout] Error 1 make[4]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' Sys.timezone() appears unknown make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running regression tests ... make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'array-subset.R' ... OK running code in 'reg-tests-1a.R' ... OK running code in 'reg-tests-1b.R' ... OK running code in 'reg-tests-1c.R' ... OK running code in 'reg-tests-1d.R' ... OK running code in 'reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ... OK running code in 'p-qbeta-strict-tst.R' ... OK running code in 'r-strict-tst.R' ... OK running code in 'reg-IO.R' ... OK comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ... OK running code in 'reg-IO2.R' ... OK comparing 'reg-IO2.Rout' to './reg-IO2.Rout.save' ... OK running code in 'reg-plot.R' ... OK comparing 'reg-plot.pdf' to './reg-plot.pdf.save' ... OK running code in 'reg-S4-examples.R' ... OK running code in 'reg-BLAS.R' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'reg-tests-3.R' ... OK comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK running code in 'reg-examples3.R' ... OK comparing 'reg-examples3.Rout' to './reg-examples3.Rout.save' ... OK running tests of plotting Latin-1 expect failure or some differences if not in a Latin-1 or UTF-8 locale running code in 'reg-plot-latin1.R' ... FAILED running code in 'reg-S4.R' ... OK comparing 'reg-S4.Rout' to './reg-S4.Rout.save' ... OK make[3]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[2]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running tests of Internet functions make[3]: Entering directory '/usr/src/RPM/BUILD/R-3.6.1/tests' running code in 'internet.R' ... OK comparing 'internet.Rout' to './internet.Rout.save' ...8,10c8,247 < Warning message: < In nsl("cran.r-project.org") : < nsl() was unable to resolve host 'cran.r-project.org' --- > > > > # test do_download (and "record" #{packages}): > > ap <- available.packages(contrib.url("http://cran.r-project.org")) > > ## IGNORE_RDIFF_END > > > > # test url connections on http > > zz <- url("http://cran.r-project.org/") > > readLines(zz) > [1] "" > [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-3.6.1/tests' make[2]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make[1]: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1/tests' make: Leaving directory '/usr/src/RPM/BUILD/R-3.6.1' + exit 0 Processing files: R-base-3.6.1-alt1 Executing(%doc): /bin/sh -e /usr/src/tmp/rpm-tmp.92082 + umask 022 + /bin/mkdir -p /usr/src/RPM/BUILD + cd /usr/src/RPM/BUILD + cd R-3.6.1 + DOCDIR=/usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + export DOCDIR + rm -rf /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + /bin/mkdir -p /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + cp -prL doc/NEWS README /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + chmod -R go-w /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + chmod -R a+rX /usr/src/tmp/R-base-buildroot/usr/share/doc/R-base-3.6.1 + exit 0 warning: File listed twice: /usr/lib64/R/library/KernSmooth/html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/00Index.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/R.css warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkde2D.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/bkfe.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpih.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpik.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/dpill.html warning: File listed twice: /usr/lib64/R/library/KernSmooth/html/locpoly.html warning: File listed twice: /usr/lib64/R/library/MASS/html warning: File listed twice: /usr/lib64/R/library/MASS/html/00Index.html warning: File listed twice: /usr/lib64/R/library/MASS/html/Aids2.html warning: File listed twice: /usr/lib64/R/library/MASS/html/Animals.html warning: File listed twice: /usr/lib64/R/library/MASS/html/Boston.html warning: File listed twice: 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/usr/lib64/R/library/utils/html/vignette.html warning: File listed twice: /usr/lib64/R/library/utils/html/warnErrList.html warning: File listed twice: /usr/lib64/R/library/utils/html/winDialog.html warning: File listed twice: /usr/lib64/R/library/utils/html/winMenus.html warning: File listed twice: /usr/lib64/R/library/utils/html/winProgressBar.html warning: File listed twice: /usr/lib64/R/library/utils/html/winextras.html warning: File listed twice: /usr/lib64/R/library/utils/html/write.table.html warning: File listed twice: /usr/lib64/R/library/utils/html/zip.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.a8XLMC find-provides: running scripts (alternatives,debuginfo,gir,lib,maven,osgi-fc,pam,perl,pkgconfig,python,shell,tcl,typelib) lib.prov: /usr/src/tmp/R-base-buildroot/usr/lib64/libR.so: 1234 symbols, 21 bpp ++ /bin/sed -e '/^libR\.so/{p;s/R/R-2.11/}' --- find-provides-deps 2024-09-29 12:27:33.719791343 +0000 +++ filter-provides-deps 2024-09-29 12:27:33.721791366 +0000 @@ -1 +1,2 @@ libR.so()(64bit) = set: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 +libR-2.11.so()(64bit) = set:odjvQNYfHFGF6Xo9rSYpedG8BII3EakgydO9cuf3TxqqZyO7yMvQ7wSiUTrcy7nNqGiflliOlRYkEVx3WbfE9EMjzuK8DfBqYQcAifd5xG3BauIcFNL1sZ76iqxUM9hRH43rPONzmSAG7LsxwROHTsK033i8b0gJi5VZjqUZdWcRCCPuZbOjbw5ZapXarSwbze7OXk9oZitxqybLaksw9aaqOHEnB223TLF9SD7vFOvsFy2WSgly51YPRTiaMlYFyDDP9NEVlf0k9nKqTQLK0oOr42ikaNO8qMDqrMqi0uEqjGkcECmkbLpzWU07KcMFZshih0Y6E9D7Q3weNKHqXKWvsn2MWmyvL1UwIIEdwUgMkJEJZzbrO0Gf6mSh3Gp4chaB6ZBSNxEBzQfo8oI3nlATtUurObODEChxiChR3Sz5BY7sZtggK1s9I2O5fbrxZD2N1MmwiZEPvpCC4E6hVwPPNKtk5Z54WqF8IIn6OpFgx9iGMheCeZlorqE8U1kuL2iKAIKZ0UJFNYT4pKMobB2SiKdfygYd6CSnmra35jIQcdWS1Fkn8XHKcv2owwi8n6H7uhZn570IKT9W2ZpUIkdh1J5OhuMGZGVVV9znzE0i5t2ad0Tp0YA0KTKt2HoP9AArXjtIyaPyexd6r1dLHgqdNeuBrNp9YprE6Yf5tYcZdXYef4Iw40nPKHzryyBdOtTAwzgqgskhonz60wMdtMRy1PP1Ud2ZuGXGZHZb9HIuB0s3UshqI9G8wHr228a7ACpd4255Mb7yVf63utFkSIashXC7ZwEXkl29yP0rQOSnjijeePeqEsvdkAuMij9Z3gnAh1y8jkuRTUgjuHRjXrw8pKjhdg4FErZgwwIzOROfiIsgr9S7TdN6Y8Lc6u2H6hsLunrMGWN4fG4gzss7UZn06ustr7hed1w5qfYzkgY55VEzWYJ229Zu0huwD0QiU0gVlRb3lWZkWDwsVMOORg2C2Wx1VrNQSnfg4DIrRL46SFbZbl2dsTQQ8MZ4RzZGzszqfwu1qp7ZhgJbkKzdLHNAtaFARBUmg0W7akSKMkVZgytPIc7FiN8r44OoFjpja3waLBnWd48yy1iszqZ6i2WHZ5JV793M2QA4OJ7Gc0ZKjTDKwZl9MA9I0NMo7bDc5ZAyVi1Cz4K1q9ah0APTZJr4H05npa53dj0S5ydzjoaLEtW0UxADMGnh1BjZiNUtCgCZvhLy29aZcIjhPwKo75pdxq17yTyONd3Lel6hCBc6g6BtYj9z8x1zko9uqFeuSZmFOUaZ3Zwx0F3yZHV4IhuloZx6DFelZLVkfZ8gZBbSBdXpDtHXNnKoMwkW83zl4ZE4UyVx47IHQIATIBiTtYT183Mx6xKQ95yFg2USYiWI6zdkPH6Zem4ylx9eBZqwW9v1B4XGv7nm0Z57bxcsMZIhCpCaUSR8gM0WOoRL9kJVOIsodv0YizyDi4e8gaPIbbm3a0iCg8lDHHkL0Wry3z1lVY4tfY6ZygnmjOXBKaEDs6EV2gFN3TzWOJdZnnkUrY6L7frBHKPTdBckoIiH8csCt9KibguLiGia8VWQxsVaW8O7P1kGUzf4Lo4ngT32e21y1JTHx5xo4mjgUee3q8fKW7gwqZCEW9h1qcrHSeErz0Ey1LJf9wN9R3dVw05ccP8xmediXyMZo74Nj2h32oRoZiwKUH2KFEQ9L8UpgfzLEA1KkCxKPYaWkKlY5Pdci0nB42Y0th6WEuVWdhhzFiQOk9xH4kDONtH01mV9zw4cZbuLx9sGH9nZwtxqza7QI0RVSgOh40vqyHFzbaO2PtUyYZwAd0dMULf5KieCdAlKVfZdCabv42EE112tc2IIYGa39ctTbpHSQoOx4kKcS9ZA7MUN0oZpqnqx2sV4vcBs0zdB5uAQsKeCh9Atc1rRm7Pv4eo1z0leEZufigxYwssXb92bbB7dSpe9deAF0WoJQShu9KE0nP4hZ2lTrIHD0D1V1C1oZmkiSx6V4miEWrDTZhcNQkPu8QvPjSLcoPdf4KFu3CioZbt6DI5FOWm4zkrdhmMnf1Qv6e1VyM0aQnLLorSU8RqZoA1CVZHa3ppCHuq530RyFJIX77eb0J54DbtSTstbWjJXgrY7yzse4yg520QbwZ8IzieQdsgz6j7ATazLZuX6g2NJhr4aIVyBhOWuLHMIvqZoSk8aw5Fo1U3EQKIT3vC1yulAYPDAcLUUe0NZ7BPX5fegeyXaudMKqduSDIVQGXmvq9NvbjjI9q9KBK1rTYHdLO4Ny7MVYqJLYFmlmztTEfCLktajpyuC4QQN79ww0WMjuhTnjPtZL5IEYM0bBQ4dJypXPx8M3KdD5MgvwhS8dFd2USvEM3idJ0vPlpoisjawpewZaEKWD2ZkO3D0ym5iO9rYXT8X3sgsIp1YVQVu3TRS2AZjj5e13cnlODiDwDVRFeVB5WuW7jblddf4Shj4a6w0ZJ3spLl2XoTdaiRVdddyqnjXm6kSZkNIa0JuXUXkMyxrodlCF18PZjkQW0vft4TXu36M7fgN0 Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.bRJ7bV find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/MASS/libs/MASS.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/foreign/libs/foreign.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grDevices/libs/grDevices.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/graphics/libs/graphics.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/grid/libs/grid.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/lattice/libs/lattice.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/nnet/libs/nnet.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/rpart/libs/rpart.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/spatial/libs/spatial.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/survival/libs/survival.so: underlinked libraries: /lib64/libm.so.6 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/library/utils/libs/utils.so: underlinked libraries: /lib64/liblzma.so.5 lib.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/lib64/R/modules/lapack.so: underlinked libraries: /lib64/libdl.so.2 shebang.req.files: executable script /usr/src/tmp/R-base-buildroot/usr/lib64/R/share/sh/echo.sh is not executable find-requires: FINDPACKAGE-COMMANDS: cat grep sh Provides: libR.so()(64bit) = set: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, libR-2.11.so()(64bit) = set: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 Requires: /bin/sh, /lib64/ld-linux-x86-64.so.2, coreutils, grep, ld-linux-x86-64.so.2()(64bit) >= set:ihbW3, ld-linux-x86-64.so.2(GLIBC_2.2.5)(64bit), libX11.so.6()(64bit) >= set:ohpSxBZ85GUbjr3ZiTS4Op7MNvybxvVcEOfOqXEF1qAwZs71CCJnKVDCNaOeQuhN2XiwdPdDviaX7NJgyWjw426Dgj994wsONU8RZq4ZjETw6Fhp3zWVUZw5ciXODiTumQluRVpoa1IvTZLG17jMAL3ACpj6Ac4oFudXhDSHmmi88f5kj4Wr9Vnm0e7EI25u1z9ZgUcSd8uJBSFYSNRimTAoZrh3ZBnylGc5tzA2LuNkPBBiUQUU6ywg3U8ZhexsVJ8zR8RTyGBSx6p5JwQZtURAFElDl8totXyLZkjPS80tH2, libXmu.so.6()(64bit) >= set:ljat5WdZ0, libXt.so.6()(64bit) >= set:miBmG8bmWeKY1r3A0IpjGJmzcnuk4L1fZ82d, libbz2.so.1()(64bit) >= set:ieU4cq8R9SL02Pd7T6CQAbuVPJLac4, libc.so.6(GLIBC_2.11)(64bit), libc.so.6(GLIBC_2.14)(64bit), libc.so.6(GLIBC_2.15)(64bit), libc.so.6(GLIBC_2.16)(64bit), libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.27)(64bit), libc.so.6(GLIBC_2.3)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libc.so.6(GLIBC_2.6)(64bit), libc.so.6(GLIBC_2.7)(64bit), libc.so.6(GLIBC_2.8)(64bit), libcairo.so.2()(64bit) >= set:mgBeCp25NOIyrlQHFsTG1phW01upHNOW8SpbeVohC5Pwchq6KplkgZIPAQh02Zr5HMxPMkimVZpVN9h6QFUdKO6OFjNsjitz641ARaZ5HZAmxdD86kgBnSaNq3ZAVlemZpcoP0tsFeDiZfuQuf3, libcurl.so.4()(64bit) >= set:kfYXC97kb1rbvpLB1zXqFhUfWcnIhYFGaimK1g7p, libdl.so.2(GLIBC_2.2.5)(64bit), libgobject-2.0.so.0()(64bit) >= set:ml6W90, libgomp.so.1()(64bit) >= set:mis5Xj4o6xrqO4ZGM8MScp68PsbwUdLBn0, libgomp.so.1(GOMP_1.0)(64bit), libgomp.so.1(GOMP_4.0)(64bit), libgomp.so.1(OMP_1.0)(64bit), libicui18n.so.65()(64bit) >= set:rolIY5WucOij1kVmNEZ6KImTd0, libicuuc.so.65()(64bit) >= set:pmfKgUVR3uSC2LbF2, libjpeg.so.62()(64bit) >= set:jfgjDuQy7g6kiGvkp5kR7Bd0, liblapack.so.4()(64bit) >= set:ohd6FWZC9Z0w5c4a9UukCXhjBhYH4Y4FFzzOsPQITkXeYooZo0Vt8WFt6QYIOIZmWow6fzRMDwp9MGO0ZhldKUzW8W1RsJZtAeHIPYhIl5WiNVlN8FgR6mScaXXLmW0FDbvWuDSCea0aj0BvFxRc15QVQjV9n85Kyco0a0SzG6SwK1cfwAyHaix50g7p00c0WMF2, liblzma.so.5()(64bit) >= set:kgIy0DJdgZuHF5yXYppdmYIDYAa1, liblzma.so.5(XZ_5.0)(64bit), libm.so.6(GLIBC_2.2.5)(64bit), libm.so.6(GLIBC_2.23)(64bit), libopenblas.so.0()(64bit) >= set:qlsiqIe00icRW574Ku0AAyAyab7fG6SOSAPoPNmLYbhPezMnFyfKftDkkVQaeAYUqnr3WgpZJxDHDDHYiTG02, libpango-1.0.so.0()(64bit) >= set:miPmiaRgNQ6cD75j31i4ky6SMMCoRQ1, libpangocairo-1.0.so.0()(64bit) >= set:jhWzZgd5, libpcre.so.3()(64bit) >= set:ieELhsZ4oFM1uTpGS8bAqz69j4, libpng16.so.16()(64bit) >= set:lhHMixNA5RSP1K7ShGvTC9MZoVYjEMOceGAeWF0, libpng16.so.16(PNG16_0)(64bit), libpthread.so.0(GLIBC_2.2.5)(64bit), libreadline.so.7()(64bit) >= set:nidQ8PMktsCwid18OsyEUS8iDQRn5631GOVow7aaRTmMg1UZho7I5k7dG1ZFel4iyBQZd1aPltLOR05Zx8IO0, librt.so.1(GLIBC_2.2.5)(64bit), libtiff.so.5()(64bit) >= set:lhyG9VP2iv3ttOWkLJhCwlrr, libz.so.1()(64bit) >= set:kgb6dgb5xDnazO8BhqfiJqdZd6eIL9, rtld(GNU_HASH), sh Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.S9KpPV Creating R-base-debuginfo package Processing files: R-full-3.6.1-alt1 Requires: R-devel = 3.6.1-alt1, R-tcltk = 3.6.1-alt1, R-doc-html = 3.6.1-alt1, gcc-c++, gcc-fortran, liblapack-devel, make Processing files: R-devel-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.bckXi1 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.OMb109 find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header # error R_ext/GraphicsEngine.h must be included first, and includes this header ^~~~~ cpp.req: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed, trying c++ mode /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h:43:4: error: #error R_ext/GraphicsEngine.h must be included first, and includes this header # error R_ext/GraphicsEngine.h must be included first, and includes this header ^~~~~ cpp.req: WARNING: /usr/src/tmp/R-base-buildroot/usr/include/R/R_ext/GraphicsDevice.h: cpp failed find-requires: FINDPACKAGE-COMMANDS: chmod mkdir rmdir Provides: pkgconfig(libR) = 3.6.1 Requires: /bin/sh, /usr/bin/libtool, /usr/lib64/R/lib/libR.so, /usr/lib64/pkgconfig, coreutils Requires(pre): R-base = 3.6.1-alt1 Requires(postun): R-base = 3.6.1-alt1 Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.BG01br Processing files: R-tcltk-3.6.1-alt1 warning: File listed twice: /usr/lib64/R/library/tcltk/html warning: File listed twice: /usr/lib64/R/library/tcltk/html/00Index.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/R.css warning: File listed twice: /usr/lib64/R/library/tcltk/html/TclInterface.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkCommands.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgetcmds.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/TkWidgets.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tclServiceMode.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-defunct.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tcltk-package.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkProgressBar.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkStartGUI.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.dir.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_choose.files.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_messageBox.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tk_select.list.html warning: File listed twice: /usr/lib64/R/library/tcltk/html/tkpager.html Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.Sj9KBL 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.5ekEe9 find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Provides: tcl(::Utility) = 1.0, tcl(::Utility::dump) = 1.0, tcl(::Utility::expand) = 1.0, tcl(::Utility::number) = 1.0, tcl(::Utility::string) = 1.0, tcl(::Utility::tk) = 1.0, tcl(Hierarchy) = 2.0, tcl(PBar) = 1.0, tcl(Widget) = 2.0 Requires: R-base = 3.6.1-alt1, libR.so()(64bit) >= set:oiZ4ZDvavdS7yJmmEm1yk76RAJNZigoIdZ4rGSanE12warZ61UkMZtzOOW0cQ6tLN8BjJrkKZnL1TEzhiItObZCaSl9pqVwPzwTv35ZmWMAXnz5WOpBZwwMBble1hwYqhmdgOF2MNqAeQO4ABz2QjcXaAt0mBDLIbcof, libc.so.6(GLIBC_2.2.5)(64bit), libc.so.6(GLIBC_2.3.4)(64bit), libc.so.6(GLIBC_2.4)(64bit), libtcl8.6.so()(64bit) >= set:nhgjl7axi5LXwZCwtKzEgR46OGPDdUhperIBMUpAQNxfXAzzCME2ZC3VjYspFcvGIvhP7CaHXaui690CwrRamfbKeqMwV4FNim2oZ0Yf9OWVxM1, libtk8.6.so()(64bit) >= set:mkluxApv1, rtld(GNU_HASH), tcl(Tk) Requires(rpmlib): rpmlib(SetVersions) Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.o58P5z Creating R-tcltk-debuginfo package Processing files: R-doc-html-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.vrZqb4 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.0FfnxB find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Requires: R-base = 3.6.1-alt1 Processing files: R-doc-pdf-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.BxAEbc 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.svqy2P find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 3.6.1, R-base < 3.6.1 Processing files: R-doc-info-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.PR2Q6w 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.0JQ1nh find-requires: running scripts (cpp,debuginfo,files,gir-js,gir-python,gir,javadoc,lib,maven,osgi-fc,pam,perl,pkgconfig,pkgconfiglib,python,rpmlib,shebang,shell,static,symlinks,systemd-services,tcl,typelib) Conflicts: R-base > 3.6.1, R-base < 3.6.1 Processing files: R-base-debuginfo-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.DgOma5 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.Qz3E9V find-requires: running scripts (debuginfo) Provides: debug64(libR.so) Requires: R-base = 3.6.1-alt1, /usr/lib/debug/lib64/ld-linux-x86-64.so.2.debug, debug64(ld-linux-x86-64.so.2), debug64(libX11.so.6), debug64(libXmu.so.6), debug64(libXt.so.6), debug64(libbz2.so.1), debug64(libc.so.6), debug64(libcairo.so.2), debug64(libcurl.so.4), debug64(libdl.so.2), debug64(libgobject-2.0.so.0), debug64(libgomp.so.1), debug64(libicui18n.so.65), debug64(libicuuc.so.65), debug64(libjpeg.so.62), debug64(liblapack.so.4), debug64(liblzma.so.5), debug64(libm.so.6), debug64(libopenblas.so.0), debug64(libpango-1.0.so.0), debug64(libpangocairo-1.0.so.0), debug64(libpcre.so.3), debug64(libpng16.so.16), debug64(libpthread.so.0), debug64(libreadline.so.7), debug64(librt.so.1), debug64(libtiff.so.5), debug64(libz.so.1) Processing files: R-tcltk-debuginfo-3.6.1-alt1 Finding Provides (using /usr/lib/rpm/find-provides) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.BgAxw3 find-provides: running scripts (debuginfo) Finding Requires (using /usr/lib/rpm/find-requires) Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.W1XT5d find-requires: running scripts (debuginfo) Requires: R-tcltk = 3.6.1-alt1, debug64(libR.so), debug64(libc.so.6), debug64(libtcl8.6.so), debug64(libtk8.6.so) Adding to R-devel a strict dependency on R-base Adding to R-tcltk a strict dependency on R-base Adding to R-doc-html a strict dependency on R-base Adding to R-base-debuginfo a strict dependency on R-base Adding to R-full a strict dependency on R-devel Adding to R-full a strict dependency on R-tcltk Adding to R-full a strict dependency on R-doc-html Adding to R-tcltk-debuginfo a strict dependency on R-tcltk Adding to R-devel a strict dependency on R-base Adding to R-tcltk-debuginfo a strict dependency on R-base-debuginfo Removing from R-tcltk-debuginfo 12 sources provided by R-base-debuginfo also prunning dir /usr/src/debug/R-3.6.1/include/R_ext also prunning dir /usr/src/debug/R-3.6.1/src/include also prunning dir /usr/src/debug/R-3.6.1/include Removing 1 extra deps from R-devel due to dependency on R-base Removing 1 extra deps from R-tcltk due to dependency on R-base Removing 1 extra deps from R-tcltk-debuginfo due to dependency on R-base-debuginfo Removing 2 extra deps from R-devel due to repentancy on R-base Removing 5 extra deps from R-tcltk due to repentancy on R-base Removing 1 extra deps from R-tcltk-debuginfo due to repentancy on R-base-debuginfo warning: Installed (but unpackaged) file(s) found: /usr/lib64/R/COPYING /usr/lib64/R/SVN-REVISION Wrote: /usr/src/RPM/RPMS/x86_64/R-base-3.6.1-alt1.x86_64.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-full-3.6.1-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-devel-3.6.1-alt1.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-3.6.1-alt1.x86_64.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-html-3.6.1-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-pdf-3.6.1-alt1.noarch.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/noarch/R-doc-info-3.6.1-alt1.noarch.rpm (w2.lzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-base-debuginfo-3.6.1-alt1.x86_64.rpm (w2T8.xzdio) Wrote: /usr/src/RPM/RPMS/x86_64/R-tcltk-debuginfo-3.6.1-alt1.x86_64.rpm (w2.lzdio) 811.11user 111.15system 12:33.46elapsed 122%CPU (0avgtext+0avgdata 961764maxresident)k 0inputs+0outputs (0major+23997218minor)pagefaults 0swaps 11.19user 3.74system 15:12.53elapsed 1%CPU (0avgtext+0avgdata 135100maxresident)k 1568inputs+0outputs (0major+371613minor)pagefaults 0swaps --- R-base-3.6.1-alt1.x86_64.rpm.repo 2021-06-21 20:06:08.000000000 +0000 +++ R-base-3.6.1-alt1.x86_64.rpm.hasher 2024-09-29 12:28:36.397478378 +0000 @@ -4435,3 +4435,3 @@ File: /usr/lib64/R/bin/Rprof 100755 root:root 8b1dc2b3c9cdfdf00b76f9bab559f740 -File: /usr/lib64/R/bin/Rscript 100755 root:root 699d3f76b6d07c4faebd9335f8965445 +File: /usr/lib64/R/bin/Rscript 100755 root:root d935289d7833788c6c5e65ab2c747430 File: /usr/lib64/R/bin/Stangle 100755 root:root 5f3ec1749e89b212df274d861d5dd1f6 @@ -4439,3 +4439,3 @@ File: /usr/lib64/R/bin/exec 40755 root:root -File: /usr/lib64/R/bin/exec/R 100755 root:root fdc3ffa02a44c62ae0333e98e2e640a8 +File: /usr/lib64/R/bin/exec/R 100755 root:root c0f31c896b493badf305066072ef758b File: /usr/lib64/R/bin/javareconf 100755 root:root f1c35ee536a466fbe7d3218f56082d17 @@ -4449,3 +4449,3 @@ File: /usr/lib64/R/library/KernSmooth 40755 root:root -File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root a7c04ebce33bf44668d3bfc5283a029e +File: /usr/lib64/R/library/KernSmooth/DESCRIPTION 100644 root:root 7f53a31e6bbc90efe197548dc7040bd9 File: /usr/lib64/R/library/KernSmooth/INDEX 100644 root:root 56080cdf3d21fa33a8cae73825b9ef9f @@ -4457,3 +4457,3 @@ File: /usr/lib64/R/library/KernSmooth/Meta/nsInfo.rds 100644 root:root 14105c52aa0a87f929490a96c046eb9b -File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 4e49a83076276b0fb5f0e8f188c20a04 +File: /usr/lib64/R/library/KernSmooth/Meta/package.rds 100644 root:root 29f36a16724c3e87ddce2e4e33753f77 File: /usr/lib64/R/library/KernSmooth/NAMESPACE 100644 root:root a93c919c53d25488f67acbe057fff7ed @@ -4465,6 +4465,6 @@ File: /usr/lib64/R/library/KernSmooth/help/AnIndex 100644 root:root 000e790525eb6d551fc2a2f3edd1f6d1 -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root 7118c7c4024fbe27b20c90560229616c -File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root b3fd52cfdfdb1f85de309508d98e8567 +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdb 100644 root:root f73bdd7007125f7621fa6a9c91813f05 +File: /usr/lib64/R/library/KernSmooth/help/KernSmooth.rdx 100644 root:root 629c74cd47a446332f22fc7276993f8d File: /usr/lib64/R/library/KernSmooth/help/aliases.rds 100644 root:root f7a179acd24bb9df14b155c528b37ad7 -File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root cce41ed35c6a3b358aaab0ca8f4f3f52 +File: /usr/lib64/R/library/KernSmooth/help/paths.rds 100644 root:root c4bc8dad97a413a24d32d388882ec52e File: /usr/lib64/R/library/KernSmooth/html 40755 root:root @@ -4480,3 +4480,3 @@ File: /usr/lib64/R/library/KernSmooth/libs 40755 root:root -File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root 2562202da933257bfd8915b48434d738 +File: /usr/lib64/R/library/KernSmooth/libs/KernSmooth.so 100644 root:root 4945c0bd6266721efaa9b8b335b46ae5 File: /usr/lib64/R/library/KernSmooth/po 40755 root:root @@ -4499,3 +4499,3 @@ File: /usr/lib64/R/library/MASS/CITATION 100644 root:root 7bf40cbb20005f08d1f9163582f0d815 -File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 4973c6c660d2e098b6ff7778922be0e3 +File: /usr/lib64/R/library/MASS/DESCRIPTION 100644 root:root 19f842e56fff16a07ed8402ed923289a File: /usr/lib64/R/library/MASS/INDEX 100644 root:root 35aff05a505ecf7e81e0473767794ca9 @@ -4508,3 +4508,3 @@ File: /usr/lib64/R/library/MASS/Meta/nsInfo.rds 100644 root:root 4ffb7e3e1f443b3678a805bfb7919c4b -File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root 42dfe7f3f8de8d9cfb364f5e1552f43f +File: /usr/lib64/R/library/MASS/Meta/package.rds 100644 root:root 2631132143777eb25c0deb3745449443 File: /usr/lib64/R/library/MASS/NAMESPACE 100644 root:root 0ac7b30ad35a4c19ea69d76a6a366b02 @@ -4521,6 +4521,6 @@ File: /usr/lib64/R/library/MASS/help/AnIndex 100644 root:root 1b15ad7a8d55d0d6c0752ef74dd744f9 -File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root 15d4306c12f243fcf7ed8a83dc20a7c2 -File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root 2c517d92562379b17d4a6c2134576fb8 +File: /usr/lib64/R/library/MASS/help/MASS.rdb 100644 root:root bad734a927011f71b9f2d9e47f1a9a57 +File: /usr/lib64/R/library/MASS/help/MASS.rdx 100644 root:root c5406fc78de2028bc49b7e596f41f18f File: /usr/lib64/R/library/MASS/help/aliases.rds 100644 root:root 9d27d9e179b3ccb72e96f84ffe3d0e55 -File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root b1fd5b8e0c31f2f5a350ea3451ff3bc1 +File: /usr/lib64/R/library/MASS/help/paths.rds 100644 root:root 57c65d0739f457cb872382ef52257c80 File: /usr/lib64/R/library/MASS/html 40755 root:root @@ -4685,3 +4685,3 @@ File: /usr/lib64/R/library/MASS/libs 40755 root:root -File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root 4445eb539750ecf4f1ab4598cef459b1 +File: /usr/lib64/R/library/MASS/libs/MASS.so 100644 root:root 740a92b5bda9d8e6b2c5480eb668d10f File: /usr/lib64/R/library/MASS/po 40755 root:root @@ -4721,3 +4721,3 @@ File: /usr/lib64/R/library/Matrix/Copyrights 100644 root:root 8734f0b040c6292983d273d4251d250a -File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root 5d096d94375afd5f6940d0be245bb29c +File: /usr/lib64/R/library/Matrix/DESCRIPTION 100644 root:root d73811c642125c5557a04a1ab69c9d54 File: /usr/lib64/R/library/Matrix/Doxyfile 100644 root:root ac3697580885d17a062ce39df01338ad @@ -4732,3 +4732,3 @@ File: /usr/lib64/R/library/Matrix/Meta/nsInfo.rds 100644 root:root 90fd1396706ec9b7a585404a83b7da82 -File: /usr/lib64/R/library/Matrix/Meta/package.rds 100644 root:root b9ab4e6293b403fb1dd94163e25ec6e7 +File: /usr/lib64/R/library/Matrix/Meta/package.rds 100644 root:root e930328a97c1b7062f612a8b98387952 File: /usr/lib64/R/library/Matrix/Meta/vignette.rds 100644 root:root f6a48395281382c8210c31d00fb9d7a7 @@ -4783,6 +4783,6 @@ File: /usr/lib64/R/library/Matrix/help/AnIndex 100644 root:root 4e35b3b25bd4de84042b1822f305eebb -File: /usr/lib64/R/library/Matrix/help/Matrix.rdb 100644 root:root 8cff1c65d784e1e85ef2be05a7618764 -File: /usr/lib64/R/library/Matrix/help/Matrix.rdx 100644 root:root 0826d3238bb1d15a94b5398256b537a6 +File: /usr/lib64/R/library/Matrix/help/Matrix.rdb 100644 root:root c7afbb2c0ddca227e332ecea2be9c702 +File: /usr/lib64/R/library/Matrix/help/Matrix.rdx 100644 root:root 5482de721c1048926eb91906dbb3caf3 File: /usr/lib64/R/library/Matrix/help/aliases.rds 100644 root:root 8417c0b779341210d44eb23b5c1d0b7a -File: /usr/lib64/R/library/Matrix/help/paths.rds 100644 root:root 8a516eeb405145334687bba23f6a60ea +File: /usr/lib64/R/library/Matrix/help/paths.rds 100644 root:root 3f50f5f6807a36eda5db10b89f28661c File: /usr/lib64/R/library/Matrix/html 40755 root:root @@ -4913,3 +4913,3 @@ File: /usr/lib64/R/library/Matrix/libs 40755 root:root -File: /usr/lib64/R/library/Matrix/libs/Matrix.so 100644 root:root c574c7543ea9e6a36330dccfccc5f83b +File: /usr/lib64/R/library/Matrix/libs/Matrix.so 100644 root:root dd233179172321ebcaabd33d4e5f12b7 File: /usr/lib64/R/library/Matrix/po 40755 root:root @@ -4939,3 +4939,3 @@ File: /usr/lib64/R/library/base/CITATION 100644 root:root 16a31abf39268631f20e1478bf64d659 -File: /usr/lib64/R/library/base/DESCRIPTION 100644 root:root 1a4520f229b709d934c30ff56aac4b76 +File: /usr/lib64/R/library/base/DESCRIPTION 100644 root:root 85891dadfc06687774f60702bcd38c3f File: /usr/lib64/R/library/base/INDEX 100644 root:root 1cdac3b4cd5dd2cdedd81985ebea7f81 @@ -4947,3 +4947,3 @@ File: /usr/lib64/R/library/base/Meta/links.rds 100644 root:root d1810ad1e508b718e3e2c4a32ff3de1c -File: /usr/lib64/R/library/base/Meta/package.rds 100644 root:root 986c94f099b12e80f450dd49b6e4e171 +File: /usr/lib64/R/library/base/Meta/package.rds 100644 root:root d4349a850b23d20aa103ecb922cd036f File: /usr/lib64/R/library/base/R 40755 root:root @@ -5401,3 +5401,3 @@ File: /usr/lib64/R/library/boot/CITATION 100644 root:root 5dc2147b194c15507379de49828222c1 -File: /usr/lib64/R/library/boot/DESCRIPTION 100644 root:root 7b80e5e2f6a1dff41b797d0db69ba0b5 +File: /usr/lib64/R/library/boot/DESCRIPTION 100644 root:root 16e02a55d7d6ceab9b4d50cc74809757 File: /usr/lib64/R/library/boot/INDEX 100644 root:root e6929f73b03924d15f3af4a4c8549a45 @@ -5410,3 +5410,3 @@ File: /usr/lib64/R/library/boot/Meta/nsInfo.rds 100644 root:root 6827d841585420cef9946487500a5dc1 -File: /usr/lib64/R/library/boot/Meta/package.rds 100644 root:root f825f83470f2426bdebf968de671c114 +File: /usr/lib64/R/library/boot/Meta/package.rds 100644 root:root 7e1a273c0a89f4e855006e0e2b0b1bfb File: /usr/lib64/R/library/boot/NAMESPACE 100644 root:root 52cc784fd6ef9af32d9586726a53bb89 @@ -5424,5 +5424,5 @@ File: /usr/lib64/R/library/boot/help/aliases.rds 100644 root:root 3a4a7e8689b33a0e13309487d73b95da -File: /usr/lib64/R/library/boot/help/boot.rdb 100644 root:root f68b781016abe2d16536e9d239a95722 -File: /usr/lib64/R/library/boot/help/boot.rdx 100644 root:root 40998a4f4d48375dd9d5c5224dda113e -File: /usr/lib64/R/library/boot/help/paths.rds 100644 root:root 764b0e63b6a75b6ad39a61bce09149ad +File: /usr/lib64/R/library/boot/help/boot.rdb 100644 root:root 9a0f948e61543e6115f62280fa754de1 +File: /usr/lib64/R/library/boot/help/boot.rdx 100644 root:root 75165fc5d8eb03ef5a5e7bb02913a41e +File: /usr/lib64/R/library/boot/help/paths.rds 100644 root:root 178784365ad6c497d7a57d826a465a40 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